Starting phenix.real_space_refine (version: dev) on Sun May 15 05:53:43 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6umm_20820/05_2022/6umm_20820.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6umm_20820/05_2022/6umm_20820.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6umm_20820/05_2022/6umm_20820.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6umm_20820/05_2022/6umm_20820.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6umm_20820/05_2022/6umm_20820.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6umm_20820/05_2022/6umm_20820.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.001 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 27": "NH1" <-> "NH2" Residue "A ARG 64": "NH1" <-> "NH2" Residue "A ASP 67": "OD1" <-> "OD2" Residue "A ASP 72": "OD1" <-> "OD2" Residue "A ARG 75": "NH1" <-> "NH2" Residue "A ASP 98": "OD1" <-> "OD2" Residue "A ARG 118": "NH1" <-> "NH2" Residue "A ARG 119": "NH1" <-> "NH2" Residue "A ASP 130": "OD1" <-> "OD2" Residue "A ARG 153": "NH1" <-> "NH2" Residue "A ARG 154": "NH1" <-> "NH2" Residue "A GLU 161": "OE1" <-> "OE2" Residue "A ASP 190": "OD1" <-> "OD2" Residue "A ASP 203": "OD1" <-> "OD2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A GLU 219": "OE1" <-> "OE2" Residue "A GLU 225": "OE1" <-> "OE2" Residue "A PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 246": "NH1" <-> "NH2" Residue "A ARG 260": "NH1" <-> "NH2" Residue "B ARG 11": "NH1" <-> "NH2" Residue "B ASP 19": "OD1" <-> "OD2" Residue "B GLU 26": "OE1" <-> "OE2" Residue "B ASP 111": "OD1" <-> "OD2" Residue "B ARG 123": "NH1" <-> "NH2" Residue "B ARG 125": "NH1" <-> "NH2" Residue "B PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 211": "OD1" <-> "OD2" Residue "B ARG 239": "NH1" <-> "NH2" Residue "B ASP 378": "OD1" <-> "OD2" Residue "B TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 406": "NH1" <-> "NH2" Residue "B TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 444": "NH1" <-> "NH2" Residue "B ARG 445": "NH1" <-> "NH2" Residue "B PHE 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 455": "OD1" <-> "OD2" Residue "B ARG 475": "NH1" <-> "NH2" Residue "C ASP 19": "OD1" <-> "OD2" Residue "C GLU 26": "OE1" <-> "OE2" Residue "C PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 114": "OD1" <-> "OD2" Residue "C PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 123": "NH1" <-> "NH2" Residue "C ARG 155": "NH1" <-> "NH2" Residue "C PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 312": "NH1" <-> "NH2" Residue "C ASP 405": "OD1" <-> "OD2" Residue "C ARG 406": "NH1" <-> "NH2" Residue "C ASP 437": "OD1" <-> "OD2" Residue "C TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 474": "OD1" <-> "OD2" Residue "D PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 29": "NH1" <-> "NH2" Residue "D PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 65": "NH1" <-> "NH2" Residue "D PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 3": "NH1" <-> "NH2" Residue "E GLU 25": "OE1" <-> "OE2" Residue "E ARG 112": "NH1" <-> "NH2" Residue "E ARG 123": "NH1" <-> "NH2" Residue "E GLU 132": "OE1" <-> "OE2" Residue "E GLU 134": "OE1" <-> "OE2" Residue "E ARG 144": "NH1" <-> "NH2" Residue "E ARG 151": "NH1" <-> "NH2" Residue "E PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 168": "OD1" <-> "OD2" Residue "E GLU 179": "OE1" <-> "OE2" Residue "E ASP 181": "OD1" <-> "OD2" Residue "E ARG 191": "NH1" <-> "NH2" Residue "E ARG 198": "NH1" <-> "NH2" Residue "E ASP 208": "OD1" <-> "OD2" Residue "E GLU 223": "OE1" <-> "OE2" Residue "E ARG 225": "NH1" <-> "NH2" Residue "E ASP 240": "OD1" <-> "OD2" Residue "E ASP 268": "OD1" <-> "OD2" Residue "E ASP 274": "OD1" <-> "OD2" Residue "E ARG 280": "NH1" <-> "NH2" Residue "E ARG 290": "NH1" <-> "NH2" Residue "E ARG 292": "NH1" <-> "NH2" Residue "E ASP 299": "OD1" <-> "OD2" Residue "E ARG 300": "NH1" <-> "NH2" Residue "E ASP 322": "OD1" <-> "OD2" Residue "E ARG 349": "NH1" <-> "NH2" Residue "E GLU 350": "OE1" <-> "OE2" Residue "E TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 354": "OD1" <-> "OD2" Residue "E ARG 361": "NH1" <-> "NH2" Residue "E ARG 366": "NH1" <-> "NH2" Residue "E ARG 395": "NH1" <-> "NH2" Residue "E ARG 399": "NH1" <-> "NH2" Residue "F ARG 27": "NH1" <-> "NH2" Residue "F ARG 64": "NH1" <-> "NH2" Residue "F ASP 67": "OD1" <-> "OD2" Residue "F ASP 72": "OD1" <-> "OD2" Residue "F ARG 75": "NH1" <-> "NH2" Residue "F ASP 98": "OD1" <-> "OD2" Residue "F ARG 118": "NH1" <-> "NH2" Residue "F ARG 119": "NH1" <-> "NH2" Residue "F ASP 127": "OD1" <-> "OD2" Residue "F ARG 153": "NH1" <-> "NH2" Residue "F ARG 154": "NH1" <-> "NH2" Residue "F GLU 161": "OE1" <-> "OE2" Residue "F ASP 173": "OD1" <-> "OD2" Residue "F GLU 182": "OE1" <-> "OE2" Residue "F ASP 190": "OD1" <-> "OD2" Residue "F ASP 206": "OD1" <-> "OD2" Residue "F GLU 211": "OE1" <-> "OE2" Residue "F GLU 219": "OE1" <-> "OE2" Residue "F PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 246": "NH1" <-> "NH2" Residue "F ARG 260": "NH1" <-> "NH2" Residue "G ARG 11": "NH1" <-> "NH2" Residue "G ASP 19": "OD1" <-> "OD2" Residue "G ASP 20": "OD1" <-> "OD2" Residue "G GLU 32": "OE1" <-> "OE2" Residue "G GLU 37": "OE1" <-> "OE2" Residue "G ASP 80": "OD1" <-> "OD2" Residue "G GLU 110": "OE1" <-> "OE2" Residue "G ASP 114": "OD1" <-> "OD2" Residue "G ARG 123": "NH1" <-> "NH2" Residue "G ARG 125": "NH1" <-> "NH2" Residue "G ASP 160": "OD1" <-> "OD2" Residue "G ASP 211": "OD1" <-> "OD2" Residue "G ARG 239": "NH1" <-> "NH2" Residue "G ARG 295": "NH1" <-> "NH2" Residue "G ASP 405": "OD1" <-> "OD2" Residue "G ARG 406": "NH1" <-> "NH2" Residue "G TYR 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 444": "NH1" <-> "NH2" Residue "G ARG 445": "NH1" <-> "NH2" Residue "G ASP 455": "OD1" <-> "OD2" Residue "G ARG 475": "NH1" <-> "NH2" Residue "H ASP 19": "OD1" <-> "OD2" Residue "H PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 84": "OD1" <-> "OD2" Residue "H GLU 121": "OE1" <-> "OE2" Residue "H ARG 123": "NH1" <-> "NH2" Residue "H ARG 155": "NH1" <-> "NH2" Residue "H ASP 211": "OD1" <-> "OD2" Residue "H ASP 306": "OD1" <-> "OD2" Residue "H ARG 312": "NH1" <-> "NH2" Residue "H ARG 