Starting phenix.real_space_refine on Thu Nov 16 21:58:53 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qh2_13960/11_2023/7qh2_13960_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qh2_13960/11_2023/7qh2_13960.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qh2_13960/11_2023/7qh2_13960.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qh2_13960/11_2023/7qh2_13960.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qh2_13960/11_2023/7qh2_13960_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qh2_13960/11_2023/7qh2_13960_updated.pdb" } resolution = 2.43 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 2 7.16 5 P 12 5.49 5 S 98 5.16 5 C 10676 2.51 5 N 2755 2.21 5 O 3265 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 91": "OE1" <-> "OE2" Residue "A GLU 122": "OE1" <-> "OE2" Residue "A GLU 247": "OE1" <-> "OE2" Residue "A ARG 311": "NH1" <-> "NH2" Residue "A ARG 322": "NH1" <-> "NH2" Residue "A ARG 330": "NH1" <-> "NH2" Residue "A GLU 393": "OE1" <-> "OE2" Residue "A GLU 396": "OE1" <-> "OE2" Residue "B GLU 32": "OE1" <-> "OE2" Residue "B ARG 170": "NH1" <-> "NH2" Residue "B ARG 187": "NH1" <-> "NH2" Residue "B GLU 216": "OE1" <-> "OE2" Residue "B GLU 244": "OE1" <-> "OE2" Residue "C GLU 7": "OE1" <-> "OE2" Residue "C GLU 16": "OE1" <-> "OE2" Residue "C ARG 22": "NH1" <-> "NH2" Residue "C GLU 37": "OE1" <-> "OE2" Residue "C ARG 74": "NH1" <-> "NH2" Residue "C GLU 139": "OE1" <-> "OE2" Residue "C ARG 156": "NH1" <-> "NH2" Residue "C GLU 178": "OE1" <-> "OE2" Residue "C GLU 231": "OE1" <-> "OE2" Residue "C GLU 265": "OE1" <-> "OE2" Residue "C GLU 294": "OE1" <-> "OE2" Residue "C GLU 319": "OE1" <-> "OE2" Residue "C ARG 320": "NH1" <-> "NH2" Residue "C ARG 328": "NH1" <-> "NH2" Residue "C GLU 333": "OE1" <-> "OE2" Residue "C GLU 367": "OE1" <-> "OE2" Residue "C ARG 371": "NH1" <-> "NH2" Residue "C GLU 398": "OE1" <-> "OE2" Residue "C ARG 407": "NH1" <-> "NH2" Residue "D GLU 91": "OE1" <-> "OE2" Residue "D GLU 122": "OE1" <-> "OE2" Residue "D ARG 183": "NH1" <-> "NH2" Residue "D GLU 247": "OE1" <-> "OE2" Residue "D ARG 311": "NH1" <-> "NH2" Residue "D ARG 330": "NH1" <-> "NH2" Residue "D GLU 393": "OE1" <-> "OE2" Residue "D GLU 396": "OE1" <-> "OE2" Residue "E ARG 170": "NH1" <-> "NH2" Residue "E GLU 216": "OE1" <-> "OE2" Residue "E GLU 244": "OE1" <-> "OE2" Residue "F GLU 7": "OE1" <-> "OE2" Residue "F GLU 16": "OE1" <-> "OE2" Residue "F ARG 22": "NH1" <-> "NH2" Residue "F GLU 37": "OE1" <-> "OE2" Residue "F GLU 56": "OE1" <-> "OE2" Residue "F ARG 74": "NH1" <-> "NH2" Residue "F GLU 139": "OE1" <-> "OE2" Residue "F ARG 156": "NH1" <-> "NH2" Residue "F GLU 178": "OE1" <-> "OE2" Residue "F GLU 265": "OE1" <-> "OE2" Residue "F GLU 294": "OE1" <-> "OE2" Residue "F GLU 319": "OE1" <-> "OE2" Residue "F ARG 320": "NH1" <-> "NH2" Residue "F GLU 333": "OE1" <-> "OE2" Residue "F GLU 344": "OE1" <-> "OE2" Residue "F ARG 351": "NH1" <-> "NH2" Residue "F ARG 371": "NH1" <-> "NH2" Residue "F GLU 398": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 16808 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2604 Classifications: {'peptide': 337} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 320} Chain: "B" Number of atoms: 2041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2041 Classifications: {'peptide': 265} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 250} Chain: "C" Number of atoms: 3603 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 467, 3593 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 18, 'TRANS': 448} Conformer: "B" Number of residues, atoms: 467, 3593 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 18, 'TRANS': 448} bond proxies already assigned to first conformer: 3643 Chain: "D" Number of atoms: 2604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2604 Classifications: {'peptide': 337} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 320} Chain: "E" Number of atoms: 2041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2041 Classifications: {'peptide': 265} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 250} Chain: "F" Number of atoms: 3593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3593 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 18, 'TRANS': 448} Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {' FE': 1, 'FAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {' FE': 1, 'FAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AHIS C 42 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS C 42 " occ=0.50 Time building chain proxies: 10.54, per 1000 atoms: 0.63 Number of scatterers: 16808 At special positions: 0 Unit cell: (162.75, 78.12, 115.