Starting phenix.real_space_refine on Sun Aug 24 14:43:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iaj_35304/08_2025/8iaj_35304.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iaj_35304/08_2025/8iaj_35304.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8iaj_35304/08_2025/8iaj_35304.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iaj_35304/08_2025/8iaj_35304.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8iaj_35304/08_2025/8iaj_35304.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iaj_35304/08_2025/8iaj_35304.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.006 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 114 5.16 5 C 13350 2.51 5 N 3470 2.21 5 O 3832 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 209 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20768 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 3861 Classifications: {'peptide': 495} Link IDs: {'PTRANS': 24, 'TRANS': 470} Chain: "B" Number of atoms: 4394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 555, 4394 Classifications: {'peptide': 555} Link IDs: {'PTRANS': 29, 'TRANS': 525} Chain: "D" Number of atoms: 1484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1484 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 8, 'TRANS': 173} Chain: "C" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 584 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain breaks: 1 Chain: "E" Number of atoms: 3861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 3861 Classifications: {'peptide': 495} Link IDs: {'PTRANS': 24, 'TRANS': 470} Chain: "F" Number of atoms: 4394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 555, 4394 Classifications: {'peptide': 555} Link IDs: {'PTRANS': 29, 'TRANS': 525} Chain: "H" Number of atoms: 1484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1484 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 8, 'TRANS': 173} Chain: "G" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 584 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain breaks: 1 Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'PLP': 1, 'Z1T': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'PLP': 1, 'Z1T': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 4.29, per 1000 atoms: 0.21 Number of scatterers: 20768 At special positions: 0 Unit cell: (171.72, 106.92, 124.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 114 16.00 P 2 15.00 O 3832 8.00 N 3470 7.00 C 13350 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 - 3.00 Amino acid : True - 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.51 Conformation dependent library (CDL) restraints added in 855.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4888 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 14 sheets defined 51.5% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 60 through 77 Processing helix chain 'A' and resid 89 through 100 Processing helix chain 'A' and resid 115 through 120 removed outlier: 3.558A pdb=" N ALA A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 175 Processing helix chain 'A' and resid 189 through 204 removed outlier: 3.700A pdb=" N TYR A 193 " --> pdb=" O GLN A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 Processing helix chain 'A' and resid 217 through 222 Processing helix chain 'A' and resid 223 through 225 No H-bonds generated for 'chain 'A' and resid 223 through 225' Processing helix chain 'A' and resid 239 through 250 removed outlier: 3.980A pdb=" N ARG A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 279 Processing helix chain 'A' and resid 302 through 314 removed outlier: 3.589A pdb=" N LEU A 306 " --> pdb=" O PRO A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 339 removed outlier: 3.527A pdb=" N HIS A 338 " --> pdb=" O GLY A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 347 Processing helix chain 'A' and resid 368 through 379 Processing helix chain 'A' and resid 379 through 384 Processing helix chain 'A' and resid 389 through 405 removed outlier: 3.744A pdb=" N VAL A 393 " --> pdb=" O PRO A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 427 removed outlier: 4.028A pdb=" N ASP A 427 " --> pdb=" O SER A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 459 removed outlier: 3.706A pdb=" N ARG A 454 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 476 Processing helix chain 'A' and resid 482 through 504 Processing helix chain 'A' and resid 534 through 554 Processing helix chain 'B' and resid 19 through 28 removed outlier: 3.533A pdb=" N GLN B 23 " --> pdb=" O PRO B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 85 removed outlier: 3.898A pdb=" N SER B 61 " --> pdb=" O PRO B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 116 removed outlier: 3.510A pdb=" N ARG B 112 " --> pdb=" O SER B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 122 removed outlier: 3.574A pdb=" N PHE B 122 " --> pdb=" O ASP B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 186 removed outlier: 3.823A pdb=" N ASP B 177 " --> pdb=" O GLY B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 215 removed outlier: 3.662A pdb=" N ILE B 204 " --> pdb=" O THR B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 237 removed outlier: 4.614A pdb=" N PHE B 233 " --> pdb=" O ASN B 229 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ASN B 234 " --> pdb=" O ALA B 230 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA B 235 " --> pdb=" O ASN B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 261 removed outlier: 3.553A pdb=" N ARG B 254 " --> pdb=" O HIS B 250 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER B 260 " --> pdb=" O GLY B 256 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY B 261 " --> pdb=" O VAL B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 286 removed outlier: 3.634A pdb=" N LEU B 275 " --> pdb=" O ASP B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 325 Processing helix chain 'B' and resid 345 through 351 Processing helix chain 'B' and resid 378 through 389 Processing helix chain 'B' and resid 390 through 395 Processing helix chain 'B' and resid 399 through 414 removed outlier: 3.516A pdb=" N LEU B 403 " --> pdb=" O PRO B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 444 removed outlier: 4.724A pdb=" N THR B 423 " --> pdb=" O PRO B 419 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG B 434 " --> pdb=" O ALA B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 476 removed outlier: 4.049A pdb=" N ALA B 468 " --> pdb=" O SER B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 522 Processing helix chain 'B' and resid 528 through 532 removed outlier: 3.869A pdb=" N SER B 531 " --> pdb=" O SER B 528 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER B 532 " --> pdb=" O GLY B 529 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 528 through 532' Processing helix chain 'B' and resid 541 through 553 Proline residue: B 550 - end of helix Processing helix chain 'D' and resid 57 through 66 Processing helix chain 'D' and resid 73 through 77 Processing helix chain 'D' and resid 79 through 98 removed outlier: 4.056A pdb=" N ILE D 88 " --> pdb=" O HIS D 84 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL