Starting phenix.real_space_refine on Sat Dec 9 00:39:24 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uva_20906/12_2023/6uva_20906.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uva_20906/12_2023/6uva_20906.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uva_20906/12_2023/6uva_20906.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uva_20906/12_2023/6uva_20906.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uva_20906/12_2023/6uva_20906.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uva_20906/12_2023/6uva_20906.pdb" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 72 5.16 5 C 6095 2.51 5 N 1657 2.21 5 O 1737 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 21": "OE1" <-> "OE2" Residue "A GLU 27": "OE1" <-> "OE2" Residue "A ASP 33": "OD1" <-> "OD2" Residue "A PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 215": "OD1" <-> "OD2" Residue "A PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 223": "OD1" <-> "OD2" Residue "A ASP 240": "OD1" <-> "OD2" Residue "A ASP 310": "OD1" <-> "OD2" Residue "A TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 314": "OE1" <-> "OE2" Residue "A PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 323": "OD1" <-> "OD2" Residue "A ASP 331": "OD1" <-> "OD2" Residue "A ARG 333": "NH1" <-> "NH2" Residue "A GLU 344": "OE1" <-> "OE2" Residue "A PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 347": "NH1" <-> "NH2" Residue "A ASP 354": "OD1" <-> "OD2" Residue "A ARG 356": "NH1" <-> "NH2" Residue "A TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B ASP 38": "OD1" <-> "OD2" Residue "B TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 154": "OD1" <-> "OD2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B ASP 228": "OD1" <-> "OD2" Residue "B ASP 246": "OD1" <-> "OD2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 267": "OD1" <-> "OD2" Residue "B PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 322": "OD1" <-> "OD2" Residue "G GLU 17": "OE1" <-> "OE2" Residue "G TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "N TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 46": "OE1" <-> "OE2" Residue "N TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 73": "OD1" <-> "OD2" Residue "N TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 109": "OD1" <-> "OD2" Residue "N TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 35": "OE1" <-> "OE2" Residue "E ARG 36": "NH1" <-> "NH2" Residue "E ASP 52": "OD1" <-> "OD2" Residue "E GLU 61": "OE1" <-> "OE2" Residue "E TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 76": "OE1" <-> "OE2" Residue "E TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 98": "NH1" <-> "NH2" Residue "E PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 108": "NH1" <-> "NH2" Residue "E ASP 113": "OD1" <-> "OD2" Residue "E ASP 116": "OD1" <-> "OD2" Residue "P ARG 7": "NH1" <-> "NH2" Residue "P ASP 35": "OD1" <-> "OD2" Residue "P ASP 40": "OD1" <-> "OD2" Residue "R ARG 38": "NH1" <-> "NH2" Residue "R GLU 47": "OE1" <-> "OE2" Residue "R TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 67": "NH1" <-> "NH2" Residue "R ASP 70": "OD1" <-> "OD2" Residue "R ASP 77": "OD1" <-> "OD2" Residue "R GLU 83": "OE1" <-> "OE2" Residue "R ASP 90": "OD1" <-> "OD2" Residue "R ASP 94": "OD1" <-> "OD2" Residue "R ASP 106": "OD1" <-> "OD2" Residue "R PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 113": "NH1" <-> "NH2" Residue "R ARG 119": "NH1" <-> "NH2" Residue "R TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 233": "OE1" <-> "OE2" Residue "R PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 248": "OE1" <-> "OE2" Residue "R TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 274": "NH1" <-> "NH2" Residue "R ASP 287": "OD1" <-> "OD2" Residue "R TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 314": "NH1" <-> "NH2" Residue "R TYR 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 362": "OE1" <-> "OE2" Residue "R TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 366": "OD1" <-> "OD2" Residue "R TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 397": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 9561 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1604 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 6, 'TRANS': 183} Chain breaks: 4 Chain: "B" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2583 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "G" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 380 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 4, 'TRANS': 44} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "E" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 888 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "P" Number of atoms: 326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 326 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 4, 'TRANS': 38} Chain: "R" Number of atoms: 2819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2819 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 9, 'TRANS': 334} Chain breaks: 4 Time building chain proxies: 5.87, per 