Starting phenix.real_space_refine on Sun Mar 17 05:38:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qh2_13960/03_2024/7qh2_13960_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qh2_13960/03_2024/7qh2_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_13960/03_2024/7qh2_13960.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qh2_13960/03_2024/7qh2_13960.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qh2_13960/03_2024/7qh2_13960_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qh2_13960/03_2024/7qh2_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-dev-5265/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: 11.12, per 1000 atoms: 0.66 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: 6.41 Conformation dependent library (CDL) restraints added in 3.7 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: 3.35 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: 4.60 Time building geometry restraints manager: 6.99 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: 10107 31.70 - 63.40: 367 63.40 - 95.10: 42 95.10 - 126.80: 0 126.80 - 158.50: 4 Dihedral angle restraints: 10520 sinusoidal: 4384 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 10517 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: 1.150 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: 5.760 Check model and map are aligned: 0.270 Set scattering table: 0.160 Process input model: 48.270 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.810 ------------------------------------------------------------------------------- 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 : 16.285 158.496 6586 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP F 397 HIS 0.007 0.001 HIS C 441 PHE 0.016 0.002 PHE C 272 TYR 0.029 0.001 TYR C 297 ARG 0.009 0.001 ARG D 322 *********************** 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 : 1.926 Fit side-chains REVERT: A 84 GLN cc_start: 0.8436 (tp-100) cc_final: 0.8224 (pp30) REVERT: A 126 TYR cc_start: 0.8935 (m-80) cc_final: 0.8407 (m-80) REVERT: A 199 THR cc_start: 0.8204 (OUTLIER) cc_final: 0.7991 (m) REVERT: A 226 CYS cc_start: 0.7892 (OUTLIER) cc_final: 0.7500 (t) REVERT: B 3 LYS cc_start: 0.7854 (OUTLIER) cc_final: 0.7533 (mmmt) REVERT: B 199 LYS cc_start: 0.4114 (OUTLIER) cc_final: 0.3104 (mmmt) REVERT: C 292 GLN cc_start: 0.8717 (tt0) cc_final: 0.8388 (tt0) REVERT: C 322 ASP cc_start: 0.7703 (m-30) cc_final: 0.7413 (m-30) REVERT: C 366 LYS cc_start: 0.8893 (ttmt) cc_final: 0.8686 (mtmt) REVERT: D 126 TYR cc_start: 0.8964 (m-80) cc_final: 0.8535 (m-80) REVERT: D 226 CYS cc_start: 0.8145 (OUTLIER) cc_final: 0.7791 (t) REVERT: E 3 LYS cc_start: 0.7515 (OUTLIER) cc_final: 0.7300 (mmmt) REVERT: E 202 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6342 (pp20) REVERT: E 216 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.6985 (tm-30) REVERT: F 266 ASP cc_start: 0.8179 (t70) cc_final: 0.7866 (t0) REVERT: F 322 ASP cc_start: 0.7930 (m-30) cc_final: 0.7639 (m-30) REVERT: F 366 LYS cc_start: 0.8726 (mttp) cc_final: 0.8425 (mttt) outliers start: 52 outliers final: 17 residues processed: 231 average time/residue: 1.5049 time to fit residues: 382.3399 Evaluate side-chains 154 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 129 time to evaluate : 1.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 226 CYS Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 3 LYS Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain D residue 226 CYS Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain E residue 3 LYS Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 28 ARG Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain E residue 248 LYS 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: 1.9990 chunk 88 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 107 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 164 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 190 optimal weight: 3.