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 2 26.01 S 98 16.00 P 12 15.00 O 3265 8.00 N 2755 7.00 C 10676 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: 5.81 Conformation dependent library (CDL) restraints added in 3.5 seconds 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3934 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 77 helices and 16 sheets defined 33.3% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.31 Creating SS restraints... Processing helix chain 'A' and resid 88 through 103 removed outlier: 3.514A pdb=" N ALA A 101 " --> pdb=" O ARG A 97 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL A 102 " --> pdb=" O GLU A 98 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 119 No H-bonds generated for 'chain 'A' and resid 117 through 119' Processing helix chain 'A' and resid 121 through 126 removed outlier: 4.137A pdb=" N TYR A 126 " --> pdb=" O GLU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 158 Processing helix chain 'A' and resid 171 through 181 removed outlier: 3.520A pdb=" N ALA A 175 " --> pdb=" O GLY A 171 " (cutoff:3.500A) Proline residue: A 176 - end of helix removed outlier: 3.546A pdb=" N ARG A 181 " --> pdb=" O ARG A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 276 No H-bonds generated for 'chain 'A' and resid 274 through 276' Processing helix chain 'A' and resid 290 through 300 removed outlier: 3.563A pdb=" N ASP A 294 " --> pdb=" O LYS A 291 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N HIS A 297 " --> pdb=" O ASP A 294 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU A 298 " --> pdb=" O MET A 295 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA A 300 " --> pdb=" O HIS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 315 Processing helix chain 'A' and resid 321 through 323 No H-bonds generated for 'chain 'A' and resid 321 through 323' Processing helix chain 'A' and resid 346 through 351 removed outlier: 4.360A pdb=" N GLY A 351 " --> pdb=" O GLN A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 371 Processing helix chain 'A' and resid 381 through 392 Proline residue: A 386 - end of helix Processing helix chain 'A' and resid 394 through 397 No H-bonds generated for 'chain 'A' and resid 394 through 397' Processing helix chain 'B' and resid 37 through 53 removed outlier: 3.726A pdb=" N PHE B 41 " --> pdb=" O PRO B 37 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY B 42 " --> pdb=" O TYR B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 77 removed outlier: 3.679A pdb=" N VAL B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU B 73 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER B 74 " --> pdb=" O LEU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing helix chain 'B' and resid 95 through 108 Processing helix chain 'B' and resid 129 through 137 removed outlier: 3.556A pdb=" N GLU B 135 " --> pdb=" O PRO B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 260 removed outlier: 3.621A pdb=" N ALA B 253 " --> pdb=" O VAL B 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 17 removed outlier: 3.655A pdb=" N LEU C 17 " --> pdb=" O ALA C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 22 No H-bonds generated for 'chain 'C' and resid 20 through 22' Processing helix chain 'C' and resid 26 through 28 No H-bonds generated for 'chain 'C' and resid 26 through 28' Processing helix chain 'C' and resid 31 through 34 Processing helix chain 'C' and resid 54 through 67 Processing helix chain 'C' and resid 119 through 128 removed outlier: 3.530A pdb=" N LYS C 124 " --> pdb=" O MET C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 149 Processing helix chain 'C' and resid 155 through 158 removed outlier: 4.346A pdb=" N VAL C 158 " --> pdb=" O MET C 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 155 through 158' Processing helix chain 'C' and resid 163 through 166 Processing helix chain 'C' and resid 195 through 199 Processing helix chain 'C' and resid 233 through 246 removed outlier: 3.681A pdb=" N ILE C 239 " --> pdb=" O ASP C 235 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N VAL C 240 " --> pdb=" O ALA C 236 " (cutoff:3.500A) Proline residue: C 241 - end of helix Processing helix chain 'C' and resid 258 through 268 removed outlier: 3.755A pdb=" N PHE C 263 " --> pdb=" O GLN C 259 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA C 264 " --> pdb=" O THR C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 307 removed outlier: 3.590A pdb=" N THR C 299 " --> pdb=" O ALA C 295 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL C 300 " --> pdb=" O GLU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 329 removed outlier: 3.747A pdb=" N SER C 326 " --> pdb=" O ASP C 322 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ALA C 327 " --> pdb=" O SER C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 337 Processing helix chain 'C' and resid 351 through 368 removed outlier: 3.621A pdb=" N ILE C 354 " --> pdb=" O ARG C 351 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N ALA C 355 " --> pdb=" O ASN C 352 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU C 356 " --> pdb=" O ARG C 353 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE C 358 " --> pdb=" O ALA C 355 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU C 359 " --> pdb=" O GLU C 356 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU C 364 " --> pdb=" O THR C 361 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA C 365 " --> pdb=" O HIS C 362 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS C 366 " --> pdb=" O ASP C 363 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N MET C 368 " --> pdb=" O ALA C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 414 Processing helix chain 'C' and resid 430 through 436 Processing helix chain 'C' and resid 439 through 452 Processing helix chain 'D' and resid 88 through 103 removed outlier: 3.514A pdb=" N ALA D 101 " --> pdb=" O ARG D 97 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL D 102 " --> pdb=" O GLU D 98 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE D 103 " --> pdb=" O LEU D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 119 No H-bonds generated for 'chain 'D' and resid 117 through 119' Processing helix chain 'D' and resid 