D 89 " --> pdb=" O ILE D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 123 removed outlier: 3.933A pdb=" N LEU D 123 " --> pdb=" O ILE D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 145 removed outlier: 3.580A pdb=" N ILE D 145 " --> pdb=" O MET D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 148 No H-bonds generated for 'chain 'D' and resid 146 through 148' Processing helix chain 'D' and resid 152 through 170 Proline residue: D 162 - end of helix Processing helix chain 'D' and resid 176 through 191 Processing helix chain 'C' and resid 13 through 22 Processing helix chain 'C' and resid 27 through 45 Processing helix chain 'C' and resid 53 through 75 Processing helix chain 'E' and resid 61 through 77 Processing helix chain 'E' and resid 89 through 100 Processing helix chain 'E' and resid 115 through 120 removed outlier: 3.558A pdb=" N ALA E 119 " --> pdb=" O SER E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 175 Processing helix chain 'E' and resid 189 through 204 removed outlier: 3.700A pdb=" N TYR E 193 " --> pdb=" O GLN E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 216 Processing helix chain 'E' and resid 217 through 222 Processing helix chain 'E' and resid 223 through 225 No H-bonds generated for 'chain 'E' and resid 223 through 225' Processing helix chain 'E' and resid 239 through 250 removed outlier: 3.980A pdb=" N ARG E 250 " --> pdb=" O LEU E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 279 Processing helix chain 'E' and resid 302 through 314 removed outlier: 3.589A pdb=" N LEU E 306 " --> pdb=" O PRO E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 334 through 339 removed outlier: 3.527A pdb=" N HIS E 338 " --> pdb=" O GLY E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 347 Processing helix chain 'E' and resid 368 through 379 Processing helix chain 'E' and resid 379 through 384 Processing helix chain 'E' and resid 389 through 405 removed outlier: 3.743A pdb=" N VAL E 393 " --> pdb=" O PRO E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 427 removed outlier: 4.028A pdb=" N ASP E 427 " --> pdb=" O SER E 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 450 through 459 removed outlier: 3.706A pdb=" N ARG E 454 " --> pdb=" O THR E 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 461 through 476 Processing helix chain 'E' and resid 482 through 504 Processing helix chain 'E' and resid 534 through 554 Processing helix chain 'F' and resid 19 through 28 removed outlier: 3.533A pdb=" N GLN F 23 " --> pdb=" O PRO F 19 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 85 removed outlier: 3.899A pdb=" N SER F 61 " --> pdb=" O PRO F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 116 removed outlier: 3.510A pdb=" N ARG F 112 " --> pdb=" O SER F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 122 removed outlier: 3.574A pdb=" N PHE F 122 " --> pdb=" O ASP F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 186 removed outlier: 3.824A pdb=" N ASP F 177 " --> pdb=" O GLY F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 215 removed outlier: 3.662A pdb=" N ILE F 204 " --> pdb=" O THR F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 237 removed outlier: 4.615A pdb=" N PHE F 233 " --> pdb=" O ASN F 229 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ASN F 234 " --> pdb=" O ALA F 230 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA F 235 " --> pdb=" O ASN F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 261 removed outlier: 3.553A pdb=" N ARG F 254 " --> pdb=" O HIS F 250 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER F 260 " --> pdb=" O GLY F 256 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY F 261 " --> pdb=" O VAL F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 286 removed outlier: 3.634A pdb=" N LEU F 275 " --> pdb=" O ASP F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 325 Processing helix chain 'F' and resid 345 through 351 Processing helix chain 'F' and resid 378 through 389 Processing helix chain 'F' and resid 390 through 395 Processing helix chain 'F' and resid 399 through 414 removed outlier: 3.516A pdb=" N LEU F 403 " --> pdb=" O PRO F 399 " (cutoff:3.500A) Processing helix chain 'F' and resid 419 through 444 removed outlier: 4.724A pdb=" N THR F 423 " --> pdb=" O PRO F 419 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG F 434 " --> pdb=" O ALA F 430 " (cutoff:3.500A) Processing helix chain 'F' and resid 464 through 476 removed outlier: 4.049A pdb=" N ALA F 468 " --> pdb=" O SER F 464 " (cutoff:3.500A) Processing helix chain 'F' and resid 504 through 522 Processing helix chain 'F' and resid 528 through 532 removed outlier: 3.869A pdb=" N SER F 531 " --> pdb=" O SER F 528 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER F 532 " --> pdb=" O GLY F 529 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 528 through 532' Processing helix chain 'F' and resid 541 through 553 Proline residue: F 550 - end of helix Processing helix chain 'H' and resid 57 through 66 Processing helix chain 'H' and resid 73 through 77 Processing helix chain 'H' and resid 79 through 98 removed outlier: 4.056A pdb=" N ILE H 88 " --> pdb=" O HIS H 84 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL H 89 " --> pdb=" O ILE H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 123 removed outlier: 3.933A pdb=" N LEU H 123 " --> pdb=" O ILE H 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 145 removed outlier: 3.580A pdb=" N ILE H 145 " --> pdb=" O MET H 141 " (cutoff:3.500A) Processing helix chain 'H' and resid 146 through 148 No H-bonds generated for 'chain 'H' and resid 146 through 148' Processing helix chain 'H' and resid 152 through 170 Proline residue: H 162 - end of helix Processing helix chain 'H' and resid 176 through 191 Processing helix chain 'G' and resid 13 through 22 Processing helix chain 'G' and resid 27 through 45 Processing helix chain 'G' and resid 53 through 75 Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 135 removed outlier: 6.913A pdb=" N ILE A 135 " --> pdb=" O THR A 145 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N THR A 145 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N LEU A 506 " --> pdb=" O ASN A 146 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N PHE A 148 " --> pdb=" O LEU A 506 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 207 through 211 removed outlier: 3.602A pdb=" N GLY A 207 " --> pdb=" O GLY A 367 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE A 364 " --> pdb=" O GLY A 352 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LYS A 286 " --> pdb=" O ARG A 316 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N PHE A 318 " --> pdb=" O LYS A 286 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ILE A 288 " --> pdb=" O PHE A 318 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ASP A 320 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N THR A 290 " --> pdb=" O ASP A 320 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL A 231 " --> pdb=" O PHE A 287 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N VAL A 289 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL A 233 