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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: 0.8248 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 17114 Z= 0.261 Angle : 0.574 8.350 23216 Z= 0.299 Chirality : 0.046 0.209 2685 Planarity : 0.006 0.070 2921 Dihedral : 13.882 177.233 2616 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.16 % Favored : 97.60 % Rotamer: Outliers : 1.77 % Allowed : 8.75 % Favored : 89.47 % 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: -2.03 (0.16), residues: 708 sheet: -1.15 (0.22), residues: 442 loop : -1.26 (0.18), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 325 HIS 0.009 0.001 HIS C 441 PHE 0.019 0.001 PHE C 272 TYR 0.025 0.001 TYR C 297 ARG 0.012 0.001 ARG D 238 *********************** 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 169 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 137 time to evaluate : 1.743 Fit side-chains REVERT: A 126 TYR cc_start: 0.8909 (m-80) cc_final: 0.8367 (m-80) REVERT: B 199 LYS cc_start: 0.5198 (OUTLIER) cc_final: 0.4884 (mmmt) REVERT: B 202 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.7040 (pm20) REVERT: B 211 MET cc_start: 0.9119 (mmt) cc_final: 0.8332 (mmt) REVERT: B 248 LYS cc_start: 0.8772 (pptt) cc_final: 0.8383 (ptpt) REVERT: C 292 GLN cc_start: 0.8397 (tt0) cc_final: 0.8002 (tt0) REVERT: C 322 ASP cc_start: 0.7833 (m-30) cc_final: 0.7571 (m-30) REVERT: C 342 MET cc_start: 0.8995 (OUTLIER) cc_final: 0.8613 (ptm) REVERT: D 126 TYR cc_start: 0.8914 (m-80) cc_final: 0.8439 (m-80) REVERT: E 248 LYS cc_start: 0.8718 (pptt) cc_final: 0.8353 (ptpt) REVERT: F 181 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7721 (mp0) REVERT: F 342 MET cc_start: 0.9069 (OUTLIER) cc_final: 0.8507 (ptm) REVERT: F 369 ASP cc_start: 0.8503 (OUTLIER) cc_final: 0.8185 (t0) REVERT: F 450 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.7968 (tt0) outliers start: 32 outliers final: 16 residues processed: 156 average time/residue: 1.3890 time to fit residues: 239.8656 Evaluate side-chains 150 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 127 time to evaluate : 1.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 240 ASN Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 28 ARG Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain F residue 342 MET Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain F residue 450 GLN 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: 0.0770 chunk 158 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 chunk 52 optimal weight: 6.9990 chunk 191 optimal weight: 0.8980 chunk 206 optimal weight: 5.9990 chunk 170 optimal weight: 3.9990 chunk 189 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 153 optimal weight: 0.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN D 115 ASN E 66 GLN E 141 HIS F 292 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17114 Z= 0.167 Angle : 0.510 7.492 23216 Z= 0.262 Chirality : 0.044 0.183 2685 Planarity : 0.005 0.069 2921 Dihedral : 12.146 179.613 2583 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.12 % Favored : 97.74 % Rotamer: Outliers : 1.72 % Allowed : 9.81 % Favored : 88.48 % 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: -1.37 (0.17), residues: 2129 helix: -0.72 (0.18), residues: 708 sheet: -0.84 (0.22), residues: 442 loop : -0.93 (0.19), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 325 HIS 0.004 0.001 HIS C 441 PHE 0.010 0.001 PHE C 272 TYR 0.017 0.001 TYR C 297 ARG 0.006 0.000 ARG B 108 *********************** 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 164 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 133 time to evaluate : 2.148 Fit side-chains REVERT: A 126 TYR cc_start: 0.8896 (m-80) cc_final: 0.8331 (m-80) REVERT: B 248 LYS cc_start: 0.8763 (pptt) cc_final: 0.8407 (ptmt) REVERT: C 292 GLN cc_start: 0.8454 (tt0) cc_final: 0.8103 (tt0) REVERT: C 322 ASP cc_start: 0.7855 (m-30) cc_final: 0.7626 (m-30) REVERT: D 126 TYR cc_start: 0.8862 (m-80) cc_final: 0.8379 (m-80) REVERT: E 248 LYS cc_start: 0.8737 (pptt) cc_final: 0.8374 (ptpt) REVERT: F 94 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8080 (tm-30) REVERT: F 181 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7700 (mp0) REVERT: F 369 ASP cc_start: 0.8481 (OUTLIER) cc_final: 0.8197 (t0) REVERT: F 450 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7857 (tt0) outliers start: 31 outliers final: 16 residues processed: 155 average time/residue: 1.4369 time to fit residues: 247.2895 Evaluate side-chains 147 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 127 time to evaluate : 1.