121 through 126 removed outlier: 4.157A pdb=" N TYR D 126 " --> pdb=" O GLU D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 158 Processing helix chain 'D' and resid 171 through 182 removed outlier: 3.519A pdb=" N ALA D 175 " --> pdb=" O GLY D 171 " (cutoff:3.500A) Proline residue: D 176 - end of helix removed outlier: 3.546A pdb=" N ARG D 181 " --> pdb=" O ARG D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 276 No H-bonds generated for 'chain 'D' and resid 274 through 276' Processing helix chain 'D' and resid 290 through 300 removed outlier: 3.563A pdb=" N ASP D 294 " --> pdb=" O LYS D 291 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N HIS D 297 " --> pdb=" O ASP D 294 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU D 298 " --> pdb=" O MET D 295 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA D 300 " --> pdb=" O HIS D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 315 Processing helix chain 'D' and resid 321 through 323 No H-bonds generated for 'chain 'D' and resid 321 through 323' Processing helix chain 'D' and resid 346 through 351 removed outlier: 4.359A pdb=" N GLY D 351 " --> pdb=" O GLN D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 371 Processing helix chain 'D' and resid 381 through 392 Proline residue: D 386 - end of helix Processing helix chain 'D' and resid 394 through 397 No H-bonds generated for 'chain 'D' and resid 394 through 397' Processing helix chain 'E' and resid 37 through 53 removed outlier: 3.726A pdb=" N PHE E 41 " --> pdb=" O PRO E 37 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY E 42 " --> pdb=" O TYR E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 77 removed outlier: 3.678A pdb=" N VAL E 70 " --> pdb=" O SER E 67 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU E 73 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER E 74 " --> pdb=" O LEU E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'E' and resid 95 through 108 Processing helix chain 'E' and resid 129 through 137 removed outlier: 3.556A pdb=" N GLU E 135 " --> pdb=" O PRO E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 194 No H-bonds generated for 'chain 'E' and resid 191 through 194' Processing helix chain 'E' and resid 248 through 260 removed outlier: 3.620A pdb=" N ALA E 253 " --> pdb=" O VAL E 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 17 removed outlier: 3.704A pdb=" N LEU F 17 " --> pdb=" O ALA F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 22 No H-bonds generated for 'chain 'F' and resid 20 through 22' Processing helix chain 'F' and resid 26 through 28 No H-bonds generated for 'chain 'F' and resid 26 through 28' Processing helix chain 'F' and resid 31 through 34 Processing helix chain 'F' and resid 54 through 67 Processing helix chain 'F' and resid 119 through 128 Processing helix chain 'F' and resid 144 through 149 Processing helix chain 'F' and resid 155 through 158 removed outlier: 4.366A pdb=" N VAL F 158 " --> pdb=" O MET F 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 155 through 158' Processing helix chain 'F' and resid 163 through 166 Processing helix chain 'F' and resid 195 through 199 Processing helix chain 'F' and resid 233 through 246 removed outlier: 3.661A pdb=" N ILE F 239 " --> pdb=" O ASP F 235 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL F 240 " --> pdb=" O ALA F 236 " (cutoff:3.500A) Proline residue: F 241 - end of helix Processing helix chain 'F' and resid 258 through 268 removed outlier: 3.663A pdb=" N PHE F 263 " --> pdb=" O GLN F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 290 through 307 removed outlier: 3.959A pdb=" N ALA F 306 " --> pdb=" O ASN F 302 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU F 307 " --> pdb=" O LEU F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 329 removed outlier: 4.531A pdb=" N ALA F 327 " --> pdb=" O SER F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 331 through 337 Processing helix chain 'F' and resid 351 through 368 removed outlier: 3.728A pdb=" N ILE F 354 " --> pdb=" O ARG F 351 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N ALA F 355 " --> pdb=" O ASN F 352 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU F 356 " --> pdb=" O ARG F 353 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE F 358 " --> pdb=" O ALA F 355 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU F 359 " --> pdb=" O GLU F 356 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU F 364 " --> pdb=" O THR F 361 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA F 365 " --> pdb=" O HIS F 362 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS F 366 " --> pdb=" O ASP F 363 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N MET F 368 " --> pdb=" O ALA F 365 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 414 Processing helix chain 'F' and resid 430 through 436 Processing helix chain 'F' and resid 439 through 452 Processing sheet with id= A, first strand: chain 'A' and resid 224 through 228 removed outlier: 5.042A pdb=" N GLY A 166 " --> pdb=" O TYR A 77 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LYS A 130 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N LEU A 111 " --> pdb=" O LYS A 130 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N PHE A 132 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ASP A 245 " --> pdb=" O VAL A 131 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N VAL A 133 " --> pdb=" O ASP A 245 