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 8.942A pdb=" N GLU A 291 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 444 through 447 removed outlier: 4.012A pdb=" N LEU A 447 " --> pdb=" O LEU A 525 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 126 through 127 removed outlier: 4.142A pdb=" N ARG B 135 " --> pdb=" O THR B 127 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP B 138 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ALA B 153 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N ILE B 140 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N SER B 151 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N HIS B 142 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N THR B 149 " --> pdb=" O HIS B 142 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ALA B 479 " --> pdb=" O PRO B 156 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N MET B 158 " --> pdb=" O ALA B 479 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 218 through 222 removed outlier: 3.538A pdb=" N ASP B 218 " --> pdb=" O ALA B 377 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N THR B 363 " --> pdb=" O GLU B 332 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP B 246 " --> pdb=" O CYS B 300 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N GLU B 302 " --> pdb=" O ASP B 246 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE B 267 " --> pdb=" O SER B 245 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 455 through 459 removed outlier: 3.702A pdb=" N ARG B 494 " --> pdb=" O VAL B 483 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 50 through 52 Processing sheet with id=AA8, first strand: chain 'E' and resid 132 through 135 removed outlier: 6.913A pdb=" N ILE E 135 " --> pdb=" O THR E 145 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N THR E 145 " --> pdb=" O ILE E 135 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N LEU E 506 " --> pdb=" O ASN E 146 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N PHE E 148 " --> pdb=" O LEU E 506 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 207 through 211 removed outlier: 3.602A pdb=" N GLY E 207 " --> pdb=" O GLY E 367 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE E 364 " --> pdb=" O GLY E 352 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LYS E 286 " --> pdb=" O ARG E 316 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N PHE E 318 " --> pdb=" O LYS E 286 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ILE E 288 " --> pdb=" O PHE E 318 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ASP E 320 " --> pdb=" O ILE E 288 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N THR E 290 " --> pdb=" O ASP E 320 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL E 231 " --> pdb=" O PHE E 287 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N VAL E 289 " --> pdb=" O VAL E 231 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL E 233 " --> pdb=" O VAL E 289 " (cutoff:3.500A) removed outlier: 8.943A pdb=" N GLU E 291 " --> pdb=" O VAL E 233 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 444 through 447 removed outlier: 4.012A pdb=" N LEU E 447 " --> pdb=" O LEU E 525 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 126 through 127 removed outlier: 4.142A pdb=" N ARG F 135 " --> pdb=" O THR F 127 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP F 138 " --> pdb=" O ALA F 153 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ALA F 153 " --> pdb=" O ASP F 138 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N ILE F 140 " --> pdb=" O SER F 151 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N SER F 151 " --> pdb=" O ILE F 140 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N HIS F 142 " --> pdb=" O THR F 149 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N THR F 149 " --> pdb=" O HIS F 142 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ALA F 479 " --> pdb=" O PRO F 156 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N MET F 158 " --> pdb=" O ALA F 479 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 218 through 222 removed outlier: 3.538A pdb=" N ASP F 218 " --> pdb=" O ALA F 377 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N THR F 363 " --> pdb=" O GLU F 332 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP F 246 " --> pdb=" O CYS F 300 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N GLU F 302 " --> pdb=" O ASP F 246 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE F 267 " --> pdb=" O SER F 245 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 455 through 459 removed outlier: 3.702A pdb=" N ARG F 494 " --> pdb=" O VAL F 483 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 50 through 52 985 hydrogen bonds defined for protein. 2889 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.97 Time building geometry restraints manager: 2.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6624 1.34 - 1.47: 5000 1.47 - 1.59: 9432 1.59 - 1.71: 2 1.71 - 1.83: 174 Bond restraints: 21232 Sorted by residual: bond pdb=" C14 Z1T F 602 " pdb=" C15 Z1T F 602 " ideal model delta sigma weight residual 1.329 1.526 -0.197 2.00e-02 2.50e+03 9.68e+01 bond pdb=" C14 Z1T B 602 " pdb=" C15 Z1T B 602 " ideal model delta sigma weight residual 1.329 1.526 -0.197 2.00e-02 2.50e+03 9.68e+01 bond pdb=" C4 PLP F 601 " pdb=" C5 PLP F 601 " ideal model delta sigma weight residual 1.390 1.486 -0.096 2.00e-02 2.50e+03 2.30e+01 bond pdb=" C4 PLP B 601 " pdb=" C5 PLP B 601 " ideal model delta sigma weight residual 1.390 1.486 -0.096 2.00e-02 2.50e+03 2.30e+01 bond pdb=" C2 PLP B 601 " pdb=" C3 PLP B 601 " ideal model delta sigma weight residual 1.390 1.484 -0.094 2.00e-02 2.50e+03 2.23e+01 ... (remaining 21227 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.54: 28668 4.54 - 9.07: 98 9.07 - 13.61: 2 13.61 - 18.15: 0 18.15 - 22.68: 4 Bond angle restraints: 28772 Sorted by residual: angle pdb=" CB MET D 70 " pdb=" CG MET D 70 " pdb=" SD MET D 70 " ideal model delta sigma weight residual 112.70 135.38 -22.68 3.00e+00 1.11e-01 5.72e+01 angle pdb=" CB MET H 70 " pdb=" CG MET H 70 " pdb=" SD MET H 70 " ideal model delta sigma weight residual 112.70 135.38 -22.68 3.00e+00 1.11e-01 5.72e+01 angle pdb=" CB MET H 177 " pdb=" CG MET H 177 " pdb=" SD MET H 177 " ideal model delta sigma weight residual 112.70 133.09 -20.39 3.00e+00 1.11e-01 4.62e+01 angle pdb=" CB MET D 177 " pdb=" CG MET D 177 " pdb=" SD MET D 177 " ideal model delta sigma weight residual 112.70 133.09 -20.39 3.00e+00 1.11e-01 4.62e+01 angle pdb=" N MET B 307 " pdb=" CA MET B 307 " pdb=" C MET B 307 " ideal model delta sigma weight residual 114.64 107.24 7.40 1.52e+00 4.33e-01 2.37e+01 ... (remaining 28767 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.06: 11796 21.06 - 42.12: 862 42.12 - 63.18: 90 63.18 - 84.24: 16 84.24 - 105.30: 6 Dihedral angle restraints: 12770 sinusoidal: 5180 harmonic: 7590 Sorted by residual: dihedral pdb=" CA GLY D 134 " pdb=" C GLY D 134 " pdb=" N ALA D 135 " pdb=" CA ALA D 135 " ideal model delta harmonic sigma weight residual 180.00 150.58 29.42 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA GLY H 134 " pdb=" C GLY H 134 " pdb=" N ALA H 135 " pdb=" CA ALA