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 240 ASN Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 28 ARG Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain F residue 450 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 188 optimal weight: 1.9990 chunk 143 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 91 optimal weight: 0.0170 chunk 128 optimal weight: 9.9990 chunk 191 optimal weight: 0.0170 chunk 202 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 181 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 overall best weight: 1.0062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN D 353 GLN E 16 ASN E 66 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 17114 Z= 0.191 Angle : 0.510 8.534 23216 Z= 0.261 Chirality : 0.044 0.180 2685 Planarity : 0.004 0.065 2921 Dihedral : 11.075 176.365 2574 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.16 % Favored : 97.70 % Rotamer: Outliers : 2.05 % Allowed : 9.92 % 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: -0.00 (0.19), residues: 712 sheet: -0.60 (0.23), residues: 448 loop : -0.75 (0.19), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 325 HIS 0.004 0.001 HIS C 441 PHE 0.011 0.001 PHE C 272 TYR 0.017 0.001 TYR C 297 ARG 0.004 0.000 ARG A 238 *********************** 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: 37 poor density : 135 time to evaluate : 2.101 Fit side-chains REVERT: A 126 TYR cc_start: 0.8835 (m-80) cc_final: 0.8294 (m-80) REVERT: B 248 LYS cc_start: 0.8765 (pptt) cc_final: 0.8451 (ptmt) REVERT: C 292 GLN cc_start: 0.8408 (tt0) cc_final: 0.8094 (tt0) REVERT: C 322 ASP cc_start: 0.7890 (m-30) cc_final: 0.7673 (m-30) REVERT: C 450 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7901 (tt0) REVERT: D 126 TYR cc_start: 0.8845 (m-80) cc_final: 0.8374 (m-80) REVERT: E 248 LYS cc_start: 0.8764 (pptt) cc_final: 0.8406 (ptpt) REVERT: F 94 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8116 (tm-30) REVERT: F 181 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7713 (mp0) REVERT: F 342 MET cc_start: 0.9065 (OUTLIER) cc_final: 0.8246 (ptm) REVERT: F 369 ASP cc_start: 0.8478 (OUTLIER) cc_final: 0.8236 (t0) REVERT: F 450 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7894 (tt0) outliers start: 37 outliers final: 15 residues processed: 157 average time/residue: 1.4984 time to fit residues: 260.3752 Evaluate side-chains 146 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 125 time to evaluate : 2.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 240 ASN Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain C residue 450 GLN Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain E residue 16 ASN Chi-restraints excluded: chain E residue 28 ARG Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain F residue 342 MET Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain F residue 450 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 2 optimal weight: 9.9990 chunk 151 optimal weight: 4.9990 chunk 83 optimal weight: 0.6980 chunk 173 optimal weight: 1.9990 chunk 140 optimal weight: 10.0000 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: 1.6986 ------------------------------------------------------------------------------- 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: 0.8249 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 17114 Z= 0.270 Angle : 0.533 8.696 23216 Z= 0.272 Chirality : 0.046 0.174 2685 Planarity : 0.004 0.065 2921 Dihedral : 10.734 174.473 2570 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.07 % Favored : 97.79 % Rotamer: Outliers : 1.94 % Allowed : 10.64 % Favored : 87.42 % 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: -0.52 (0.18), residues: 2129 helix: 0.34 (0.19), residues: 714 sheet: -0.58 (0.23), residues: 454 loop : -0.62 (0.20), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 325 HIS 0.006 0.001 HIS C 441 PHE 0.016 0.001 PHE C 272 TYR 0.020 0.001 TYR F 297 ARG 0.003 0.000 ARG B 108 *********************** 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 163 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 128 time to evaluate : 1.863 Fit side-chains REVERT: A 126 TYR cc_start: 0.8900 (m-80) cc_final: 0.8399 (m-80) REVERT: B 35 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8509 (tt) REVERT: B 154 LYS cc_start: 0.8632 (mtmm) cc_final: 0.8353 (mttm) REVERT: B 248 LYS cc_start: 0.8763 (pptt) cc_final: 0.8457 (ptmt) REVERT: C 292 GLN cc_start: 0.8381 (tt0) cc_final: 0.8032 (tt0) REVERT: C 322 ASP cc_start: 0.7928 (m-30) cc_final: 0.7727 (m-30) REVERT: C 366 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8432 (ttmt) REVERT: C 450 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.7957 (tt0) REVERT: D 126 TYR cc_start: 