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLU A 247 " --> pdb=" O VAL A 133 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 212 through 217 removed outlier: 7.066A pdb=" N CYS A 190 " --> pdb=" O PRO A 206 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 306 through 309 removed outlier: 6.466A pdb=" N LEU A 336 " --> pdb=" O ILE A 280 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N ALA A 282 " --> pdb=" O LEU A 336 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ILE A 338 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N CYS A 375 " --> pdb=" O ALA A 360 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N ASN A 362 " --> pdb=" O CYS A 375 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N MET A 377 " --> pdb=" O ASN A 362 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 166 through 171 removed outlier: 3.732A pdb=" N LYS B 147 " --> pdb=" O GLN B 159 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN B 161 " --> pdb=" O VAL B 145 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL B 145 " --> pdb=" O ASN B 161 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N THR B 56 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N VAL B 6 " --> pdb=" O THR B 56 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N THR B 58 " --> pdb=" O VAL B 6 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLU B 81 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N SER B 61 " --> pdb=" O GLU B 81 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N CYS B 83 " --> pdb=" O SER B 61 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 23 through 25 Processing sheet with id= F, first strand: chain 'C' and resid 101 through 105 removed outlier: 6.510A pdb=" N THR C 112 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N LEU C 104 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N THR C 110 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LYS C 215 " --> pdb=" O VAL C 167 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N VAL C 167 " --> pdb=" O LYS C 215 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 313 through 315 removed outlier: 3.630A pdb=" N ALA C 279 " --> pdb=" O PHE C 230 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA C 252 " --> pdb=" O THR C 284 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 342 through 345 Processing sheet with id= I, first strand: chain 'D' and resid 224 through 228 removed outlier: 5.042A pdb=" N GLY D 166 " --> pdb=" O TYR D 77 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LYS D 130 " --> pdb=" O ALA D 109 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N LEU D 111 " --> pdb=" O LYS D 130 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N PHE D 132 " --> pdb=" O LEU D 111 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ASP D 245 " --> pdb=" O VAL D 131 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N VAL D 133 " --> pdb=" O ASP D 245 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLU D 247 " --> pdb=" O VAL D 133 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 212 through 217 removed outlier: 7.065A pdb=" N CYS D 190 " --> pdb=" O PRO D 206 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 306 through 309 removed outlier: 6.466A pdb=" N LEU D 336 " --> pdb=" O ILE D 280 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ALA D 282 " --> pdb=" O LEU D 336 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ILE D 338 " --> pdb=" O ALA D 282 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N CYS D 375 " --> pdb=" O ALA D 360 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N ASN D 362 " --> pdb=" O CYS D 375 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N MET D 377 " --> pdb=" O ASN D 362 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 166 through 171 removed outlier: 3.732A pdb=" N LYS E 147 " --> pdb=" O GLN E 159 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASN E 161 " --> pdb=" O VAL E 145 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL E 145 " --> pdb=" O ASN E 161 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU E 114 " --> pdb=" O LYS E 3 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N THR E 56 " --> pdb=" O ILE E 4 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N VAL E 6 " --> pdb=" O THR E 56 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N THR E 58 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLU E 81 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N SER E 61 " --> pdb=" O GLU E 81 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N CYS E 83 " --> pdb=" O SER E 61 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 23 through 25 Processing sheet with id= N, first strand: chain 'F' and resid 101 through 105 removed outlier: 6.515A pdb=" N THR F 112 " --> pdb=" O LEU F 102 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N LEU F 104 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR F 110 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LYS F 215 " --> pdb=" O VAL F 167 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL F 167 " --> pdb=" O LYS F 215 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'F' and resid 313 through 315 removed outlier: 3.630A pdb=" N ALA F 279 " --> pdb=" O PHE F 230 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA F 252 " --> pdb=" O THR F 284 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 342 through 345 515 hydrogen bonds defined for protein. 