H 135 " ideal model delta harmonic sigma weight residual 180.00 150.58 29.42 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA PHE A 256 " pdb=" C PHE A 256 " pdb=" N ASN A 257 " pdb=" CA ASN A 257 " ideal model delta harmonic sigma weight residual -180.00 -154.64 -25.36 0 5.00e+00 4.00e-02 2.57e+01 ... (remaining 12767 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2338 0.048 - 0.095: 749 0.095 - 0.143: 153 0.143 - 0.190: 12 0.190 - 0.238: 4 Chirality restraints: 3256 Sorted by residual: chirality pdb=" CA LEU B 91 " pdb=" N LEU B 91 " pdb=" C LEU B 91 " pdb=" CB LEU B 91 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA LEU F 91 " pdb=" N LEU F 91 " pdb=" C LEU F 91 " pdb=" CB LEU F 91 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" C17 Z1T F 602 " pdb=" C16 Z1T F 602 " pdb=" C18 Z1T F 602 " pdb=" N1 Z1T F 602 " both_signs ideal model delta sigma weight residual False 2.47 2.69 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 3253 not shown) Planarity restraints: 3652 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 86 " 0.045 5.00e-02 4.00e+02 6.91e-02 7.65e+00 pdb=" N PRO A 87 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO A 87 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 87 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG E 86 " -0.045 5.00e-02 4.00e+02 6.91e-02 7.65e+00 pdb=" N PRO E 87 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO E 87 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO E 87 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE G 48 " -0.011 2.00e-02 2.50e+03 2.32e-02 5.38e+00 pdb=" C PHE G 48 " 0.040 2.00e-02 2.50e+03 pdb=" O PHE G 48 " -0.015 2.00e-02 2.50e+03 pdb=" N TYR G 49 " -0.014 2.00e-02 2.50e+03 ... (remaining 3649 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 1062 2.72 - 3.27: 20149 3.27 - 3.81: 32021 3.81 - 4.36: 38933 4.36 - 4.90: 70221 Nonbonded interactions: 162386 Sorted by model distance: nonbonded pdb=" CD LYS A 85 " pdb=" OE1 GLN H 55 " model vdw 2.176 3.440 nonbonded pdb=" NH2 ARG A 228 " pdb=" OD2 ASP D 63 " model vdw 2.184 3.120 nonbonded pdb=" NH2 ARG E 228 " pdb=" OD2 ASP H 63 " model vdw 2.184 3.120 nonbonded pdb=" OE1 GLN D 55 " pdb=" CD LYS E 85 " model vdw 2.193 3.440 nonbonded pdb=" OG1 THR F 342 " pdb=" OE2 GLU F 348 " model vdw 2.204 3.040 ... (remaining 162381 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.090 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: 0.220 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 16.070 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 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 0.463 21234 Z= 0.528 Angle : 0.858 22.682 28772 Z= 0.485 Chirality : 0.047 0.238 3256 Planarity : 0.005 0.069 3652 Dihedral : 13.913 105.296 7882 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.44 % Favored : 92.49 % Rotamer: Outliers : 0.61 % Allowed : 0.78 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.16), residues: 2582 helix: 1.50 (0.15), residues: 1218 sheet: -0.46 (0.32), residues: 258 loop : -2.21 (0.16), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 42 TYR 0.022 0.002 TYR F 533 PHE 0.036 0.002 PHE C 62 TRP 0.010 0.001 TRP D 106 HIS 0.004 0.001 HIS G 45 Details of bonding type rmsd covalent geometry : bond 0.00612 (21232) covalent geometry : angle 0.85779 (28772) hydrogen bonds : bond 0.15985 ( 985) hydrogen bonds : angle 5.88274 ( 2889) Misc. bond : bond 0.46243 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 266 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 39 THR cc_start: 0.8399 (p) cc_final: 0.8098 (p) REVERT: F 466 MET cc_start: 0.8273 (ttp) cc_final: 0.7822 (ttp) REVERT: H 39 THR cc_start: 0.8395 (p) cc_final: 0.8078 (p) outliers start: 14 outliers final: 5 residues processed: 270 average time/residue: 0.1329 time to fit residues: 56.1133 Evaluate side-chains 212 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 207 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain H residue 70 MET Chi-restraints excluded: chain G residue 59 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 0.4980 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 9.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 GLN ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 HIS B 145 ASN E 130 GLN E 237 GLN ** E 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 HIS F 145 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.123589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.097336 restraints weight = 28511.246| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.67 r_work: 0.2919 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21234 Z= 0.145 Angle : 0.600 6.980 28772 Z= 0.319 Chirality : 0.043 0.179 3256 Planarity : 0.005 0.046 3652 Dihedral : 7.450 100.431 2933 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.96 % Allowed : 6.13 % Favored : 92.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.17), residues: 2582 helix: 1.77 (0.15), residues: 1228 sheet: 0.09 (0.31), residues: 280 loop : -2.12 (0.17), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 174 TYR 0.016 0.001 TYR B 510 PHE 0.017 0.001 PHE E 256 TRP 0.009 0.001 TRP D 142 HIS 0.003 0.001 HIS C 45 Details of bonding type rmsd covalent geometry : bond 0.00332 (21232) covalent geometry : angle 0.59989 (28772) hydrogen bonds : bond 0.05403 ( 985) hydrogen bonds : angle 4.65906 ( 2889) Misc. bond : bond 0.00083 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 252 time to evaluate : 0.803 Fit side-chains REVERT: A 94 ASP cc_start: 0.8353 (m-30) cc_final: 0.7929 (m-30) REVERT: B 396 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.7870 (pp20) REVERT: D 39 THR cc_start: 0.8393 (p) cc_final: 0.8068 (p) REVERT: D 73 THR cc_start: 0.9175 (m) cc_final: 0.8858 (p) REVERT: C 59 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8542 (tp) REVERT: E 94 ASP cc_start: 0.8327 (m-30) cc_final: 0.7886 (m-30) REVERT: F 396 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.7845 (pp20) REVERT: F 520 ASP cc_start: 0.8118 (t0) cc_final: 0.7900 (m-30) REVERT: H 39 THR cc_start: 0.8406 (p) cc_final: 0.8087 (p) REVERT: H 73 THR cc_start: 0.9176 (m) cc_final: 0.8838 (p) REVERT: G 59 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8524 (tp) outliers start: 22 outliers final: 12 residues processed: 267 average time/residue: 0.1270 time to fit residues: 53.4609 Evaluate side-chains 229 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 213 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 375 ILE Chi-restraints excluded: chain F residue 396 GLU Chi-restraints excluded: chain G residue 59 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 26 optimal weight: 3.9990 chunk 182 optimal weight: 3.9990 chunk 243 optimal weight: 0.8980 chunk 145 optimal weight: 7.9990 chunk 50 optimal weight: 0.8980 chunk 79 optimal weight: 6.9990 chunk 202 optimal weight: 7.9990 chunk 114 optimal weight: 5.9990 chunk 160 optimal weight: 0.0070 chunk 66 optimal weight: 0.6980 chunk 1 optimal weight: 9.9990 overall best weight: 1.3000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.124968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.098703 restraints weight = 