1000 atoms: 0.61 Number of scatterers: 9561 At special positions: 0 Unit cell: (115.37, 97.11, 146.08, 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 72 16.00 O 1737 8.00 N 1657 7.00 C 6095 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 72 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 104 " distance=2.03 Simple disulfide: pdb=" SG CYS P 10 " - pdb=" SG CYS P 15 " distance=2.03 Simple disulfide: pdb=" SG CYS R 48 " - pdb=" SG CYS R 74 " distance=2.03 Simple disulfide: pdb=" SG CYS R 65 " - pdb=" SG CYS R 105 " distance=2.03 Simple disulfide: pdb=" SG CYS R 88 " - pdb=" SG CYS R 127 " distance=2.03 Simple disulfide: pdb=" SG CYS R 212 " - pdb=" SG CYS R 282 " distance=2.02 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: 3.93 Conformation dependent library (CDL) restraints added in 2.1 seconds 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2258 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 11 sheets defined 40.2% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 16 through 39 removed outlier: 3.803A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.637A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.746A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.788A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 391 Processing helix chain 'B' and resid 7 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 15 through 23 Processing helix chain 'G' and resid 29 through 43 removed outlier: 3.509A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.714A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'E' and resid 36 through 48 removed outlier: 4.188A pdb=" N CYS E 40 " --> pdb=" O ARG E 36 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA E 43 " --> pdb=" O LEU E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 58 removed outlier: 3.632A pdb=" N TRP E 56 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N CYS E 57 " --> pdb=" O TRP E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 76 Processing helix chain 'E' and resid 86 through 99 removed outlier: 4.531A pdb=" N GLY E 91 " --> pdb=" O PRO E 87 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N PHE E 92 " --> pdb=" O LEU E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 142 Proline residue: E 126 - end of helix removed outlier: 3.951A pdb=" N LYS E 142 " --> pdb=" O VAL E 138 " (cutoff:3.500A) Processing helix chain 'P' and resid 15 through 28 Processing helix chain 'R' and resid 36 through 52 Processing helix chain 'R' and resid 124 through 128 removed outlier: 3.551A pdb=" N CYS R 127 " --> pdb=" O TYR R 124 " (cutoff:3.500A) Processing helix chain 'R' and resid 130 through 167 removed outlier: 3.707A pdb=" N LYS R 134 " --> pdb=" O ASN R 130 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS R 167 " --> pdb=" O PHE R 163 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 198 Processing helix chain 'R' and resid 204 through 208 removed outlier: 4.205A pdb=" N THR R 207 " --> pdb=" O LEU R 204 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN R 208 " --> pdb=" O VAL R 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 204 through 208' Processing helix chain 'R' and resid 210 through 242 Processing helix chain 'R' and resid 252 through 261 Processing helix chain 'R' and resid 263 through 277 Processing helix chain 'R' and resid 280 through 284 removed outlier: 3.670A pdb=" N TRP R 283 " --> pdb=" O ASP R 280 " (cutoff:3.500A) Processing helix chain 'R' and resid 288 through 290 No H-bonds generated for 'chain 'R' and resid 288 through 290' Processing helix chain 'R' and resid 291 through 321 Proline residue: R 297 - end of helix Processing helix chain 'R' and resid 330 through 346 Proline residue: R 343 - end of helix Processing helix chain 'R' and resid 347 through 350 Processing helix chain 'R' and resid 363 through 385 removed outlier: 5.205A pdb=" N GLY R 377 " --> pdb=" O MET R 373 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N LEU R 378 " --> pdb=" O HIS R 374 " (cutoff:3.500A) Processing helix chain 'R' and resid 388 through 399 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 3.970A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 9.350A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.528A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.501A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.670A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.202A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.775A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.523A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.527A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 5 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60 removed outlier: 3.672A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 84 through 87 456 hydrogen bonds defined for protein. 