1386 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.98 Time building geometry restraints manager: 6.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 2887 1.28 - 1.42: 3865 1.42 - 1.55: 10159 1.55 - 1.68: 38 1.68 - 1.82: 165 Bond restraints: 17114 Sorted by residual: bond pdb=" N PRO E 201 " pdb=" CA PRO E 201 " ideal model delta sigma weight residual 1.469 1.699 -0.230 1.28e-02 6.10e+03 3.23e+02 bond pdb=" N PRO F 460 " pdb=" CA PRO F 460 " ideal model delta sigma weight residual 1.467 1.674 -0.207 1.21e-02 6.83e+03 2.92e+02 bond pdb=" C ASN F 459 " pdb=" N PRO F 460 " ideal model delta sigma weight residual 1.332 1.435 -0.103 1.30e-02 5.92e+03 6.30e+01 bond pdb=" C2 FAD C 501 " pdb=" N3 FAD C 501 " ideal model delta sigma weight residual 1.399 1.259 0.140 2.00e-02 2.50e+03 4.89e+01 bond pdb=" C2 FAD F 501 " pdb=" N3 FAD F 501 " ideal model delta sigma weight residual 1.399 1.260 0.139 2.00e-02 2.50e+03 4.82e+01 ... (remaining 17109 not shown) Histogram of bond angle deviations from ideal: 96.69 - 106.07: 492 106.07 - 115.45: 10771 115.45 - 124.83: 11666 124.83 - 134.22: 281 134.22 - 143.60: 6 Bond angle restraints: 23216 Sorted by residual: angle pdb=" C ASN E 200 " pdb=" N PRO E 201 " pdb=" CA PRO E 201 " ideal model delta sigma weight residual 119.84 141.31 -21.47 1.25e+00 6.40e-01 2.95e+02 angle pdb=" C ASN F 459 " pdb=" N PRO F 460 " pdb=" CA PRO F 460 " ideal model delta sigma weight residual 119.76 136.90 -17.14 1.03e+00 9.43e-01 2.77e+02 angle pdb=" O CYS C 464 " pdb=" C CYS C 464 " pdb=" N GLN C 465 " ideal model delta sigma weight residual 121.89 105.44 16.45 1.55e+00 4.16e-01 1.13e+02 angle pdb=" CA PRO E 201 " pdb=" N PRO E 201 " pdb=" CD PRO E 201 " ideal model delta sigma weight residual 112.00 97.90 14.10 1.40e+00 5.10e-01 1.01e+02 angle pdb=" N SER E 198 " pdb=" CA SER E 198 " pdb=" C SER E 198 " ideal model delta sigma weight residual 113.18 102.12 11.06 1.33e+00 5.65e-01 6.92e+01 ... (remaining 23211 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.70: 9939 31.70 - 63.40: 297 63.40 - 95.10: 22 95.10 - 126.80: 0 126.80 - 158.50: 4 Dihedral angle restraints: 10262 sinusoidal: 4126 harmonic: 6136 Sorted by residual: dihedral pdb=" CA ILE E 197 " pdb=" C ILE E 197 " pdb=" N SER E 198 " pdb=" CA SER E 198 " ideal model delta harmonic sigma weight residual 180.00 145.48 34.52 0 5.00e+00 4.00e-02 4.77e+01 dihedral pdb=" CA SER E 198 " pdb=" C SER E 198 " pdb=" N LYS E 199 " pdb=" CA LYS E 199 " ideal model delta harmonic sigma weight residual 180.00 148.92 31.08 0 5.00e+00 4.00e-02 3.87e+01 dihedral pdb=" CA GLU E 22 " pdb=" C GLU E 22 " pdb=" N THR E 23 " pdb=" CA THR E 23 " ideal model delta harmonic sigma weight residual 180.00 154.54 25.46 0 5.00e+00 4.00e-02 2.59e+01 ... (remaining 10259 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 2283 0.081 - 0.163: 375 0.163 - 0.244: 22 0.244 - 0.326: 4 0.326 - 0.407: 1 Chirality restraints: 2685 Sorted by residual: chirality pdb=" CA PRO F 460 " pdb=" N PRO F 460 " pdb=" C PRO F 460 " pdb=" CB PRO F 460 " both_signs ideal model delta sigma weight residual False 2.72 3.13 -0.41 2.00e-01 2.50e+01 4.15e+00 chirality pdb=" CA ILE E 27 " pdb=" N ILE E 27 " pdb=" C ILE E 27 " pdb=" CB ILE E 27 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.32 2.00e-01 2.50e+01 2.48e+00 chirality pdb=" CA ARG C 351 " pdb=" N ARG C 351 " pdb=" C ARG C 351 " pdb=" CB ARG C 351 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.11e+00 ... (remaining 2682 not shown) Planarity restraints: 2921 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS C 464 " -0.083 2.00e-02 2.50e+03 1.52e-01 2.31e+02 pdb=" C CYS C 464 " 0.263 2.00e-02 2.50e+03 pdb=" O CYS C 464 " -0.094 2.00e-02 2.50e+03 pdb=" N GLN C 465 " -0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' FAD C 501 " 0.010 2.00e-02 2.50e+03 2.06e-02 2.02e+01 pdb=" C10 FAD C 501 " -0.011 2.00e-02 2.50e+03 pdb=" C2 FAD C 501 " 0.028 2.00e-02 2.50e+03 pdb=" C4 FAD C 501 " -0.013 2.00e-02 2.50e+03 pdb=" C4X FAD C 501 " -0.009 2.00e-02 2.50e+03 pdb=" C5X FAD C 501 " -0.003 2.00e-02 2.50e+03 pdb=" C6 FAD C 501 " -0.001 2.00e-02 2.50e+03 pdb=" C7 FAD C 501 " 0.027 2.00e-02 2.50e+03 pdb=" C7M FAD C 501 " 0.038 2.00e-02 2.50e+03 pdb=" C8 FAD C 501 " -0.012 2.00e-02 2.50e+03 pdb=" C8M FAD C 501 " 0.011 2.00e-02 2.50e+03 pdb=" C9 FAD C 501 " -0.019 2.00e-02 2.50e+03 pdb=" C9A FAD C 501 " -0.021 2.00e-02 2.50e+03 pdb=" N1 FAD C 501 " -0.002 2.00e-02 2.50e+03 pdb=" N10 FAD C 501 " -0.034 2.00e-02 2.50e+03 pdb=" N3 FAD C 501 " 0.003 2.00e-02 2.50e+03 pdb=" N5 FAD C 501 " -0.024 2.00e-02 2.50e+03 pdb=" O2 FAD C 501 " 0.041 2.00e-02 2.50e+03 pdb=" O4 FAD C 501 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' FAD F 501 " -0.010 2.00e-02 2.50e+03 2.06e-02 2.02e+01 pdb=" C10 FAD F 501 " 0.011 2.00e-02 2.50e+03 pdb=" C2 FAD F 501 " -0.029 2.00e-02 2.50e+03 pdb=" C4 FAD F 501 " 0.013 2.00e-02 2.50e+03 pdb=" C4X FAD F 501 " 0.009 2.00e-02 2.50e+03 pdb=" C5X FAD F 501 " 0.003 2.00e-02 2.50e+03 pdb=" C6 FAD F 501 " 0.001 2.00e-02 2.50e+03 pdb=" C7 FAD F 501 " -0.027 2.00e-02 2.50e+03 pdb=" C7M FAD F 501 " -0.038 2.00e-02 2.50e+03 pdb=" C8 FAD F 501 " 0.012 2.00e-02 2.50e+03 pdb=" C8M FAD F 501 " -0.011 2.00e-02 2.50e+03 pdb=" C9 FAD F 501 " 0.019 2.00e-02 2.50e+03 pdb=" C9A FAD F 501 " 0.022 2.00e-02 2.50e+03 pdb=" N1 FAD F 501 " 0.002 2.00e-02 2.50e+03 pdb=" N10 FAD F 501 " 0.035 2.00e-02 2.50e+03 pdb=" N3 FAD F 501 " -0.003 2.00e-02 2.50e+03 pdb=" N5 FAD F 501 " 0.024 2.00e-02 2.50e+03 pdb=" O2 FAD F 501 " -0.041 2.00e-02 2.50e+03 pdb=" O4 FAD F 501 " 0.007 2.00e-02 2.50e+03 ... (remaining 2918 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.32: 29 2.32 - 2.96: 7387 2.96 - 3.61: 23944 3.61 - 4.25: 42804 4.25 - 4.90: 68635 Nonbonded interactions: 142799 Sorted by model distance: nonbonded pdb=" OE2 GLU C 422 " pdb="FE FE C 502 " model vdw 1.674 2.260 nonbonded pdb=" OE2 GLU F 422 " pdb="FE FE F 502 " model vdw 1.704 2.260 nonbonded pdb=" NE2 HIS C 377 " pdb="FE FE C 502 " model vdw 1.730 2.340 nonbonded pdb="FE FE C 502 " pdb=" O HOH C 601 " model vdw 1.775 2.260 nonbonded pdb="FE FE F 502 " pdb=" O HOH F 601 " model vdw 1.866 2.260 ... (remaining 142794 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 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = (chain 'C' and (resid 1 through 41 or resid 43 through 467 or resid 501 through \ 502)) selection = (chain 'F' and (resid 1 through 41 or resid 43 through 467 or resid 501 through \ 502)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.340 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: 5.850 Check model and map are aligned: 0.230 Set scattering table: 0.130 Process input model: 46.300 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.130 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:11.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 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 : 0.008 0.230 17114 Z= 0.499 Angle : 1.008 21.466 23216 Z= 0.599 Chirality : 0.057 0.407 2685 Planarity : 0.008 0.152 2921 Dihedral : 15.057 158.496 6328 Min Nonbonded Distance : 1.674 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.34 % Favored : 96.43 % Rotamer: Outliers : 2.88 % Allowed : 4.27 % Favored : 92.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -4.15 (0.14), residues: 2129 helix: -4.40 (0.07), residues: 694 sheet: -1.53 (0.21), residues: 430 loop : -1.91 (0.16), residues: 1005 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 190 time to evaluate : 1.951 Fit side-chains outliers start: 52 outliers final: 17 residues processed: 231 average time/residue: 1.4950 time to fit residues: 380.4196 Evaluate side-chains 144 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 127 time to evaluate : 2.221 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 16 residues processed: 1 average time/residue: 0.1777 time to fit residues: 3.2963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 0.9990 chunk 159 optimal weight: 5.9990 chunk 88 optimal weight: 0.6980 chunk 54 optimal weight: 0.5980 chunk 107 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 164 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 122 optimal weight: 0.0770 chunk 190 optimal weight: 3.9990 overall best weight: 1.2742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 GLN A 353 GLN A 354 ASN A 397 ASN B 16 ASN B 200 ASN C 382 ASN D 115 ASN D 324 GLN D 354 ASN D 397 ASN F 292 GLN F 382 ASN F 394 GLN F 423 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 17114 Z= 0.230 Angle : 0.574 9.681 23216 Z= 0.302 Chirality : 0.045 0.218 2685 Planarity : 0.006 0.070 2921 Dihedral : 8.938 178.454 2300 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.26 % Favored : 97.51 % Rotamer: Outliers : 1.72 % Allowed : 8.98 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.38 (0.16), residues: 2129 helix: -2.01 (0.16), residues: 708 sheet: -1.19 (0.22), residues: 442 loop : -1.26 (0.18), residues: 979 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 137 time to evaluate : 1.975 Fit side-chains outliers start: 31 outliers final: 17 residues processed: 156 average time/residue: 1.4370 time to fit residues: 249.5022 Evaluate side-chains 144 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 127 time to evaluate : 1.962 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 15 residues processed: 3 average time/residue: 0.2033 time to fit residues: 3.8111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 105 optimal weight: 10.0000 chunk 59 optimal weight: 0.7980 chunk 158 optimal weight: 0.0030 chunk 129 optimal weight: 10.0000 chunk 52 optimal weight: 0.8980 chunk 191 optimal weight: 5.9990 chunk 206 optimal weight: 4.9990 chunk 170 optimal weight: 3.9990 chunk 189 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN B 66 GLN D 115 ASN D 353 GLN E 66 GLN E 141 HIS F 292 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 17114 Z= 0.181 Angle : 0.513 8.067 23216 Z= 0.265 Chirality : 0.044 0.188 2685 Planarity : 0.005 0.066 2921 Dihedral : 8.597 178.706 2300 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.35 % Favored : 97.51 % Rotamer: Outliers : 1.61 % Allowed : 10.19 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.28 (0.17), residues: 2129 helix: -0.64 (0.18), residues: 708 sheet: -0.83 (0.22), residues: 442 loop : -0.85 (0.19), residues: 979 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 132 time to evaluate : 2.055 Fit side-chains outliers start: 29 outliers final: 19 residues processed: 155 average time/residue: 1.3861 time to fit residues: 239.6899 Evaluate side-chains 144 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 125 time to evaluate : 1.996 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 17 residues processed: 3 average time/residue: 0.1973 time to fit residues: 3.6721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 188 optimal weight: 0.7980 chunk 143 optimal weight: 0.3980 chunk 