406": "NH1" <-> "NH2" Residue "H ASP 437": "OD1" <-> "OD2" Residue "H TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 474": "OD1" <-> "OD2" Residue "I ASP 62": "OD1" <-> "OD2" Residue "I ARG 65": "NH1" <-> "NH2" Residue "I ARG 69": "NH1" <-> "NH2" Residue "J ARG 3": "NH1" <-> "NH2" Residue "J GLU 25": "OE1" <-> "OE2" Residue "J ARG 32": "NH1" <-> "NH2" Residue "J GLU 95": "OE1" <-> "OE2" Residue "J ASP 103": "OD1" <-> "OD2" Residue "J ARG 112": "NH1" <-> "NH2" Residue "J ASP 113": "OD1" <-> "OD2" Residue "J GLU 121": "OE1" <-> "OE2" Residue "J ARG 123": "NH1" <-> "NH2" Residue "J ARG 144": "NH1" <-> "NH2" Residue "J ASP 149": "OD1" <-> "OD2" Residue "J ARG 151": "NH1" <-> "NH2" Residue "J PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 168": "OD1" <-> "OD2" Residue "J ASP 181": "OD1" <-> "OD2" Residue "J ARG 191": "NH1" <-> "NH2" Residue "J ARG 198": "NH1" <-> "NH2" Residue "J GLU 220": "OE1" <-> "OE2" Residue "J ARG 225": "NH1" <-> "NH2" Residue "J ARG 280": "NH1" <-> "NH2" Residue "J ARG 290": "NH1" <-> "NH2" Residue "J ARG 292": "NH1" <-> "NH2" Residue "J ARG 300": "NH1" <-> "NH2" Residue "J ASP 322": "OD1" <-> "OD2" Residue "J GLU 345": "OE1" <-> "OE2" Residue "J ARG 349": "NH1" <-> "NH2" Residue "J TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 361": "NH1" <-> "NH2" Residue "J ASP 364": "OD1" <-> "OD2" Residue "J ARG 366": "NH1" <-> "NH2" Residue "J ARG 395": "NH1" <-> "NH2" Residue "J ARG 399": "NH1" <-> "NH2" Residue "J ASP 401": "OD1" <-> "OD2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 23658 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2169 Classifications: {'peptide': 285} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 268} Chain: "B" Number of atoms: 3162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3162 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 415} Chain breaks: 2 Chain: "C" Number of atoms: 3238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3238 Classifications: {'peptide': 452} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 422} Chain breaks: 1 Chain: "D" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 644 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "E" Number of atoms: 2698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2698 Classifications: {'peptide': 343} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 313} Chain breaks: 1 Chain: "F" Number of atoms: 2169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2169 Classifications: {'peptide': 285} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 268} Chain: "G" Number of atoms: 3162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3162 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 415} Chain breaks: 2 Chain: "H" Number of atoms: 3238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3238 Classifications: {'peptide': 452} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 422} Chain breaks: 1 Chain: "I" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 480 Classifications: {'peptide': 61} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 58} Chain: "J" Number of atoms: 2698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2698 Classifications: {'peptide': 343} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 313} Chain breaks: 1 Time building chain proxies: 12.92, per 1000 atoms: 0.55 Number of scatterers: 23658 At special positions: 0 Unit cell: (188.6, 141.86, 154.98, 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 60 16.00 O 4227 8.00 N 4240 7.00 C 15131 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: 10.07 Conformation dependent library (CDL) restraints added in 3.6 seconds 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5908 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 19 sheets defined 58.3% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 1 through 17 Processing helix chain 'A' and resid 23 through 41 Processing helix chain 'A' and resid 48 through 65 Processing helix chain 'A' and resid 89 through 95 removed outlier: 3.671A pdb=" N VAL A 93 " --> pdb=" O GLN A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 139 removed outlier: 3.793A pdb=" N LEU A 135 " --> pdb=" O ASN A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 163 Processing helix chain 'A' and resid 204 through 214 Processing helix chain 'A' and resid 263 through 270 Processing helix chain 'B' and resid 34 through 47 removed outlier: 3.796A pdb=" N ILE B 38 " --> pdb=" O PRO B 34 " (cutoff:3.500A) Proline residue: B 40 - end of helix Processing helix chain 'B' and resid 111 through 120 Processing helix chain 'B' and resid 121 through 124 Processing helix chain 'B' and resid 127 through 159 removed outlier: 3.803A pdb=" N HIS B 131 " --> pdb=" O TRP B 127 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE B 132 " --> pdb=" O GLY B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 181 removed outlier: 3.675A pdb=" N LEU B 179 " --> pdb=" O VAL B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 196 Processing helix chain 'B' and resid 196 through 206 Processing helix chain 'B' and resid 213 through 234 removed outlier: 3.553A pdb=" N GLY B 234 " --> pdb=" O ILE B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 264 Processing helix chain 'B' and resid 267 through 285 removed outlier: 3.556A pdb=" N ILE B 271 " --> pdb=" O SER B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 294 Processing helix chain 'B' and resid 319 through 351 Processing helix chain 'B' and resid 356 through 374 removed outlier: 3.556A pdb=" N TRP B 360 " --> pdb=" O SER B 356 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL B 363 " --> pdb=" O ALA B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 404 removed outlier: 4.396A pdb=" N SER B 390 " --> pdb=" O LEU B 386 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N TYR B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 430 Processing helix chain 'B' and resid 430 through 435 Processing helix chain 'B' and resid 436 through 439 removed outlier: 3.540A pdb=" N TYR B 439 " --> pdb=" O PRO B 436 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 436 through 439' Processing helix chain 'B' and resid 440 