1293 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.61 Time building geometry restraints manager: 4.21 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: 3099 1.34 - 1.46: 2237 1.46 - 1.58: 4344 1.58 - 1.70: 0 1.70 - 1.81: 100 Bond restraints: 9780 Sorted by residual: bond pdb=" C ASP P 40 " pdb=" N PRO P 41 " ideal model delta sigma weight residual 1.334 1.356 -0.023 2.34e-02 1.83e+03 9.30e-01 bond pdb=" CA GLY B 244 " pdb=" C GLY B 244 " ideal model delta sigma weight residual 1.520 1.514 0.006 7.30e-03 1.88e+04 7.45e-01 bond pdb=" CA GLU E 74 " pdb=" C GLU E 74 " ideal model delta sigma weight residual 1.523 1.534 -0.011 1.28e-02 6.10e+03 6.82e-01 bond pdb=" C VAL E 124 " pdb=" N ILE E 125 " ideal model delta sigma weight residual 1.329 1.338 -0.009 1.13e-02 7.83e+03 6.31e-01 bond pdb=" CA VAL E 51 " pdb=" CB VAL E 51 " ideal model delta sigma weight residual 1.538 1.546 -0.008 1.10e-02 8.26e+03 5.83e-01 ... (remaining 9775 not shown) Histogram of bond angle deviations from ideal: 100.09 - 106.88: 247 106.88 - 113.68: 5352 113.68 - 120.47: 3760 120.47 - 127.27: 3779 127.27 - 134.06: 124 Bond angle restraints: 13262 Sorted by residual: angle pdb=" CA TYR R 367 " pdb=" CB TYR R 367 " pdb=" CG TYR R 367 " ideal model delta sigma weight residual 113.90 119.60 -5.70 1.80e+00 3.09e-01 1.00e+01 angle pdb=" N VAL R 205 " pdb=" CA VAL R 205 " pdb=" C VAL R 205 " ideal model delta sigma weight residual 112.29 109.46 2.83 9.40e-01 1.13e+00 9.08e+00 angle pdb=" C THR E 73 " pdb=" N GLU E 74 " pdb=" CA GLU E 74 " ideal model delta sigma weight residual 122.37 118.02 4.35 1.54e+00 4.22e-01 7.97e+00 angle pdb=" C PHE R 166 " pdb=" N LYS R 167 " pdb=" CA LYS R 167 " ideal model delta sigma weight residual 121.54 126.14 -4.60 1.91e+00 2.74e-01 5.81e+00 angle pdb=" CA LEU R 395 " pdb=" CB LEU R 395 " pdb=" CG LEU R 395 " ideal model delta sigma weight residual 116.30 124.61 -8.31 3.50e+00 8.16e-02 5.63e+00 ... (remaining 13257 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 4970 17.98 - 35.96: 561 35.96 - 53.94: 193 53.94 - 71.92: 49 71.92 - 89.89: 15 Dihedral angle restraints: 5788 sinusoidal: 2300 harmonic: 3488 Sorted by residual: dihedral pdb=" CB CYS E 57 " pdb=" SG CYS E 57 " pdb=" SG CYS E 104 " pdb=" CB CYS E 104 " ideal model delta sinusoidal sigma weight residual -86.00 -167.11 81.11 1 1.00e+01 1.00e-02 8.12e+01 dihedral pdb=" CB CYS R 88 " pdb=" SG CYS R 88 " pdb=" SG CYS R 127 " pdb=" CB CYS R 127 " ideal model delta sinusoidal sigma weight residual 93.00 142.59 -49.59 1 1.00e+01 1.00e-02 3.38e+01 dihedral pdb=" CB CYS R 48 " pdb=" SG CYS R 48 " pdb=" SG CYS R 74 " pdb=" CB CYS R 74 " ideal model delta sinusoidal sigma weight residual 93.00 52.92 40.08 1 1.00e+01 1.00e-02 2.25e+01 ... (remaining 5785 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 915 0.030 - 0.060: 377 0.060 - 0.091: 109 0.091 - 0.121: 68 0.121 - 0.151: 6 Chirality restraints: 1475 Sorted by residual: chirality pdb=" CA LYS E 42 " pdb=" N LYS E 42 " pdb=" C LYS E 42 " pdb=" CB LYS E 42 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.71e-01 chirality pdb=" CA ILE R 352 " pdb=" N ILE R 352 " pdb=" C ILE R 352 " pdb=" CB ILE R 352 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.99e-01 chirality pdb=" CA ILE E 123 " pdb=" N ILE E 123 " pdb=" C ILE E 123 " pdb=" CB ILE E 123 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.86e-01 ... (remaining 1472 not shown) Planarity restraints: 1684 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR R 367 " 0.016 2.00e-02 2.50e+03 1.22e-02 2.99e+00 pdb=" CG TYR R 367 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR R 367 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR R 367 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR R 367 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR R 367 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR R 367 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR R 367 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO E 114 " -0.022 5.00e-02 4.00e+02 3.33e-02 1.78e+00 pdb=" N PRO E 115 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO E 115 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO E 115 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 113 " -0.020 5.00e-02 4.00e+02 3.05e-02 1.49e+00 pdb=" N PRO E 114 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO E 114 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO E 114 " -0.017 5.00e-02 4.00e+02 ... (remaining 1681 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 887 2.75 - 3.28: 9414 3.28 - 3.82: 16408 3.82 - 4.36: 19653 4.36 - 4.90: 32748 Nonbonded interactions: 79110 Sorted by model distance: nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.207 2.440 nonbonded pdb=" O TRP R 72 " pdb=" OH TYR R 91 " model vdw 2.296 2.440 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.307 2.440 nonbonded pdb=" OG SER B 227 " pdb=" O PRO N 100 " model vdw 2.318 2.440 nonbonded pdb=" O HIS R 370 " pdb=" ND1 HIS R 374 " model vdw 2.321 2.520 ... (remaining 79105 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.320 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 29.860 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 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:12.