99 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 128 optimal weight: 9.9990 chunk 191 optimal weight: 5.9990 chunk 202 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 181 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN B 66 GLN D 353 GLN E 16 ASN E 66 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 17114 Z= 0.234 Angle : 0.529 8.050 23216 Z= 0.272 Chirality : 0.045 0.183 2685 Planarity : 0.004 0.065 2921 Dihedral : 8.561 176.375 2300 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.21 % Favored : 97.65 % Rotamer: Outliers : 2.11 % Allowed : 9.86 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.79 (0.17), residues: 2129 helix: -0.02 (0.19), residues: 712 sheet: -0.61 (0.23), residues: 448 loop : -0.73 (0.19), residues: 969 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 134 time to evaluate : 1.986 Fit side-chains outliers start: 38 outliers final: 22 residues processed: 159 average time/residue: 1.4392 time to fit residues: 254.1874 Evaluate side-chains 146 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 124 time to evaluate : 1.972 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 19 residues processed: 4 average time/residue: 0.2153 time to fit residues: 4.0603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 3.9990 chunk 115 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 chunk 151 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 chunk 173 optimal weight: 0.2980 chunk 140 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 chunk 182 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN A 371 ASN B 66 GLN D 353 GLN E 66 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 17114 Z= 0.263 Angle : 0.542 8.578 23216 Z= 0.276 Chirality : 0.046 0.178 2685 Planarity : 0.004 0.064 2921 Dihedral : 8.533 172.877 2300 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.30 % Favored : 97.55 % Rotamer: Outliers : 1.99 % Allowed : 10.64 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.47 (0.18), residues: 2129 helix: 0.35 (0.19), residues: 716 sheet: -0.59 (0.23), residues: 454 loop : -0.54 (0.20), residues: 959 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 132 time to evaluate : 1.991 Fit side-chains outliers start: 36 outliers final: 23 residues processed: 159 average time/residue: 1.3944 time to fit residues: 247.4365 Evaluate side-chains 146 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 123 time to evaluate : 1.952 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 20 residues processed: 3 average time/residue: 0.1831 time to fit residues: 3.5308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 68 optimal weight: 3.9990 chunk 182 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 203 optimal weight: 1.9990 chunk 168 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN B 66 GLN D 353 GLN D 371 ASN E 66 GLN F 456 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 17114 Z= 0.285 Angle : 0.543 9.447 23216 Z= 0.277 Chirality : 0.046 0.178 2685 Planarity : 0.004 0.065 2921 Dihedral : 8.501 168.475 2300 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.26 % Favored : 97.60 % Rotamer: Outliers : 1.88 % Allowed : 10.97 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.32 (0.18), residues: 2129 helix: 0.52 (0.19), residues: 716 sheet: -0.52 (0.23), residues: 454 loop : -0.49 (0.20), residues: 959 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 130 time to evaluate : 1.793 Fit side-chains outliers start: 34 outliers final: 23 residues processed: 154 average time/residue: 1.4687 time to fit residues: 251.7102 Evaluate side-chains 148 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 125 time to evaluate : 1.915 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 20 residues processed: 4 average time/residue: 0.2924 time to fit residues: 4.2420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 115 optimal weight: 0.8980 chunk 148 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 171 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 202 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 123 optimal weight: 9.9990 chunk 93 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN B 66 GLN D 353 GLN E 66 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 17114 Z= 0.334 Angle : 0.564 10.847 23216 Z= 0.286 Chirality : 0.047 0.177 2685 Planarity : 0.004 0.065 2921 Dihedral : 8.572 166.077 2300 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.54 % Favored : 97.32 % Rotamer: Outliers : 1.77 % Allowed : 11.14 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.27 (0.18), residues: 2129 helix: 0.55 (0.19), residues: 720 sheet: -0.51 (0.23), residues: 454 loop : -0.44 (0.20), residues: 955 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 130 time to evaluate : 2.060 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 24 residues processed: 155 average time/residue: 1.4218 time to fit residues: 245.1306 Evaluate side-chains 150 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 126 time to evaluate : 1.843 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 20 residues processed: 4 average time/residue: 0.2074 time to fit residues: 4.0077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 125 optimal weight: 7.9990 chunk 80 optimal weight: 0.9980 chunk 120 optimal weight: 9.9990 chunk 60 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 128 optimal weight: 8.9990 chunk 137 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 