through 455 Processing helix chain 'B' and resid 457 through 466 removed outlier: 3.984A pdb=" N VAL B 461 " --> pdb=" O SER B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 473 Processing helix chain 'C' and resid 34 through 47 Proline residue: C 40 - end of helix Processing helix chain 'C' and resid 82 through 87 Processing helix chain 'C' and resid 115 through 123 removed outlier: 3.926A pdb=" N ARG C 123 " --> pdb=" O PHE C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 158 Processing helix chain 'C' and resid 161 through 182 Processing helix chain 'C' and resid 185 through 196 removed outlier: 3.543A pdb=" N ALA C 189 " --> pdb=" O SER C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 208 removed outlier: 3.889A pdb=" N LEU C 206 " --> pdb=" O ALA C 202 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N VAL C 208 " --> pdb=" O PHE C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 233 removed outlier: 3.587A pdb=" N VAL C 217 " --> pdb=" O GLY C 213 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA C 233 " --> pdb=" O LEU C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 264 removed outlier: 3.753A pdb=" N VAL C 243 " --> pdb=" O ARG C 239 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TRP C 264 " --> pdb=" O ALA C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 285 Processing helix chain 'C' and resid 285 through 294 Processing helix chain 'C' and resid 313 through 351 removed outlier: 3.667A pdb=" N LEU C 317 " --> pdb=" O PRO C 313 " (cutoff:3.500A) Proline residue: C 321 - end of helix Processing helix chain 'C' and resid 356 through 373 Processing helix chain 'C' and resid 374 through 376 No H-bonds generated for 'chain 'C' and resid 374 through 376' Processing helix chain 'C' and resid 379 through 404 removed outlier: 4.648A pdb=" N SER C 390 " --> pdb=" O LEU C 386 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N TYR C 391 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 430 Processing helix chain 'C' and resid 435 through 439 Processing helix chain 'C' and resid 440 through 466 removed outlier: 4.443A pdb=" N ILE C 459 " --> pdb=" O ASP C 455 " (cutoff:3.500A) Proline residue: C 460 - end of helix Processing helix chain 'C' and resid 467 through 474 Processing helix chain 'D' and resid 34 through 54 Processing helix chain 'D' and resid 62 through 92 Processing helix chain 'E' and resid 95 through 130 Processing helix chain 'E' and resid 134 through 139 removed outlier: 3.540A pdb=" N ILE E 139 " --> pdb=" O LEU E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 197 Processing helix chain 'E' and resid 210 through 212 No H-bonds generated for 'chain 'E' and resid 210 through 212' Processing helix chain 'E' and resid 220 through 237 Processing helix chain 'E' and resid 258 through 264 Processing helix chain 'E' and resid 285 through 298 Proline residue: E 295 - end of helix Processing helix chain 'E' and resid 386 through 399 removed outlier: 3.953A pdb=" N ARG E 399 " --> pdb=" O ARG E 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 17 Processing helix chain 'F' and resid 23 through 41 Processing helix chain 'F' and resid 48 through 65 Processing helix chain 'F' and resid 89 through 96 Processing helix chain 'F' and resid 132 through 137 Processing helix chain 'F' and resid 143 through 163 Processing helix chain 'F' and resid 204 through 215 removed outlier: 3.638A pdb=" N VAL F 208 " --> pdb=" O ARG F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 263 through 271 Processing helix chain 'G' and resid 34 through 37 Processing helix chain 'G' and resid 38 through 47 Processing helix chain 'G' and resid 112 through 121 removed outlier: 3.585A pdb=" N GLU G 121 " --> pdb=" O VAL G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 128 through 159 Processing helix chain 'G' and resid 161 through 181 removed outlier: 3.805A pdb=" N PHE G 165 " --> pdb=" O LEU G 161 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 208 removed outlier: 3.664A pdb=" N ALA G 189 " --> pdb=" O SER G 185 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N VAL G 198 " --> pdb=" O VAL G 194 " (cutoff:3.500A) Proline residue: G 199 - end of helix removed outlier: 3.993A pdb=" N VAL G 208 " --> pdb=" O PHE G 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 213 through 235 removed outlier: 3.616A pdb=" N VAL G 217 " --> pdb=" O GLY G 213 " (cutoff:3.500A) Processing helix chain 'G' and resid 240 through 264 Processing helix chain 'G' and resid 267 through 285 removed outlier: 3.501A pdb=" N ILE G 271 " --> pdb=" O SER G 267 " (cutoff:3.500A) Processing helix chain 'G' and resid 285 through 294 Processing helix chain 'G' and resid 319 through 349 Processing helix chain 'G' and resid 356 through 374 Processing helix chain 'G' and resid 379 through 404 removed outlier: 3.518A pdb=" N TRP G 385 " --> pdb=" O ALA G 381 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N SER G 390 " --> pdb=" O LEU G 386 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N TYR G 391 " --> pdb=" O LEU G 387 " (cutoff:3.500A) Processing helix chain 'G' and resid 406 through 430 removed outlier: 3.552A pdb=" N ALA G 410 " --> pdb=" O ARG G 406 " (cutoff:3.500A) Processing helix chain 'G' and resid 430 through 435 removed outlier: 3.634A pdb=" N ALA G 434 " --> pdb=" O ASN G 430 " (cutoff:3.500A) Processing helix chain 'G' and resid 440 through 466 removed outlier: 5.280A pdb=" N ILE G 459 " --> pdb=" O ASP G 455 " (cutoff:3.500A) Proline residue: G 460 - end of helix Processing helix chain 'G' and resid 469 through 474 Processing helix chain 'H' and resid 34 through 47 removed outlier: 3.980A pdb=" N ILE H 38 " --> pdb=" O PRO H 34 " (cutoff:3.500A) Proline residue: H 40 - end of helix removed outlier: 3.518A pdb=" N GLN H 47 " --> pdb=" O GLN H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 87 Processing helix chain 'H' and resid 115 through 123 Processing helix chain 'H' and resid 128 through 158 Processing helix chain 'H' and resid 160 through 181 removed outlier: 4.408A pdb=" N GLN H 164 " --> pdb=" O ASP H 160 " (cutoff:3.500A) Processing helix chain 'H' and resid 182 through 184 No H-bonds generated