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 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 : 0.002 0.030 9780 Z= 0.140 Angle : 0.547 8.305 13262 Z= 0.313 Chirality : 0.040 0.151 1475 Planarity : 0.003 0.033 1684 Dihedral : 18.040 89.894 3503 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.36 % Allowed : 26.30 % Favored : 70.35 % 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: -2.29 (0.22), residues: 1169 helix: -0.89 (0.22), residues: 434 sheet: -1.42 (0.30), residues: 225 loop : -2.05 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 234 HIS 0.004 0.001 HIS R 374 PHE 0.011 0.001 PHE R 308 TYR 0.030 0.001 TYR R 367 ARG 0.006 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 136 time to evaluate : 1.180 Fit side-chains outliers start: 35 outliers final: 9 residues processed: 164 average time/residue: 1.4137 time to fit residues: 246.0326 Evaluate side-chains 114 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 105 time to evaluate : 1.152 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 9 residues processed: 0 time to fit residues: 1.5644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.1980 chunk 88 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 55 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 chunk 106 optimal weight: 0.0870 overall best weight: 0.8564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 218 ASN A 357 HIS A 387 HIS B 88 ASN B 259 GLN N 82 GLN E 86 ASN E 110 HIS ** P 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 250 GLN ** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9780 Z= 0.185 Angle : 0.584 7.990 13262 Z= 0.310 Chirality : 0.043 0.147 1475 Planarity : 0.004 0.036 1684 Dihedral : 4.610 20.172 1298 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 4.89 % Allowed : 24.38 % Favored : 70.73 % 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: -1.01 (0.24), residues: 1169 helix: 0.36 (0.24), residues: 441 sheet: -0.80 (0.31), residues: 232 loop : -1.50 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 169 HIS 0.004 0.001 HIS A 362 PHE 0.015 0.002 PHE E 100 TYR 0.010 0.001 TYR R 227 ARG 0.006 0.001 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 118 time to evaluate : 1.227 Fit side-chains outliers start: 51 outliers final: 19 residues processed: 158 average time/residue: 1.5101 time to fit residues: 254.8611 Evaluate side-chains 127 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 108 time to evaluate : 1.205 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 17 residues processed: 2 average time/residue: 1.0127 time to fit residues: 3.6597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 88 optimal weight: 7.9990 chunk 72 optimal weight: 2.9990 chunk 29 optimal weight: 0.0040 chunk 106 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 overall best weight: 1.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 264 ASN A 267 GLN A 357 HIS B 220 GLN B 266 HIS N 35 ASN E 71 ASN E 86 ASN ** E 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 187 ASN ** R 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9780 Z= 0.278 Angle : 0.677 7.583 13262 Z= 0.362 Chirality : 0.047 0.222 1475 Planarity : 0.005 0.046 1684 Dihedral : 5.367 26.895 1298 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 5.85 % Allowed : 24.66 % Favored : 69.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.24), residues: 1169 helix: 0.50 (0.24), residues: 446 sheet: -0.40 (0.32), residues: 239 loop : -1.30 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.006 0.001 HIS E 97 PHE 0.016 0.002 PHE B 199 TYR 0.012 0.002 TYR R 227 ARG 0.007 0.001 ARG N 72 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 105 time to evaluate : 1.156 Fit side-chains outliers start: 61 outliers final: 28 residues processed: 155 average time/residue: 1.3969 time to fit residues: 230.8853 Evaluate side-chains 132 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 104 time to evaluate : 1.150 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 23 residues processed: 5 average time/residue: 0.6984 time to fit residues: 5.4695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 105 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 11 optimal weight: 0.0370 chunk 50 optimal weight: 0.6980 chunk 71 optimal weight: 6.9990 chunk 106 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 94 optimal weight: 0.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 264 ASN A 357 HIS ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 ASN ** E 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 86 ASN ** E 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9780 Z= 0.162 Angle : 0.554 7.274 13262 Z= 0.293 Chirality : 0.042 0.137 1475 Planarity : 0.004 0.039 1684 Dihedral : 4.884 30.794 1298 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 4.70 % Allowed : 25.53 % Favored : 69.