0.8869 (m-80) cc_final: 0.8435 (m-80) REVERT: E 28 ARG cc_start: 0.5781 (OUTLIER) cc_final: 0.4981 (mtp-110) REVERT: E 35 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8525 (tt) REVERT: E 209 LYS cc_start: 0.8853 (mmpt) cc_final: 0.8627 (mmmt) REVERT: E 248 LYS cc_start: 0.8775 (pptt) cc_final: 0.8429 (ptpt) REVERT: F 1 MET cc_start: 0.6042 (OUTLIER) cc_final: 0.5392 (ppp) REVERT: F 94 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8116 (tm-30) REVERT: F 181 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7736 (mp0) REVERT: F 369 ASP cc_start: 0.8497 (OUTLIER) cc_final: 0.8234 (t0) REVERT: F 450 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7929 (tt0) outliers start: 35 outliers final: 17 residues processed: 150 average time/residue: 1.4322 time to fit residues: 237.6506 Evaluate side-chains 152 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 125 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain C residue 366 LYS Chi-restraints excluded: chain C residue 450 GLN Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain E residue 28 ARG Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain F residue 297 TYR Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain F residue 450 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 68 optimal weight: 1.9990 chunk 182 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 203 optimal weight: 0.8980 chunk 168 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 F 456 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 17114 Z= 0.225 Angle : 0.507 10.161 23216 Z= 0.259 Chirality : 0.045 0.173 2685 Planarity : 0.004 0.065 2921 Dihedral : 10.434 170.299 2570 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.21 % Favored : 97.65 % Rotamer: Outliers : 2.16 % Allowed : 10.47 % 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: -0.29 (0.18), residues: 2129 helix: 0.60 (0.20), residues: 714 sheet: -0.50 (0.23), residues: 454 loop : -0.52 (0.20), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 325 HIS 0.005 0.001 HIS C 441 PHE 0.011 0.001 PHE C 272 TYR 0.017 0.001 TYR C 297 ARG 0.002 0.000 ARG A 238 *********************** 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 174 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 135 time to evaluate : 2.013 Fit side-chains REVERT: B 26 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7634 (mt) REVERT: B 28 ARG cc_start: 0.5418 (OUTLIER) cc_final: 0.4576 (mtp-110) REVERT: B 248 LYS cc_start: 0.8776 (pptt) cc_final: 0.8473 (ptmt) REVERT: C 94 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7812 (tm-30) REVERT: C 292 GLN cc_start: 0.8365 (tt0) cc_final: 0.8018 (tt0) REVERT: C 322 ASP cc_start: 0.7921 (m-30) cc_final: 0.7717 (m-30) REVERT: C 342 MET cc_start: 0.9076 (OUTLIER) cc_final: 0.8248 (ptm) REVERT: C 366 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8432 (ttmt) REVERT: C 450 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7939 (tt0) REVERT: E 28 ARG cc_start: 0.5448 (OUTLIER) cc_final: 0.5173 (mtp180) REVERT: E 35 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8476 (tt) REVERT: E 209 LYS cc_start: 0.8870 (mmpt) cc_final: 0.8664 (mmmt) REVERT: E 248 LYS cc_start: 0.8811 (pptt) cc_final: 0.8462 (ptpt) REVERT: F 94 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8105 (tm-30) REVERT: F 181 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7697 (mp0) REVERT: F 342 MET cc_start: 0.9045 (OUTLIER) cc_final: 0.8222 (ptm) REVERT: F 450 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7912 (tt0) outliers start: 39 outliers final: 15 residues processed: 158 average time/residue: 1.4622 time to fit residues: 255.7285 Evaluate side-chains 153 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 126 time to evaluate : 2.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 240 ASN Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 366 LYS Chi-restraints excluded: chain C residue 450 GLN Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain E residue 28 ARG Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain F residue 297 TYR Chi-restraints excluded: chain F residue 342 MET Chi-restraints excluded: chain F residue 450 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 115 optimal weight: 0.7980 chunk 148 optimal weight: 0.5980 chunk 114 optimal weight: 0.9990 chunk 171 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 202 optimal weight: 3.9990 chunk 126 optimal