for 'chain 'H' and resid 182 through 184' Processing helix chain 'H' and resid 186 through 196 Processing helix chain 'H' and resid 196 through 206 Processing helix chain 'H' and resid 213 through 233 removed outlier: 4.021A pdb=" N VAL H 217 " --> pdb=" O GLY H 213 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA H 233 " --> pdb=" O LEU H 229 " (cutoff:3.500A) Processing helix chain 'H' and resid 239 through 264 removed outlier: 3.534A pdb=" N TRP H 264 " --> pdb=" O ALA H 260 " (cutoff:3.500A) Processing helix chain 'H' and resid 267 through 285 removed outlier: 3.527A pdb=" N ILE H 271 " --> pdb=" O SER H 267 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN H 285 " --> pdb=" O ILE H 281 " (cutoff:3.500A) Processing helix chain 'H' and resid 285 through 294 Processing helix chain 'H' and resid 313 through 351 removed outlier: 3.531A pdb=" N LEU H 317 " --> pdb=" O PRO H 313 " (cutoff:3.500A) Proline residue: H 321 - end of helix Processing helix chain 'H' and resid 356 through 373 Processing helix chain 'H' and resid 380 through 404 removed outlier: 3.846A pdb=" N ALA H 384 " --> pdb=" O ALA H 380 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N SER H 390 " --> pdb=" O LEU H 386 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N TYR H 391 " --> pdb=" O LEU H 387 " (cutoff:3.500A) Processing helix chain 'H' and resid 407 through 430 Processing helix chain 'H' and resid 435 through 439 Processing helix chain 'H' and resid 440 through 466 removed outlier: 4.331A pdb=" N ILE H 459 " --> pdb=" O ASP H 455 " (cutoff:3.500A) Proline residue: H 460 - end of helix Processing helix chain 'H' and resid 468 through 475 Processing helix chain 'I' and resid 34 through 51 Processing helix chain 'I' and resid 62 through 92 Processing helix chain 'J' and resid 95 through 130 Processing helix chain 'J' and resid 132 through 136 Processing helix chain 'J' and resid 183 through 197 Processing helix chain 'J' and resid 210 through 212 No H-bonds generated for 'chain 'J' and resid 210 through 212' Processing helix chain 'J' and resid 220 through 237 Processing helix chain 'J' and resid 255 through 260 removed outlier: 4.226A pdb=" N TRP J 260 " --> pdb=" O GLY J 256 " (cutoff:3.500A) Processing helix chain 'J' and resid 261 through 263 No H-bonds generated for 'chain 'J' and resid 261 through 263' Processing helix chain 'J' and resid 285 through 294 Processing helix chain 'J' and resid 295 through 297 No H-bonds generated for 'chain 'J' and resid 295 through 297' Processing helix chain 'J' and resid 324 through 328 removed outlier: 3.623A pdb=" N ILE J 328 " --> pdb=" O PRO J 325 " (cutoff:3.500A) Processing helix chain 'J' and resid 386 through 398 Processing sheet with id=AA1, first strand: chain 'A' and resid 166 through 169 removed outlier: 4.401A pdb=" N VAL A 79 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N SER A 120 " --> pdb=" O VAL A 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 99 removed outlier: 7.305A pdb=" N ASP A 105 " --> pdb=" O GLY A 228 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N GLY A 228 " --> pdb=" O ASP A 105 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU A 219 " --> pdb=" O ARG A 242 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N VAL A 237 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL A 199 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS A 181 " --> pdb=" O ALA A 188 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 181 through 183 removed outlier: 3.647A pdb=" N LYS A 181 " --> pdb=" O ALA A 188 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 166 through 169 removed outlier: 4.401A pdb=" N VAL A 79 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ASP A 127 " --> pdb=" O CYS A 104 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N CYS A 104 " --> pdb=" O ASP A 127 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N ASP A 105 " --> pdb=" O GLY A 228 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N GLY A 228 " --> pdb=" O ASP A 105 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU A 219 " --> pdb=" O ARG A 242 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N VAL A 237 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL A 199 " --> pdb=" O VAL A 237 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 67 through 71 removed outlier: 8.836A pdb=" N LEU B 94 " --> pdb=" O ARG B 11 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA B 13 " --> pdb=" O LEU B 94 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N LEU B 96 " --> pdb=" O ALA B 13 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N LEU B 15 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 9.457A pdb=" N ALA B 98 " --> pdb=" O LEU B 15 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 9 through 14 Processing sheet with id=AA7, first strand: chain 'C' and resid 68 through 70 Processing sheet with id=AA8, first strand: chain 'E' and resid 22 through 24 removed outlier: 6.039A pdb=" N ILE E 22 " --> pdb=" O LYS E 172 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 157 through 166 removed outlier: 6.793A pdb=" N VAL E 157 " --> pdb=" O ASP E 208 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASP E 208 " --> pdb=" O VAL E 157 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ARG E 159 " --> pdb=" O GLY E 206 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLY E 206 " --> pdb=" O ARG E 159 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N GLY E 161 " --> pdb=" O PRO E 204 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N HIS E 163 " --> pdb=" O ASP E 202 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP E 202 " --> pdb=" O HIS E 163 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 246 through 249 removed outlier: 6.225A pdb=" N ALA E 247 " --> pdb=" O VAL E 317 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL E 316 " --> pdb=" O ILE E 340 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ARG E 342 " --> pdb=" O VAL E 316 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LEU E 318 " --> pdb=" O ARG E 342 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N LEU E 360 " --> pdb=" O ARG E 214 