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.25), residues: 1169 helix: 1.13 (0.25), residues: 433 sheet: -0.29 (0.32), residues: 241 loop : -1.15 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 139 HIS 0.007 0.001 HIS E 97 PHE 0.013 0.001 PHE B 199 TYR 0.009 0.001 TYR B 59 ARG 0.006 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 109 time to evaluate : 1.142 Fit side-chains outliers start: 49 outliers final: 23 residues processed: 148 average time/residue: 1.3753 time to fit residues: 217.1412 Evaluate side-chains 125 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 102 time to evaluate : 0.977 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 22 residues processed: 1 average time/residue: 0.2492 time to fit residues: 1.8429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 64 optimal weight: 0.4980 chunk 1 optimal weight: 0.9980 chunk 84 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 101 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 264 ASN A 357 HIS B 176 GLN E 71 ASN E 86 ASN ** E 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9780 Z= 0.178 Angle : 0.570 7.247 13262 Z= 0.301 Chirality : 0.042 0.142 1475 Planarity : 0.004 0.039 1684 Dihedral : 4.905 28.879 1298 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 4.41 % Allowed : 26.49 % Favored : 69.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.25), residues: 1169 helix: 1.23 (0.25), residues: 434 sheet: -0.31 (0.31), residues: 251 loop : -1.01 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 139 HIS 0.005 0.001 HIS E 97 PHE 0.014 0.001 PHE B 199 TYR 0.021 0.001 TYR N 60 ARG 0.004 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 104 time to evaluate : 1.193 Fit side-chains outliers start: 46 outliers final: 31 residues processed: 141 average time/residue: 1.3286 time to fit residues: 200.0859 Evaluate side-chains 133 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 102 time to evaluate : 1.127 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 27 residues processed: 4 average time/residue: 1.1162 time to fit residues: 6.3167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 101 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 113 optimal weight: 0.0270 chunk 93 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 37 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 overall best weight: 1.1242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 264 ASN A 357 HIS B 176 GLN E 71 ASN E 86 ASN ** E 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9780 Z= 0.206 Angle : 0.609 13.769 13262 Z= 0.319 Chirality : 0.043 0.150 1475 Planarity : 0.004 0.041 1684 Dihedral : 5.065 33.165 1298 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 5.28 % Allowed : 25.62 % Favored : 69.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.25), residues: 1169 helix: 1.27 (0.25), residues: 433 sheet: -0.34 (0.31), residues: 253 loop : -0.95 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 139 HIS 0.005 0.001 HIS E 97 PHE 0.014 0.002 PHE B 199 TYR 0.022 0.001 TYR N 60 ARG 0.006 0.001 ARG E 143 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 106 time to evaluate : 1.149 Fit side-chains outliers start: 55 outliers final: 33 residues processed: 148 average time/residue: 1.2858 time to fit residues: 203.8568 Evaluate side-chains 136 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 103 time to evaluate : 1.019 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 30 residues processed: 3 average time/residue: 0.1523 time to fit residues: 2.0794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 0.3980 chunk 64 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 112 optimal weight: 0.0270 chunk 70 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.8842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 264 ASN A 357 HIS B 32 GLN B 176 GLN E 71 ASN E 86 ASN ** E 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9780 Z= 0.180 Angle : 0.568 7.050 13262 Z= 0.300 Chirality : 0.042 0.146 1475 Planarity : 0.004 0.039 1684 Dihedral : 4.972 32.209 1298 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 4.70 % Allowed : 26.58 % Favored : 68.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.25), residues: 1169 helix: 1.36 (0.25), residues: 433 sheet: -0.31 (0.32), residues: 249 loop : -0.90 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 139 HIS 0.005 0.001 HIS E 97 PHE 0.013 0.001 PHE B 199 TYR 0.024 0.001 TYR N 60 ARG 0.006 0.000 ARG E 143 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 103 time to evaluate : 1.091 Fit side-chains revert: symmetry clash outliers start: 49 outliers final: 34 residues processed: 145 average time/residue: 1.2666 time to fit residues: 197.0681 Evaluate side-chains 133 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 99 time to evaluate : 1.167 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 32 residues processed: 2 average time/residue: 1.1332 time to fit residues: 3.9530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 22 optimal weight: 0.0270 chunk 21 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 102 optimal weight: 0.0040 chunk 108 optimal weight: 0.5980 overall best weight: 0.4650 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 264 ASN A 357 HIS B 259 GLN E 71 ASN E 86 ASN E 97 HIS ** P 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 50 GLN ** R 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9780 Z= 0.149 Angle : 0.547 12.101 13262 Z= 0.285 Chirality : 0.041 0.139 1475 Planarity : 0.004 0.039 1684 Dihedral : 4.704 29.774 1298 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 4.22 % Allowed : 27.06 % Favored : 68.