159 optimal weight: 5.9990 chunk 184 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN B 66 GLN D 353 GLN E 66 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 17114 Z= 0.237 Angle : 0.535 11.462 23216 Z= 0.272 Chirality : 0.045 0.171 2685 Planarity : 0.004 0.064 2921 Dihedral : 8.393 161.656 2300 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.54 % Favored : 97.27 % Rotamer: Outliers : 1.66 % Allowed : 11.36 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.16 (0.18), residues: 2129 helix: 0.71 (0.20), residues: 716 sheet: -0.48 (0.23), residues: 454 loop : -0.42 (0.20), residues: 959 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 137 time to evaluate : 1.935 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 22 residues processed: 160 average time/residue: 1.3397 time to fit residues: 239.3636 Evaluate side-chains 152 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 130 time to evaluate : 1.877 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 22 residues processed: 1 average time/residue: 0.2991 time to fit residues: 3.0020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 0.8980 chunk 176 optimal weight: 2.9990 chunk 188 optimal weight: 0.9980 chunk 113 optimal weight: 6.9990 chunk 82 optimal weight: 0.0020 chunk 148 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 170 optimal weight: 2.9990 chunk 178 optimal weight: 0.8980 chunk 187 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 overall best weight: 0.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN B 66 GLN D 353 GLN E 66 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17114 Z= 0.168 Angle : 0.502 7.573 23216 Z= 0.258 Chirality : 0.044 0.171 2685 Planarity : 0.004 0.063 2921 Dihedral : 8.180 159.851 2300 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.40 % Favored : 97.41 % Rotamer: Outliers : 1.55 % Allowed : 11.86 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.03 (0.18), residues: 2129 helix: 0.87 (0.20), residues: 714 sheet: -0.44 (0.23), residues: 454 loop : -0.37 (0.20), residues: 961 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 137 time to evaluate : 1.850 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 25 residues processed: 158 average time/residue: 1.4244 time to fit residues: 250.8712 Evaluate side-chains 156 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 131 time to evaluate : 2.046 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 22 residues processed: 4 average time/residue: 0.2247 time to fit residues: 4.2576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 199 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 138 optimal weight: 5.9990 chunk 209 optimal weight: 0.5980 chunk 192 optimal weight: 3.9990 chunk 166 optimal weight: 0.0010 chunk 17 optimal weight: 9.9990 chunk 128 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 132 optimal weight: 0.3980 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN B 66 GLN D 353 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 17114 Z= 0.147 Angle : 0.488 6.546 23216 Z= 0.250 Chirality : 0.044 0.168 2685 Planarity : 0.004 0.062 2921 Dihedral : 8.012 156.680 2300 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.54 % Favored : 97.27 % Rotamer: Outliers : 1.39 % Allowed : 12.13 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.11 (0.18), residues: 2129 helix: 1.04 (0.20), residues: 714 sheet: -0.38 (0.23), residues: 454 loop : -0.31 (0.20), residues: 961 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 141 time to evaluate : 1.911 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 22 residues processed: 163 average time/residue: 1.4033 time to fit residues: 255.1443 Evaluate side-chains 153 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 131 time to evaluate : 2.092 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 21 residues processed: 2 average time/residue: 0.2676 time to fit residues: 3.6413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 46 optimal weight: 0.9990 chunk 166 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 171 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 30 optimal weight: 0.3980 chunk 146 optimal weight: 10.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN B 66 GLN D 353 GLN E 66 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.095385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.064310 restraints weight = 33261.178| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 2.53 r_work: 0.2709 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2567 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2573 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2573 r_free = 0.2573 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2573 r_free = 0.2573 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2573 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17114 Z= 0.171 Angle : 0.511 7.583 23216 Z= 0.259 Chirality : 0.044 0.168 2685 Planarity : 0.004 0.060 2921 Dihedral : 8.004 156.807 2300 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.49 % Favored : 97.32 % Rotamer: Outliers : 1.33 % Allowed : 12.30 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 (0.18), residues: 2129 helix: 1.08 (0.20), residues: 714 sheet: -0.28 (0.23), residues: 450 loop : -0.26 (0.21), residues: 965 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5625.02 seconds wall clock time: 101 minutes 19.47 seconds (6079.47 seconds total)