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N THR E 216 " --> pdb=" O LEU E 360 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL E 362 " --> pdb=" O THR E 216 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE E 218 " --> pdb=" O VAL E 362 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ILE E 359 " --> pdb=" O TRP E 370 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 166 through 168 removed outlier: 3.868A pdb=" N SER F 120 " --> pdb=" O VAL F 82 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS F 106 " --> pdb=" O THR F 125 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N SER F 229 " --> pdb=" O GLU F 232 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N VAL F 237 " --> pdb=" O VAL F 199 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 98 through 99 Processing sheet with id=AB4, first strand: chain 'F' and resid 181 through 182 Processing sheet with id=AB5, first strand: chain 'G' and resid 67 through 71 removed outlier: 8.471A pdb=" N LEU G 94 " --> pdb=" O ARG G 11 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ALA G 13 " --> pdb=" O LEU G 94 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N LEU G 96 " --> pdb=" O ALA G 13 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N LEU G 15 " --> pdb=" O LEU G 96 " (cutoff:3.500A) removed outlier: 9.179A pdb=" N ALA G 98 " --> pdb=" O LEU G 15 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG G 23 " --> pdb=" O ALA G 16 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 24 through 30 removed outlier: 3.918A pdb=" N LEU H 96 " --> pdb=" O LEU H 15 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 23 through 24 Processing sheet with id=AB8, first strand: chain 'J' and resid 157 through 163 removed outlier: 6.938A pdb=" N THR J 205 " --> pdb=" O ALA J 160 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ARG J 162 " --> pdb=" O ALA J 203 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ALA J 203 " --> pdb=" O ARG J 162 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 216 through 219 removed outlier: 5.824A pdb=" N THR J 216 " --> pdb=" O LEU J 360 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N VAL J 362 " --> pdb=" O THR J 216 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE J 218 " --> pdb=" O VAL J 362 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ILE J 359 " --> pdb=" O TRP J 370 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 246 through 248 removed outlier: 6.429A pdb=" N ALA J 247 " --> pdb=" O VAL J 317 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N LEU J 314 " --> pdb=" O THR J 338 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ILE J 340 " --> pdb=" O LEU J 314 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL J 316 " --> pdb=" O ILE J 340 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 1531 hydrogen bonds defined for protein. 4485 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: 8.09 Time building geometry restraints manager: 10.70 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: 7885 1.34 - 1.45: 3036 1.45 - 1.57: 13116 1.57 - 1.69: 0 1.69 - 1.81: 104 Bond restraints: 24141 Sorted by residual: bond pdb=" C LEU A 270 " pdb=" N ASN A 271 " ideal model delta sigma weight residual 1.327 1.246 0.081 2.31e-02 1.87e+03 1.23e+01 bond pdb=" N VAL G 350 " pdb=" CA VAL G 350 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.92e+00 bond pdb=" N LEU G 349 " pdb=" CA LEU G 349 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.10e-02 8.26e+03 7.90e+00 bond pdb=" N ARG C 312 " pdb=" CA ARG C 312 " ideal model delta sigma weight residual 1.452 1.489 -0.037 1.41e-02 5.03e+03 6.75e+00 bond pdb=" N SER G 351 " pdb=" CA SER G 351 " ideal model delta sigma weight residual 1.458 1.487 -0.030 1.22e-02 6.72e+03 6.00e+00 ... (remaining 24136 not shown) Histogram of bond angle deviations from ideal: 98.64 - 105.74: 737 105.74 - 112.84: 14013 112.84 - 119.93: 7508 119.93 - 127.03: 10420 127.03 - 134.13: 423 Bond angle restraints: 33101 Sorted by residual: angle pdb=" N ILE E 328 " pdb=" CA ILE E 328 " pdb=" C ILE E 328 " ideal model delta sigma weight residual 113.71 107.40 6.31 9.50e-01 1.11e+00 4.41e+01 angle pdb=" N ARG J 151 " pdb=" CA ARG J 151 " pdb=" C ARG J 151 " ideal model delta sigma weight residual 114.64 105.58 9.06 1.52e+00 4.33e-01 3.55e+01 angle pdb=" N ILE J 328 " pdb=" CA ILE J 328 " pdb=" C ILE J 328 " ideal model delta sigma weight residual 111.62 108.19 3.43 7.90e-01 1.60e+00 1.88e+01 angle pdb=" N ASP H 19 " pdb=" CA ASP H 19 " pdb=" C ASP H 19 " ideal model delta sigma weight residual 114.39 108.40 5.99 1.45e+00 4.76e-01 1.71e+01 angle pdb=" N TRP E 258 " pdb=" CA TRP E 258 " pdb=" C TRP E 258 " ideal model delta sigma weight residual 114.64 108.46 6.18 1.52e+00 4.33e-01 1.66e+01 ... (remaining 33096 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 13337 17.86 - 35.71: 913 35.71 - 53.57: 130 53.57 - 71.43: 43 71.43 - 89.28: 24 Dihedral angle restraints: 14447 sinusoidal: 5342 harmonic: 9105 Sorted by residual: dihedral pdb=" CA SER D 15 " pdb=" C SER D 15 " pdb=" N ARG D 16 " pdb=" CA ARG D 16 " ideal model delta harmonic sigma weight residual -180.00 -158.17 -21.83 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA ARG E 349 " pdb=" C ARG E 349 " pdb=" N GLU E 350 " pdb=" CA GLU E 350 " ideal model delta harmonic sigma weight residual 180.00 159.32 20.68 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA ASP E 364 " pdb=" C ASP E 364 " pdb=" N GLY E 365 " pdb=" CA GLY E 365 " ideal model delta harmonic sigma weight residual 180.00 -159.40 -20.60 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 14444 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 3260 0.053 - 0.106: 689 0.106 - 0.159: 104 0.159 - 0.212: 5 0.212 - 0.265: 1 Chirality restraints: 4059 Sorted by residual: chirality pdb=" CB ILE H 459 " pdb=" CA ILE H 459 " pdb=" CG1 ILE H 459 " pdb=" CG2 ILE H 459 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CB ILE J 180 " pdb=" CA ILE J 180 " pdb=" CG1 ILE J 180 " pdb=" CG2 ILE J 180 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB VAL C 167 " pdb=" CA VAL C 167 " pdb=" CG1 VAL C 167 " pdb=" CG2 VAL C 167 