weight: 0.6980 chunk 123 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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: 0.8231 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 17114 Z= 0.188 Angle : 0.492 10.426 23216 Z= 0.251 Chirality : 0.044 0.173 2685 Planarity : 0.004 0.063 2921 Dihedral : 10.211 167.717 2568 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.21 % Favored : 97.65 % Rotamer: Outliers : 2.05 % Allowed : 10.75 % Favored : 87.20 % 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: -0.12 (0.18), residues: 2129 helix: 0.75 (0.20), residues: 714 sheet: -0.43 (0.23), residues: 454 loop : -0.42 (0.20), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 325 HIS 0.004 0.001 HIS C 441 PHE 0.009 0.001 PHE F 255 TYR 0.016 0.001 TYR C 297 ARG 0.003 0.000 ARG E 108 *********************** 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 175 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 138 time to evaluate : 1.932 Fit side-chains revert: symmetry clash REVERT: A 126 TYR cc_start: 0.8804 (m-80) cc_final: 0.8483 (m-80) REVERT: B 26 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7660 (mt) REVERT: B 28 ARG cc_start: 0.5391 (OUTLIER) cc_final: 0.4505 (mtp-110) REVERT: B 154 LYS cc_start: 0.8612 (mtmm) cc_final: 0.8343 (mttm) REVERT: B 209 LYS cc_start: 0.8868 (mmpt) cc_final: 0.8666 (mmmt) REVERT: B 248 LYS cc_start: 0.8754 (pptt) cc_final: 0.8475 (ptmt) REVERT: C 94 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7810 (tm-30) REVERT: C 292 GLN cc_start: 0.8345 (tt0) cc_final: 0.8005 (tt0) REVERT: C 342 MET cc_start: 0.9080 (OUTLIER) cc_final: 0.8268 (ptm) REVERT: C 366 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8440 (ttmt) REVERT: C 450 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7943 (tt0) REVERT: D 126 TYR cc_start: 0.8811 (m-80) cc_final: 0.8429 (m-80) REVERT: E 35 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8445 (tt) REVERT: E 248 LYS cc_start: 0.8783 (pptt) cc_final: 0.8472 (ptpt) REVERT: F 94 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8100 (tm-30) REVERT: F 181 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7698 (mp0) REVERT: F 342 MET cc_start: 0.9018 (OUTLIER) cc_final: 0.8212 (ptm) REVERT: F 450 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.7888 (tt0) outliers start: 37 outliers final: 14 residues processed: 161 average time/residue: 1.4359 time to fit residues: 255.6805 Evaluate side-chains 155 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 130 time to evaluate : 1.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 240 ASN Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 366 LYS Chi-restraints excluded: chain C residue 450 GLN Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain F residue 297 TYR Chi-restraints excluded: chain F residue 342 MET Chi-restraints excluded: chain F residue 450 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 125 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 120 optimal weight: 7.9990 chunk 60 optimal weight: 0.1980 chunk 39 optimal weight: 0.2980 chunk 128 optimal weight: 6.9990 chunk 137 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 159 optimal weight: 4.9990 chunk 184 optimal weight: 0.2980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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: 0.8226 moved from start: 0.2278 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 : 0.494 7.402 23216 Z= 0.253 Chirality : 0.044 0.167 2685 Planarity : 0.004 0.062 2921 Dihedral : 10.017 167.252 2562 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.02 % Favored : 97.84 % Rotamer: Outliers : 1.83 % Allowed : 11.08 % 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: -0.01 (0.18), residues: 2129 helix: 0.86 (0.20), residues: 714 sheet: -0.39 (0.23), residues: 454 loop : -0.34 (0.20), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 325 HIS 0.004 0.001 HIS C 441 PHE 0.008 0.001 PHE F 255 TYR 0.016 0.001 TYR C 297 ARG 0.002 0.000 ARG E 108 *********************** 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 171 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 138 time to evaluate : 1.735 Fit side-chains REVERT: A 126 TYR cc_start: 0.8802 (m-80) cc_final: 0.8486 (m-80) REVERT: B 26 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7694 (mt) REVERT: B 28 ARG cc_start: 0.5327 (OUTLIER) cc_final: 0.4255 (mtp-110) REVERT: B 154 LYS cc_start: 