28418.095| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 1.67 r_work: 0.2927 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21234 Z= 0.126 Angle : 0.555 6.263 28772 Z= 0.295 Chirality : 0.042 0.182 3256 Planarity : 0.005 0.050 3652 Dihedral : 7.194 96.867 2927 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.91 % Allowed : 8.61 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.17), residues: 2582 helix: 1.90 (0.15), residues: 1230 sheet: 0.27 (0.32), residues: 280 loop : -1.99 (0.17), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 137 TYR 0.015 0.001 TYR B 510 PHE 0.016 0.001 PHE A 256 TRP 0.007 0.001 TRP H 142 HIS 0.003 0.001 HIS C 45 Details of bonding type rmsd covalent geometry : bond 0.00289 (21232) covalent geometry : angle 0.55507 (28772) hydrogen bonds : bond 0.04733 ( 985) hydrogen bonds : angle 4.42436 ( 2889) Misc. bond : bond 0.00082 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 236 time to evaluate : 0.562 Fit side-chains REVERT: A 85 LYS cc_start: 0.8611 (tppt) cc_final: 0.8333 (mmtp) REVERT: A 98 ASP cc_start: 0.8177 (m-30) cc_final: 0.7877 (m-30) REVERT: B 271 ASP cc_start: 0.8334 (t0) cc_final: 0.8123 (t0) REVERT: B 483 VAL cc_start: 0.8761 (m) cc_final: 0.8551 (t) REVERT: B 520 ASP cc_start: 0.8159 (t0) cc_final: 0.7716 (m-30) REVERT: D 39 THR cc_start: 0.8335 (p) cc_final: 0.8011 (p) REVERT: C 59 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8642 (tp) REVERT: E 85 LYS cc_start: 0.8607 (tppt) cc_final: 0.8328 (mmtp) REVERT: E 98 ASP cc_start: 0.8203 (m-30) cc_final: 0.7935 (m-30) REVERT: E 261 MET cc_start: 0.8162 (mmp) cc_final: 0.7765 (mmp) REVERT: F 483 VAL cc_start: 0.8756 (m) cc_final: 0.8543 (t) REVERT: F 520 ASP cc_start: 0.8070 (t0) cc_final: 0.7625 (m-30) REVERT: H 39 THR cc_start: 0.8358 (p) cc_final: 0.8032 (p) REVERT: G 59 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8623 (tp) outliers start: 21 outliers final: 19 residues processed: 249 average time/residue: 0.1343 time to fit residues: 52.7110 Evaluate side-chains 244 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 223 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 514 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 388 ASP Chi-restraints excluded: chain H residue 98 PHE Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain G residue 59 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 110 optimal weight: 10.0000 chunk 195 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 126 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 chunk 80 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 239 optimal weight: 10.0000 chunk 53 optimal weight: 0.0470 chunk 31 optimal weight: 3.9990 overall best weight: 0.8880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 GLN ** E 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 171 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.126891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.100782 restraints weight = 28496.835| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.67 r_work: 0.2949 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 21234 Z= 0.109 Angle : 0.517 6.469 28772 Z= 0.274 Chirality : 0.041 0.182 3256 Planarity : 0.005 0.050 3652 Dihedral : 7.030 94.469 2927 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.35 % Allowed : 9.70 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.17), residues: 2582 helix: 2.03 (0.15), residues: 1232 sheet: 0.36 (0.32), residues: 280 loop : -1.79 (0.17), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 174 TYR 0.013 0.001 TYR B 510 PHE 0.017 0.001 PHE G 62 TRP 0.006 0.001 TRP H 106 HIS 0.003 0.001 HIS G 45 Details of bonding type rmsd covalent geometry : bond 0.00243 (21232) covalent geometry : angle 0.51715 (28772) hydrogen bonds : bond 0.04030 ( 985) hydrogen bonds : angle 4.24871 ( 2889) Misc. bond : bond 0.00063 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 231 time to evaluate : 0.761 Fit side-chains REVERT: A 94 ASP cc_start: 0.8130 (m-30) cc_final: 0.7821 (m-30) REVERT: A 98 ASP cc_start: 0.8208 (m-30) cc_final: 0.7825 (m-30) REVERT: A 308 LYS cc_start: 0.8647 (ttmt) cc_final: 0.8313 (ttmm) REVERT: B 271 ASP cc_start: 0.8243 (t0) cc_final: 0.7957 (t0) REVERT: B 396 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.7784 (pp20) REVERT: B 483 VAL cc_start: 0.8677 (m) cc_final: 0.8455 (t) REVERT: B 520 ASP cc_start: 0.8114 (t0) cc_final: 0.7685 (m-30) REVERT: D 39 THR cc_start: 0.8434 (p) cc_final: 0.8072 (p) REVERT: D 42 ARG cc_start: 0.7702 (ttm110) cc_final: 0.7209 (mtm180) REVERT: C 59 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8699 (tp) REVERT: E 94 ASP cc_start: 0.8113 (m-30) cc_final: 0.7818 (m-30) REVERT: E 98 ASP cc_start: 0.8224 (m-30) cc_final: 0.7874 (m-30) REVERT: E 308 LYS cc_start: 0.8576 (ttmt) cc_final: 0.8318 (ttmm) REVERT: E 341 MET cc_start: 0.8551 (mtt) cc_final: 0.8271 (mtp) REVERT: F 396 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.7779 (pp20) REVERT: F 466 MET cc_start: 0.8576 (ttp) cc_final: 0.8318 (ttp) REVERT: F 483 VAL cc_start: 0.8661 (m) cc_final: 0.8413 (t) REVERT: F 520 ASP cc_start: 0.8117 (t0) cc_final: 0.7684 (m-30) REVERT: H 39 THR cc_start: 0.8320 (p) cc_final: 0.7991 (p) REVERT: H 42 ARG cc_start: 0.7698 (ttm110) cc_final: 0.7191 (mtm180) REVERT: G 59 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8686 (tp) outliers start: 31 outliers final: 20 residues processed: 253 average time/residue: 0.1224 time to fit residues: 49.2681 Evaluate side-chains 243 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 219 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain E residue 130 GLN Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 514 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 396 GLU Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain H residue 98 PHE Chi-restraints excluded: chain G residue 59 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 57 optimal weight: 10.0000 chunk 224 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 206 optimal weight: 7.9990 chunk 221 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 236 optimal weight: 4.9990 chunk 153 optimal weight: 0.9980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 GLN ** E 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.125019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.097522 restraints weight = 28013.068| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.78 r_work: 0.2938 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21234 Z= 0.141 Angle : 0.557 7.670 28772 Z= 0.294 Chirality : 0.043 0.174 3256 Planarity : 0.005 0.053 3652 Dihedral : 7.042 94.298 2926 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 1.74 % Allowed : 10.61 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.17), residues: 2582 helix: 1.98 (0.15), residues: 1234 sheet: 0.44 (0.33), residues: 254 loop : -1.74 (0.18), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 174 TYR 0.017 0.001 TYR B 510 PHE 0.019 0.001 PHE E 256 TRP 0.008 0.001 TRP D 142 HIS 0.003 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00337 (21232) covalent geometry : angle 0.55702 (28772) hydrogen bonds : bond 0.04806 ( 