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.77e-01 ... (remaining 4056 not shown) Planarity restraints: 4231 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL E 200 " -0.010 2.00e-02 2.50e+03 2.12e-02 4.47e+00 pdb=" C VAL E 200 " 0.037 2.00e-02 2.50e+03 pdb=" O VAL E 200 " -0.014 2.00e-02 2.50e+03 pdb=" N ARG E 201 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER H 435 " -0.031 5.00e-02 4.00e+02 4.65e-02 3.46e+00 pdb=" N PRO H 436 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO H 436 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO H 436 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 441 " -0.030 5.00e-02 4.00e+02 4.54e-02 3.30e+00 pdb=" N PRO C 442 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO C 442 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 442 " -0.026 5.00e-02 4.00e+02 ... (remaining 4228 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3222 2.74 - 3.28: 24920 3.28 - 3.82: 39502 3.82 - 4.36: 44139 4.36 - 4.90: 76758 Nonbonded interactions: 188541 Sorted by model distance: nonbonded pdb=" OG SER C 352 " pdb=" OD1 ASN C 354 " model vdw 2.203 2.440 nonbonded pdb=" O THR C 82 " pdb=" OG1 THR C 85 " model vdw 2.227 2.440 nonbonded pdb=" NH1 ARG J 225 " pdb=" OD2 ASP J 257 " model vdw 2.230 2.520 nonbonded pdb=" OG SER G 31 " pdb=" OD1 ASP G 84 " model vdw 2.231 2.440 nonbonded pdb=" NE ARG A 138 " pdb=" OE2 GLU C 110 " model vdw 2.237 2.520 ... (remaining 188536 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 'F' } ncs_group { reference = (chain 'B' and (resid 7 through 49 or resid 67 through 475)) selection = (chain 'C' and (resid 7 through 295 or resid 313 through 475)) selection = (chain 'G' and (resid 7 through 49 or resid 67 through 475)) selection = (chain 'H' and (resid 7 through 295 or resid 313 through 475)) } ncs_group { reference = chain 'E' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 15131 2.51 5 N 4240 2.21 5 O 4227 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 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: 5.020 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: 0.030 Extract box with map and model: 19.370 Check model and map are aligned: 0.380 Convert atoms to be neutral: 0.220 Process input model: 62.630 Find NCS groups from input model: 1.570 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5559 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 0.081 24141 Z= 0.429 Angle : 0.793 13.638 33101 Z= 0.455 Chirality : 0.043 0.265 4059 Planarity : 0.005 0.046 4231 Dihedral : 13.227 89.283 8539 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer Outliers : 0.17 % 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: -2.07 (0.13), residues: 3148 helix: -0.54 (0.11), residues: 1748 sheet: -2.31 (0.25), residues: 283 loop : -2.33 (0.16), residues: 1117 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 599 time to evaluate : 2.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 600 average time/residue: 0.3199 time to fit residues: 305.1350 Evaluate side-chains 367 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 366 time to evaluate : 2.677 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.7471 time to fit residues: 4.3486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 266 optimal weight: 0.9990 chunk 239 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 81 optimal weight: 0.7980 chunk 161 optimal weight: 7.9990 chunk 127 optimal weight: 9.9990 chunk 247 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 150 optimal weight: 6.9990 chunk 184 optimal weight: 8.9990 chunk 286 optimal weight: 5.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN A 89 GLN ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 HIS ** B 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 GLN C 154 HIS C 216 ASN C 328 GLN E 130 HIS E 187 HIS ** E 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 271 ASN E 313 HIS F 74 HIS ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 271 ASN G 47 GLN G 328 GLN ** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 234 GLN ** J 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 313 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5724 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.065 24141 Z= 0.248 Angle : 0.733 10.307 33101 Z= 0.357 Chirality : 0.045 0.380 4059 Planarity : 0.005 0.077 4231 Dihedral : 4.843 73.935 3452 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer Outliers : 3.15 % 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: -0.54 (0.15), residues: 3148 helix: 0.63 (0.12), residues: 1761 sheet: -1.83 (0.27), residues: 288 loop : -1.46 (0.18), residues: 1099 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 396 time to evaluate : 2.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 76 outliers final: 34 residues processed: 437 average time/residue: 0.3007 time to fit residues: 215.1389 Evaluate side-chains 361 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 327 time to evaluate : 2.783 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.2438 time to fit residues: 18.3533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 159 optimal weight: 40.0000 chunk 89 optimal weight: 4.9990 chunk 238 optimal weight: 2.9990 chunk 195 optimal weight: 30.0000 chunk 79 optimal weight: 1.9990 chunk 287 optimal weight: 5.9990 chunk 310 optimal weight: 30.0000 chunk 256 optimal weight: 8.9990 chunk 285 optimal weight: 9.9990 chunk 98 optimal weight: 6.9990 chunk 230 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 234 GLN ** E 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 89 GLN ** F 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 43 GLN H 131 HIS ** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 408 GLN ** J 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5831 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.080 24141 Z= 0.278 Angle : 0.751 12.203 33101 Z= 0.362 Chirality : 0.044 0.287 4059 Planarity : 0.005 0.050 4231 Dihedral : 4.709 70.900 3452 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 19.