0.8564 (mtmm) cc_final: 0.8294 (mttm) REVERT: B 209 LYS cc_start: 0.8859 (mmpt) cc_final: 0.8656 (mmmt) REVERT: B 248 LYS cc_start: 0.8733 (pptt) cc_final: 0.8480 (ptmt) REVERT: C 94 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7791 (tm-30) REVERT: C 292 GLN cc_start: 0.8339 (tt0) cc_final: 0.8006 (tt0) REVERT: C 342 MET cc_start: 0.9078 (OUTLIER) cc_final: 0.8253 (ptm) REVERT: C 366 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8443 (ttmt) REVERT: C 450 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.7930 (tt0) REVERT: D 126 TYR cc_start: 0.8806 (m-80) cc_final: 0.8489 (m-80) REVERT: E 35 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8456 (tt) REVERT: E 248 LYS cc_start: 0.8783 (pptt) cc_final: 0.8498 (ptpt) REVERT: F 94 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8103 (tm-30) REVERT: F 181 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7684 (mp0) REVERT: F 342 MET cc_start: 0.9006 (OUTLIER) cc_final: 0.8227 (ptm) REVERT: F 450 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7859 (tt0) outliers start: 33 outliers final: 16 residues processed: 155 average time/residue: 1.5124 time to fit residues: 258.0515 Evaluate side-chains 161 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 134 time to evaluate : 1.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 366 LYS Chi-restraints excluded: chain C residue 450 GLN Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain F residue 297 TYR Chi-restraints excluded: chain F residue 342 MET Chi-restraints excluded: chain F residue 450 GLN 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: 4.9990 chunk 113 optimal weight: 6.9990 chunk 82 optimal weight: 0.6980 chunk 148 optimal weight: 0.5980 chunk 57 optimal weight: 0.6980 chunk 170 optimal weight: 2.9990 chunk 178 optimal weight: 0.7980 chunk 187 optimal weight: 0.9990 chunk 123 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.8216 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 17114 Z= 0.160 Angle : 0.487 7.291 23216 Z= 0.248 Chirality : 0.044 0.168 2685 Planarity : 0.004 0.060 2921 Dihedral : 9.878 165.542 2562 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.21 % Favored : 97.65 % 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: 0.10 (0.18), residues: 2129 helix: 1.00 (0.20), residues: 714 sheet: -0.38 (0.23), residues: 454 loop : -0.30 (0.20), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 325 HIS 0.003 0.001 HIS C 441 PHE 0.009 0.001 PHE F 255 TYR 0.015 0.001 TYR A 230 ARG 0.002 0.000 ARG E 108 *********************** 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 169 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 141 time to evaluate : 1.838 Fit side-chains revert: symmetry clash REVERT: A 126 TYR cc_start: 0.8795 (m-80) cc_final: 0.8473 (m-80) REVERT: B 26 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7693 (mt) REVERT: B 28 ARG cc_start: 0.5137 (OUTLIER) cc_final: 0.4790 (mtp180) REVERT: B 154 LYS cc_start: 0.8557 (mtmm) cc_final: 0.8301 (mttm) REVERT: B 248 LYS cc_start: 0.8743 (pptt) cc_final: 0.8478 (ptmt) REVERT: C 94 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.7772 (tm-30) REVERT: C 292 GLN cc_start: 0.8325 (tt0) cc_final: 0.7995 (tt0) REVERT: C 342 MET cc_start: 0.9068 (OUTLIER) cc_final: 0.8822 (ppp) REVERT: C 366 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8434 (ttmt) REVERT: C 450 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7929 (tt0) REVERT: D 126 TYR cc_start: 0.8791 (m-80) cc_final: 0.8465 (m-80) REVERT: E 162 MET cc_start: 0.7855 (mpp) cc_final: 0.7617 (mmm) REVERT: E 248 LYS cc_start: 0.8798 (pptt) cc_final: 0.8441 (ptmt) REVERT: F 94 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8079 (tm-30) REVERT: F 181 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7703 (mp0) REVERT: F 222 MET cc_start: 0.8007 (mmm) cc_final: 0.7616 (mtm) REVERT: F 450 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7853 (tt0) outliers start: 28 outliers final: 12 residues processed: 156 average time/residue: 1.5080 time to fit residues: 260.1095 Evaluate side-chains 154 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 133 time to evaluate : 1.