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.25), residues: 1169 helix: 1.56 (0.25), residues: 433 sheet: -0.27 (0.32), residues: 249 loop : -0.85 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP E 139 HIS 0.005 0.001 HIS E 97 PHE 0.014 0.001 PHE E 69 TYR 0.027 0.001 TYR N 60 ARG 0.006 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 101 time to evaluate : 1.195 Fit side-chains revert: symmetry clash outliers start: 44 outliers final: 30 residues processed: 140 average time/residue: 1.2561 time to fit residues: 188.6232 Evaluate side-chains 130 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 100 time to evaluate : 1.053 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 29 residues processed: 1 average time/residue: 0.0883 time to fit residues: 1.7366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 99 optimal weight: 0.0970 chunk 104 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 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 31 GLN A 264 ASN A 357 HIS E 71 ASN E 86 ASN ** P 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9780 Z= 0.276 Angle : 0.656 8.339 13262 Z= 0.350 Chirality : 0.046 0.167 1475 Planarity : 0.005 0.040 1684 Dihedral : 5.341 33.052 1298 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.65 % Allowed : 27.54 % Favored : 68.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.25), residues: 1169 helix: 1.23 (0.25), residues: 434 sheet: -0.30 (0.32), residues: 249 loop : -0.94 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP E 139 HIS 0.006 0.001 HIS R 374 PHE 0.014 0.002 PHE B 199 TYR 0.026 0.002 TYR N 60 ARG 0.006 0.001 ARG N 72 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 100 time to evaluate : 1.193 Fit side-chains outliers start: 38 outliers final: 27 residues processed: 134 average time/residue: 1.2832 time to fit residues: 185.0175 Evaluate side-chains 122 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 95 time to evaluate : 1.232 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 27 residues processed: 0 time to fit residues: 1.3732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 111 optimal weight: 0.7980 chunk 67 optimal weight: 0.4980 chunk 52 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 73 optimal weight: 0.0670 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 264 ASN A 357 HIS E 71 ASN E 86 ASN ** R 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9780 Z= 0.155 Angle : 0.555 6.809 13262 Z= 0.292 Chirality : 0.042 0.142 1475 Planarity : 0.004 0.039 1684 Dihedral : 4.931 31.446 1298 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.98 % Allowed : 28.50 % Favored : 68.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.25), residues: 1169 helix: 1.47 (0.25), residues: 435 sheet: -0.29 (0.32), residues: 249 loop : -0.84 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP E 139 HIS 0.005 0.001 HIS R 374 PHE 0.012 0.001 PHE B 199 TYR 0.029 0.001 TYR N 60 ARG 0.007 0.000 ARG B 197 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 98 time to evaluate : 1.123 Fit side-chains outliers start: 31 outliers final: 27 residues processed: 128 average time/residue: 1.3504 time to fit residues: 185.4379 Evaluate side-chains 124 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 97 time to evaluate : 1.206 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 27 residues processed: 0 time to fit residues: 1.3982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 13 optimal weight: 0.0070 chunk 25 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 11 optimal weight: 0.0980 chunk 17 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 overall best weight: 0.8202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 264 ASN A 357 HIS E 71 ASN E 86 ASN ** R 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.215786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.164615 restraints weight = 9683.785| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 1.34 r_work: 0.3763 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3663 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9780 Z= 0.177 Angle : 0.579 8.462 13262 Z= 0.304 Chirality : 0.042 0.146 1475 Planarity : 0.004 0.039 1684 Dihedral : 4.974 30.738 1298 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.26 % Allowed : 28.12 % Favored : 68.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.25), residues: 1169 helix: 1.46 (0.25), residues: 435 sheet: -0.29 (0.32), residues: 249 loop : -0.83 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP E 139 HIS 0.005 0.001 HIS R 374 PHE 0.019 0.002 PHE E 100 TYR 0.028 0.001 TYR N 60 ARG 0.007 0.000 ARG B 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4354.70 seconds wall clock time: 78 minutes 2.72 seconds (4682.72 seconds total)