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer Outliers : 3.06 % 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: -0.07 (0.15), residues: 3148 helix: 0.95 (0.12), residues: 1768 sheet: -1.65 (0.27), residues: 294 loop : -1.14 (0.18), residues: 1086 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 353 time to evaluate : 2.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 74 outliers final: 33 residues processed: 399 average time/residue: 0.3155 time to fit residues: 210.2920 Evaluate side-chains 348 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 315 time to evaluate : 2.650 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.2108 time to fit residues: 16.9654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 284 optimal weight: 0.1980 chunk 216 optimal weight: 4.9990 chunk 149 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 137 optimal weight: 9.9990 chunk 193 optimal weight: 7.9990 chunk 288 optimal weight: 3.9990 chunk 305 optimal weight: 5.9990 chunk 150 optimal weight: 4.9990 chunk 273 optimal weight: 5.9990 chunk 82 optimal weight: 0.2980 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 GLN C 126 GLN ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5822 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.066 24141 Z= 0.219 Angle : 0.745 13.592 33101 Z= 0.348 Chirality : 0.044 0.343 4059 Planarity : 0.005 0.051 4231 Dihedral : 4.647 68.416 3452 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 18.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer Outliers : 2.28 % 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: 0.29 (0.15), residues: 3148 helix: 1.18 (0.12), residues: 1769 sheet: -1.51 (0.27), residues: 290 loop : -0.87 (0.19), residues: 1089 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 345 time to evaluate : 2.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 23 residues processed: 378 average time/residue: 0.2781 time to fit residues: 176.6769 Evaluate side-chains 335 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 312 time to evaluate : 2.800 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.2152 time to fit residues: 12.5060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 254 optimal weight: 5.9990 chunk 173 optimal weight: 10.0000 chunk 4 optimal weight: 7.9990 chunk 227 optimal weight: 0.2980 chunk 126 optimal weight: 20.0000 chunk 260 optimal weight: 10.0000 chunk 211 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 155 optimal weight: 8.9990 chunk 274 optimal weight: 5.9990 chunk 77 optimal weight: 20.0000 overall best weight: 4.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 GLN ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 HIS ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5902 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.073 24141 Z= 0.268 Angle : 0.754 14.042 33101 Z= 0.359 Chirality : 0.045 0.402 4059 Planarity : 0.005 0.054 4231 Dihedral : 4.617 64.423 3452 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 21.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer Outliers : 2.15 % 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: 0.43 (0.15), residues: 3148 helix: 1.25 (0.12), residues: 1770 sheet: -1.43 (0.27), residues: 290 loop : -0.74 (0.19), residues: 1088 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 327 time to evaluate : 2.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 23 residues processed: 359 average time/residue: 0.2909 time to fit residues: 175.8937 Evaluate side-chains 325 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 302 time to evaluate : 2.874 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.2208 time to fit residues: 13.3465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 102 optimal weight: 0.9980 chunk 275 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 179 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 305 optimal weight: 8.9990 chunk 253 optimal weight: 0.9990 chunk 141 optimal weight: 8.9990 chunk 25 optimal weight: 0.3980 chunk 101 optimal weight: 2.9990 chunk 160 optimal weight: 3.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 GLN ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5840 moved from start: 0.4330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 24141 Z= 0.192 Angle : 0.771 13.924 33101 Z= 0.350 Chirality : 0.045 0.404 4059 Planarity : 0.004 0.056 4231 Dihedral : 4.524 61.219 3452 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 19.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer Outliers : 1.53 % 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: 0.52 (0.15), residues: 3148 helix: 1.25 (0.12), residues: 1772 sheet: -1.27 (0.28), residues: 289 loop : -0.61 (0.19), residues: 1087 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 337 time to evaluate : 2.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 11 residues processed: 359 average time/residue: 0.2797 time to fit residues: 171.0597 Evaluate side-chains 318 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 307 time to evaluate : 2.803 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2144 time to fit residues: 8.1335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 294 optimal weight: 8.9990 chunk 34 optimal weight: 0.5980 chunk 174 optimal weight: 10.0000 chunk 223 optimal weight: 5.9990 chunk 172 optimal weight: 7.9990 chunk 257 optimal weight: 8.9990 chunk 170 optimal weight: 8.9990 chunk 304 optimal weight: 4.9990 chunk 190 optimal weight: 2.9990 chunk 185 optimal weight: 20.0000 chunk 140 optimal weight: 7.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5936 moved from start: 0.4678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 24141 Z= 0.277 Angle : 0.804 13.843 33101 Z= 0.378 Chirality : 0.046 0.398 4059 Planarity : 0.005 0.055 4231 Dihedral : 4.570 56.130 3452 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 22.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer Outliers : 1.49 % 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: 0.63 (0.15), residues: 3148 helix: 1.36 (0.12), residues: 1759 sheet: -1.19 (0.27), residues: 292 loop : -0.58 (0.19), residues: 1097 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 318 time to evaluate : 2.