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 366 LYS Chi-restraints excluded: chain C residue 450 GLN Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain F residue 297 TYR Chi-restraints excluded: chain F residue 450 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 199 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 138 optimal weight: 5.9990 chunk 209 optimal weight: 0.9990 chunk 192 optimal weight: 4.9990 chunk 166 optimal weight: 0.3980 chunk 17 optimal weight: 0.9980 chunk 128 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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: 0.8226 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 17114 Z= 0.199 Angle : 0.505 12.784 23216 Z= 0.256 Chirality : 0.045 0.162 2685 Planarity : 0.004 0.060 2921 Dihedral : 9.928 165.387 2562 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.07 % Favored : 97.79 % Rotamer: Outliers : 1.39 % Allowed : 12.24 % 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: 0.19 (0.18), residues: 2129 helix: 1.10 (0.20), residues: 702 sheet: -0.36 (0.23), residues: 454 loop : -0.24 (0.20), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 325 HIS 0.003 0.001 HIS C 441 PHE 0.009 0.001 PHE C 272 TYR 0.016 0.001 TYR C 297 ARG 0.002 0.000 ARG E 108 ********************** 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 159 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 134 time to evaluate : 2.089 Fit side-chains revert: symmetry clash REVERT: A 126 TYR cc_start: 0.8795 (m-80) cc_final: 0.8477 (m-80) REVERT: B 26 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7709 (mt) REVERT: B 28 ARG cc_start: 0.5028 (OUTLIER) cc_final: 0.4669 (mtp180) REVERT: B 154 LYS cc_start: 0.8521 (mtmm) cc_final: 0.8315 (mttm) REVERT: B 248 LYS cc_start: 0.8728 (pptt) cc_final: 0.8476 (ptmt) REVERT: C 94 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7794 (tm-30) REVERT: C 292 GLN cc_start: 0.8340 (tt0) cc_final: 0.8009 (tt0) REVERT: C 342 MET cc_start: 0.9061 (OUTLIER) cc_final: 0.8811 (ppp) REVERT: C 450 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7947 (tt0) REVERT: D 126 TYR cc_start: 0.8789 (m-80) cc_final: 0.8466 (m-80) REVERT: E 35 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8490 (tt) REVERT: E 248 LYS cc_start: 0.8773 (pptt) cc_final: 0.8441 (ptmt) REVERT: F 94 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8108 (tm-30) REVERT: F 181 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7707 (mp0) REVERT: F 450 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7890 (tt0) outliers start: 25 outliers final: 11 residues processed: 149 average time/residue: 1.4801 time to fit residues: 243.4724 Evaluate side-chains 150 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 130 time to evaluate : 1.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 450 GLN Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain F residue 297 TYR Chi-restraints excluded: chain F residue 450 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 153 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 166 optimal weight: 0.0170 chunk 69 optimal weight: 0.7980 chunk 171 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 146 optimal weight: 10.0000 overall best weight: 0.8420 ------------------------------------------------------------------------------- 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 = 0.3429 r_free = 0.3429 target = 0.096103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.063843 restraints weight = 33826.036| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 2.64 r_work: 0.2698 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2556 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2567 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2567 r_free = 0.2567 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 = 0.2567 r_free = 0.2567 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2567 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17114 Z= 0.170 Angle : 0.491 7.693 23216 Z= 0.251 Chirality : 0.044 0.166 2685 Planarity : 0.004 0.060 2921 Dihedral : 9.840 165.216 2562 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.30 % Favored : 97.55 % Rotamer: Outliers : 1.33 % Allowed : 12.41 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.20 (0.18), residues: 2129 helix: 1.09 (0.20), residues: 714 sheet: -0.31 (0.23), residues: 450 loop : -0.27 (0.20), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 325 HIS 0.003 0.001 HIS C 441 PHE 0.008 0.001 PHE F 255 TYR 0.015 0.001 TYR C 297 ARG 0.002 0.000 ARG E 108 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5659.10 seconds wall clock time: 101 minutes 4.46 seconds (6064.46 seconds total)