985) hydrogen bonds : angle 4.26013 ( 2889) Misc. bond : bond 0.00074 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 210 time to evaluate : 0.527 Fit side-chains REVERT: A 85 LYS cc_start: 0.8588 (tppt) cc_final: 0.8221 (tppt) REVERT: A 94 ASP cc_start: 0.8094 (m-30) cc_final: 0.7764 (m-30) REVERT: A 98 ASP cc_start: 0.8188 (m-30) cc_final: 0.7895 (m-30) REVERT: A 261 MET cc_start: 0.8193 (mmp) cc_final: 0.7789 (mmp) REVERT: A 308 LYS cc_start: 0.8607 (ttmt) cc_final: 0.8338 (ttmm) REVERT: B 271 ASP cc_start: 0.8303 (t0) cc_final: 0.8081 (t0) REVERT: B 396 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.7740 (pp20) REVERT: B 483 VAL cc_start: 0.8843 (m) cc_final: 0.8621 (t) REVERT: D 39 THR cc_start: 0.8439 (p) cc_final: 0.8093 (p) REVERT: C 59 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8546 (tp) REVERT: E 85 LYS cc_start: 0.8535 (tppt) cc_final: 0.8168 (tppt) REVERT: F 116 MET cc_start: 0.8589 (mmm) cc_final: 0.8288 (mmp) REVERT: F 396 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.7738 (pp20) REVERT: F 483 VAL cc_start: 0.8816 (m) cc_final: 0.8595 (t) REVERT: H 39 THR cc_start: 0.8280 (p) cc_final: 0.7953 (p) REVERT: G 59 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8613 (tp) outliers start: 40 outliers final: 27 residues processed: 239 average time/residue: 0.1260 time to fit residues: 47.5507 Evaluate side-chains 238 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 207 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 514 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 396 GLU Chi-restraints excluded: chain F residue 560 VAL Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain H residue 98 PHE Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain G residue 59 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 208 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 128 optimal weight: 7.9990 chunk 194 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 217 optimal weight: 5.9990 chunk 152 optimal weight: 6.9990 chunk 133 optimal weight: 0.7980 chunk 200 optimal weight: 0.8980 chunk 191 optimal weight: 6.9990 chunk 233 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 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 GLN ** E 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 171 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.126768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.099375 restraints weight = 28115.214| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.79 r_work: 0.2942 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21234 Z= 0.111 Angle : 0.528 10.309 28772 Z= 0.276 Chirality : 0.041 0.179 3256 Planarity : 0.005 0.054 3652 Dihedral : 6.929 93.600 2926 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.74 % Allowed : 11.22 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.17), residues: 2582 helix: 2.09 (0.15), residues: 1234 sheet: 0.52 (0.33), residues: 256 loop : -1.64 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 174 TYR 0.014 0.001 TYR B 510 PHE 0.018 0.001 PHE C 62 TRP 0.007 0.001 TRP B 294 HIS 0.003 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00251 (21232) covalent geometry : angle 0.52804 (28772) hydrogen bonds : bond 0.04117 ( 985) hydrogen bonds : angle 4.18229 ( 2889) Misc. bond : bond 0.00061 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 227 time to evaluate : 0.717 Fit side-chains REVERT: A 261 MET cc_start: 0.8235 (mmp) cc_final: 0.7864 (mmt) REVERT: A 308 LYS cc_start: 0.8619 (ttmt) cc_final: 0.8363 (mtpt) REVERT: B 116 MET cc_start: 0.8419 (mmm) cc_final: 0.8109 (mmp) REVERT: B 139 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.7901 (mtm180) REVERT: B 239 LYS cc_start: 0.8557 (ptmm) cc_final: 0.8226 (tttm) REVERT: B 271 ASP cc_start: 0.8235 (t0) cc_final: 0.8007 (t0) REVERT: B 323 LYS cc_start: 0.8396 (tttt) cc_final: 0.8151 (tttp) REVERT: B 396 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.7673 (pp20) REVERT: D 39 THR cc_start: 0.8400 (p) cc_final: 0.8038 (p) REVERT: D 42 ARG cc_start: 0.7641 (ttm110) cc_final: 0.7112 (mtm180) REVERT: C 59 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8494 (tp) REVERT: E 125 MET cc_start: 0.7401 (mtm) cc_final: 0.6656 (mtm) REVERT: E 308 LYS cc_start: 0.8609 (ttmt) cc_final: 0.8233 (ttmm) REVERT: F 116 MET cc_start: 0.8553 (mmm) cc_final: 0.8267 (mmp) REVERT: F 139 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.7943 (mtm180) REVERT: F 239 LYS cc_start: 0.8536 (ptmm) cc_final: 0.8202 (tttm) REVERT: F 396 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.7673 (pp20) REVERT: H 39 THR cc_start: 0.8240 (p) cc_final: 0.7897 (p) REVERT: H 42 ARG cc_start: 0.7639 (ttm110) cc_final: 0.7103 (mtm180) REVERT: G 59 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8507 (tp) outliers start: 40 outliers final: 30 residues processed: 257 average time/residue: 0.1332 time to fit residues: 53.1168 Evaluate side-chains 251 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 215 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 514 LEU Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 139 ARG Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain F residue 396 GLU Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain H residue 98 PHE Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain G residue 59 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 176 optimal weight: 9.9990 chunk 3 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 231 optimal weight: 2.9990 chunk 184 optimal weight: 5.9990 chunk 112 optimal weight: 0.9990 chunk 183 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 223 optimal weight: 0.6980 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 GLN ** E 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 477 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.125170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.097612 restraints weight = 28303.228| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 1.79 r_work: 0.2920 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 21234 Z= 0.138 Angle : 0.558 9.661 28772 Z= 0.293 Chirality : 0.042 0.173 3256 Planarity : 0.005 0.057 3652 Dihedral : 6.981 93.892 2926 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.00 % Allowed : 11.61 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.17), residues: 2582 helix: 2.07 (0.15), residues: 1234 sheet: 0.51 (0.33), residues: 254 loop : -1.66 (0.18), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 437 TYR 0.017 0.001 TYR F 510 PHE 0.020 0.001 PHE C 62 TRP 0.008 0.001 TRP H 142 HIS 0.004 0.001 HIS C 45 Details of bonding type rmsd covalent geometry : bond 0.00328 (21232) covalent geometry : angle 0.55794 (28772) hydrogen bonds : bond 0.04675 ( 985) hydrogen bonds : angle 4.21159 ( 2889) Misc. bond : bond 0.00069 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 221 time to evaluate : 0.810 Fit side-chains REVERT: A 85 LYS cc_start: 0.8593 (tppt) cc_final: 0.8267 (tppt) REVERT: A 261 MET cc_start: 0.8236 (mmp) cc_final: 0.7865 (mmp) REVERT: A 308 LYS cc_start: 0.8577 (ttmt) cc_final: 0.8309 (mtpt) REVERT: B 116 MET cc_start: 0.8471 (mmm) cc_final: 0.7988 (mmm) REVERT: B 139 