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 18 residues processed: 336 average time/residue: 0.2872 time to fit residues: 164.0203 Evaluate side-chains 317 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 299 time to evaluate : 2.680 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2122 time to fit residues: 10.5113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 188 optimal weight: 0.9990 chunk 121 optimal weight: 0.0970 chunk 181 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 chunk 193 optimal weight: 6.9990 chunk 207 optimal weight: 7.9990 chunk 150 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 239 optimal weight: 5.9990 chunk 277 optimal weight: 3.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 HIS ** B 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 GLN ** C 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 55 HIS ** J 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5888 moved from start: 0.4834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 24141 Z= 0.212 Angle : 0.823 17.031 33101 Z= 0.374 Chirality : 0.047 0.437 4059 Planarity : 0.004 0.054 4231 Dihedral : 4.532 51.806 3452 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 20.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer Outliers : 0.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.15), residues: 3148 helix: 1.36 (0.12), residues: 1757 sheet: -1.14 (0.27), residues: 292 loop : -0.55 (0.19), residues: 1099 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 318 time to evaluate : 2.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 11 residues processed: 329 average time/residue: 0.2976 time to fit residues: 164.8894 Evaluate side-chains 312 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 301 time to evaluate : 2.963 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2180 time to fit residues: 8.2691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 291 optimal weight: 2.9990 chunk 266 optimal weight: 1.9990 chunk 283 optimal weight: 5.9990 chunk 170 optimal weight: 9.9990 chunk 123 optimal weight: 2.9990 chunk 222 optimal weight: 7.9990 chunk 87 optimal weight: 9.9990 chunk 256 optimal weight: 4.9990 chunk 268 optimal weight: 5.9990 chunk 282 optimal weight: 20.0000 chunk 186 optimal weight: 20.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5946 moved from start: 0.5112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 24141 Z= 0.257 Angle : 0.856 17.621 33101 Z= 0.393 Chirality : 0.049 0.428 4059 Planarity : 0.005 0.054 4231 Dihedral : 4.548 46.930 3452 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 22.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer Outliers : 0.33 % 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: 0.73 (0.15), residues: 3148 helix: 1.37 (0.12), residues: 1741 sheet: -1.16 (0.27), residues: 292 loop : -0.35 (0.20), residues: 1115 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 312 time to evaluate : 2.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 317 average time/residue: 0.2941 time to fit residues: 159.5862 Evaluate side-chains 297 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 292 time to evaluate : 2.537 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2085 time to fit residues: 5.7080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 300 optimal weight: 8.9990 chunk 183 optimal weight: 0.0870 chunk 142 optimal weight: 3.9990 chunk 208 optimal weight: 4.9990 chunk 314 optimal weight: 9.9990 chunk 289 optimal weight: 4.9990 chunk 250 optimal weight: 5.9990 chunk 26 optimal weight: 20.0000 chunk 193 optimal weight: 2.9990 chunk 153 optimal weight: 7.9990 chunk 199 optimal weight: 20.0000 overall best weight: 3.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5936 moved from start: 0.5290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.080 24141 Z= 0.240 Angle : 0.864 16.918 33101 Z= 0.396 Chirality : 0.050 0.483 4059 Planarity : 0.005 0.052 4231 Dihedral : 4.524 42.597 3452 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 22.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer Outliers : 0.21 % 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: 0.75 (0.15), residues: 3148 helix: 1.36 (0.12), residues: 1735 sheet: -1.12 (0.27), residues: 292 loop : -0.30 (0.20), residues: 1121 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 307 time to evaluate : 2.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 309 average time/residue: 0.2931 time to fit residues: 153.6969 Evaluate side-chains 297 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 294 time to evaluate : 2.954 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2132 time to fit residues: 4.8129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 267 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 231 optimal weight: 6.9990 chunk 37 optimal weight: 20.0000 chunk 69 optimal weight: 6.9990 chunk 251 optimal weight: 0.9980 chunk 105 optimal weight: 5.9990 chunk 257 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 220 optimal weight: 6.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 330 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 = 0.3166 r_free = 0.3166 target = 0.043087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.036305 restraints weight = 234751.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.036983 restraints weight = 158046.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.037439 restraints weight = 120470.502| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.5462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.081 24141 Z= 0.263 Angle : 0.872 16.603 33101 Z= 0.403 Chirality : 0.050 0.478 4059 Planarity : 0.005 0.059 4231 Dihedral : 4.525 39.507 3452 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 24.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer Outliers : 0.62 % 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: 0.76 (0.15), residues: 3148 helix: 1.35 (0.12), residues: 1739 sheet: -1.12 (0.28), residues: 290 loop : -0.27 (0.20), residues: 1119 =============================================================================== Job complete usr+sys time: 4501.10 seconds wall clock time: 82 minutes 43.99 seconds (4963.99 seconds total)