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.7791 (mtm180) REVERT: B 396 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.7700 (pp20) REVERT: D 39 THR cc_start: 0.8411 (p) cc_final: 0.8071 (p) REVERT: C 14 THR cc_start: 0.7753 (p) cc_final: 0.7509 (p) REVERT: C 59 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8497 (tp) REVERT: E 85 LYS cc_start: 0.8543 (tppt) cc_final: 0.8214 (tppt) REVERT: E 125 MET cc_start: 0.7551 (mtm) cc_final: 0.6823 (mtm) REVERT: E 308 LYS cc_start: 0.8630 (ttmt) cc_final: 0.8254 (ttmm) REVERT: E 479 ASN cc_start: 0.7998 (t0) cc_final: 0.7767 (t0) REVERT: F 116 MET cc_start: 0.8614 (mmm) cc_final: 0.8317 (mmp) REVERT: F 139 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.7817 (mtm180) REVERT: F 396 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.7697 (pp20) REVERT: F 483 VAL cc_start: 0.8722 (m) cc_final: 0.8519 (t) REVERT: H 39 THR cc_start: 0.8247 (p) cc_final: 0.7927 (p) REVERT: G 14 THR cc_start: 0.7755 (p) cc_final: 0.7510 (p) REVERT: G 59 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8514 (tp) outliers start: 46 outliers final: 31 residues processed: 258 average time/residue: 0.1405 time to fit residues: 56.6096 Evaluate side-chains 247 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 210 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 514 LEU Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 139 ARG Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 332 GLU Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain F residue 396 GLU Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 560 VAL Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain H residue 98 PHE Chi-restraints excluded: chain H residue 205 SER Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain G residue 59 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 141 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 152 optimal weight: 0.9990 chunk 87 optimal weight: 6.9990 chunk 189 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 136 optimal weight: 6.9990 chunk 177 optimal weight: 8.9990 chunk 36 optimal weight: 9.9990 chunk 49 optimal weight: 8.9990 chunk 16 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 GLN ** E 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 171 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.126091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.098616 restraints weight = 28113.554| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.78 r_work: 0.2928 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21234 Z= 0.121 Angle : 0.535 8.875 28772 Z= 0.281 Chirality : 0.042 0.175 3256 Planarity : 0.005 0.056 3652 Dihedral : 6.940 93.735 2926 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.22 % Allowed : 11.83 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.17), residues: 2582 helix: 2.14 (0.15), residues: 1234 sheet: 0.59 (0.33), residues: 256 loop : -1.60 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 456 TYR 0.015 0.001 TYR F 510 PHE 0.020 0.001 PHE C 62 TRP 0.008 0.001 TRP D 142 HIS 0.003 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00282 (21232) covalent geometry : angle 0.53544 (28772) hydrogen bonds : bond 0.04309 ( 985) hydrogen bonds : angle 4.17270 ( 2889) Misc. bond : bond 0.00062 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 220 time to evaluate : 0.754 Fit side-chains REVERT: A 261 MET cc_start: 0.8227 (mmp) cc_final: 0.7841 (mmp) REVERT: A 308 LYS cc_start: 0.8646 (ttmt) cc_final: 0.8438 (mtpt) REVERT: A 479 ASN cc_start: 0.7986 (t0) cc_final: 0.7772 (t0) REVERT: B 8 THR cc_start: 0.8361 (OUTLIER) cc_final: 0.7999 (t) REVERT: B 116 MET cc_start: 0.8462 (mmm) cc_final: 0.7986 (mmm) REVERT: B 139 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.7933 (mtm180) REVERT: B 323 LYS cc_start: 0.8419 (tttt) cc_final: 0.8180 (tttp) REVERT: B 396 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.7680 (pp20) REVERT: B 548 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.6806 (ttp-110) REVERT: D 39 THR cc_start: 0.8418 (p) cc_final: 0.8058 (p) REVERT: C 14 THR cc_start: 0.7742 (p) cc_final: 0.7499 (p) REVERT: C 59 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8489 (tp) REVERT: E 125 MET cc_start: 0.7561 (mtm) cc_final: 0.6888 (mtm) REVERT: E 308 LYS cc_start: 0.8593 (ttmt) cc_final: 0.8219 (ttmm) REVERT: E 479 ASN cc_start: 0.8005 (t0) cc_final: 0.7766 (t0) REVERT: F 8 THR cc_start: 0.8334 (OUTLIER) cc_final: 0.7981 (t) REVERT: F 116 MET cc_start: 0.8601 (mmm) cc_final: 0.8228 (mmp) REVERT: F 139 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.7941 (mtm180) REVERT: F 323 LYS cc_start: 0.8416 (tttt) cc_final: 0.8180 (tttp) REVERT: F 396 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.7685 (pp20) REVERT: F 483 VAL cc_start: 0.8720 (m) cc_final: 0.8484 (t) REVERT: F 548 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.6781 (ttp-110) REVERT: H 39 THR cc_start: 0.8251 (p) cc_final: 0.7913 (p) REVERT: G 14 THR cc_start: 0.7741 (p) cc_final: 0.7494 (p) REVERT: G 59 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8505 (tp) outliers start: 51 outliers final: 32 residues processed: 261 average time/residue: 0.1285 time to fit residues: 52.2564 Evaluate side-chains 258 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 216 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 548 ARG Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 514 LEU Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 139 ARG Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain F residue 396 GLU Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 548 ARG Chi-restraints excluded: chain F residue 560 VAL Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain H residue 98 PHE Chi-restraints excluded: chain H residue 205 SER Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain G residue 59 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 182 optimal weight: 1.9990 chunk 124 optimal weight: 10.0000 chunk 209 optimal weight: 5.9990 chunk 232 optimal weight: 9.9990 chunk 41 optimal weight: 0.0050 chunk 72 optimal weight: 1.9990 chunk 217 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 216 optimal weight: 3.9990 chunk 157 optimal weight: 0.4980 chunk 175 optimal weight: 0.8980 overall best weight: 1.0798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.126914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.099479 restraints weight = 28169.372| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 1.78 r_work: 0.2937 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21234 Z= 0.112 Angle : 0.530 8.628 28772 Z= 0.278 Chirality : 0.041 0.177 3256 Planarity : 0.005 0.053 3652 Dihedral : 6.886 93.443 2926 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.00 % Allowed : 12.04 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.17), residues: 2582 helix: 2.19 (0.15), residues: 1238 sheet: 0.70 (0.33), residues: 256 loop : -1.54 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 456 TYR 0.014 0.001 TYR B 510 PHE 0.020 0.001 PHE C 62 TRP 0.007 0.001 TRP B 294 HIS 0.003 0.001 HIS G 45 Details of bonding type rmsd covalent geometry : bond 0.00252 (21232) covalent geometry : angle 0.53002 (28772) hydrogen bonds : bond 0.04052 ( 985) hydrogen bonds : angle 4.13772 ( 2889) Misc. bond : bond 0.00059 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 216 time to evaluate : 0.771 Fit side-chains REVERT: A 85 LYS cc_start: 0.8603 (tppt) cc_final: 0.8322 (tppt) REVERT: A 261 MET cc_start: 0.8281 (mmp) cc_final: 0.7864 (mmp) REVERT: A 479 ASN cc_start: 0.8015 (t0) cc_final: 0.7755 (t0) REVERT: B 8 THR cc_start: 0.8344 (OUTLIER) cc_final: 0.7989 (t) REVERT: B 116 MET cc_start: 0.8455 (mmm) cc_final: 0.7993 (mmm) REVERT: B 139 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.7908 (mtm180) REVERT: B 323 LYS cc_start: 0.8417 (tttt) cc_final: 0.8181 (tttp) REVERT: B 396 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.7690 (pp20) REVERT: B 548 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.6784 (ttp-110) REVERT: D 39 THR cc_start: 0.8400 (p) cc_final: 0.8033 (p) REVERT: C 59 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8456 (tp) REVERT: E 85 LYS cc_start: 0.8618 (tppt) cc_final: 0.8339 (tppt) REVERT: E 125 MET cc_start: 0.7523 (mtm) cc_final: 0.7299 (mtm) REVERT: E 308 LYS cc_start: 0.8587 (ttmt) cc_final: 0.8314 (mtpt) REVERT: E 479 ASN cc_start: 0.8008 (t0) cc_final: 0.7799 (t0) REVERT: F 8 THR cc_start: 0.8321 (OUTLIER) cc_final: 0.7980 (t) REVERT: F 116 MET cc_start: 0.8546 (mmm) cc_final: 0.8107 (mmm) REVERT: F 323 LYS cc_start: 0.8411 (tttt) cc_final: 0.8182 (tttp) REVERT: F 396 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.7697 (pp20) REVERT: F 548 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.6769 (ttp-110) REVERT: H 39 THR cc_start: 0.8396 (p) cc_final: 0.8023 (p) REVERT: G 59 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8466 (tp) outliers start: 46 outliers final: 32 residues processed: 248 average time/residue: 0.1376 time to fit residues: 53.3309 Evaluate side-chains 249 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 208 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 548 ARG Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 514 LEU Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 375 ILE Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain F residue 396 GLU Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 548 ARG Chi-restraints excluded: chain F residue 560 VAL Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain G residue 59 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 91 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 chunk 164 optimal weight: 9.9990 chunk 26 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 chunk 223 optimal weight: 1.9990 chunk 90 optimal weight: 0.3980 chunk 156 optimal weight: 7.9990 chunk 208 optimal weight: 3.9990 chunk 190 optimal weight: 7.9990 chunk 201 optimal weight: 0.0770 overall best weight: 1.4142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.126063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.098542 restraints weight = 28129.151| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 1.78 r_work: 0.2931 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21234 Z= 0.123 Angle : 0.540 8.499 28772 Z= 0.283 Chirality : 0.042 0.174 3256 Planarity : 0.005 0.054 3652 Dihedral : 6.916 93.750 2926 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.04 % Allowed : 12.26 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.17), residues: 2582 helix: 2.19 (0.15), residues: 1238 sheet: 0.66 (0.33), residues: 256 loop : -1.55 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 456 TYR 0.016 0.001 TYR B 510 PHE 0.022 0.001 PHE C 62 TRP 0.007 0.001 TRP H 142 HIS 0.003 0.001 HIS G 45 Details of bonding type rmsd covalent geometry : bond 0.00287 (21232) covalent geometry : angle 0.54005 (28772) hydrogen bonds : bond 0.04323 ( 985) hydrogen bonds : angle 4.13719 ( 2889) Misc. bond : bond 0.00064 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 215 time to evaluate : 0.791 Fit side-chains REVERT: A 261 MET cc_start: 0.8353 (mmp) cc_final: 0.7962 (mmp) REVERT: A 479 ASN cc_start: 0.8045 (t0) cc_final: 0.7820 (t0) REVERT: B 8 THR cc_start: 0.8360 (OUTLIER) cc_final: 0.8005 (t) REVERT: B 116 MET cc_start: 0.8475 (mmm) cc_final: 0.8027 (mmm) REVERT: B 139 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.7935 (mtm180) REVERT: B 323 LYS cc_start: 0.8440 (tttt) cc_final: 0.8203 (tttp) REVERT: B 396 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.7680 (pp20) REVERT: B 548 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.6888 (ttp-110) REVERT: D 39 THR cc_start: 0.8401 (p) cc_final: 0.8032 (p) REVERT: C 59 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8500 (tp) REVERT: E 308 LYS cc_start: 0.8596 (ttmt) cc_final: 0.8321 (mtpt) REVERT: E 533 MET cc_start: 0.8141 (OUTLIER) cc_final: 0.7743 (mtm) REVERT: F 8 THR cc_start: 0.8335 (OUTLIER) cc_final: 0.7989 (t) REVERT: F 116 MET cc_start: 0.8560 (mmm) cc_final: 0.8117 (mmm) REVERT: F 119 ASP cc_start: 0.8709 (OUTLIER) cc_final: 0.8383 (m-30) REVERT: F 139 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.7951 (mtm180) REVERT: F 323 LYS cc_start: 0.8431 (tttt) cc_final: 0.8192 (tttp) REVERT: F 396 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.7697 (pp20) REVERT: F 548 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.6860 (ttp-110) REVERT: H 39 THR cc_start: 0.8233 (p) cc_final: 0.7888 (p) REVERT: G 59 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8468 (tp) outliers start: 47 outliers final: 34 residues processed: 249 average time/residue: 0.1389 time to fit residues: 53.6650 Evaluate side-chains 256 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 210 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 332 GLU Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 548 ARG Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 514 LEU Chi-restraints excluded: chain E residue 533 MET Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 119 ASP Chi-restraints excluded: chain F residue 139 ARG Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 332 GLU Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 391 THR Chi-restraints excluded: chain F residue 396 GLU Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 548 ARG Chi-restraints excluded: chain F residue 560 VAL Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain H residue 98 PHE Chi-restraints excluded: chain H residue 205 SER Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain G residue 59 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 65 optimal weight: 3.9990 chunk 211 optimal weight: 0.0060 chunk 177 optimal weight: 0.0060 chunk 217 optimal weight: 0.9990 chunk 161 optimal weight: 0.6980 chunk 142 optimal weight: 3.9990 chunk 175 optimal weight: 0.9990 chunk 127 optimal weight: 4.9990 chunk 146 optimal weight: 0.4980 chunk 156 optimal weight: 0.9980 chunk 210 optimal weight: 0.7980 overall best weight: 0.4012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 HIS ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 516 GLN D 55 GLN D 171 GLN E 421 HIS E 464 GLN F 78 HIS H 55 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.130547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.103388 restraints weight = 28150.941| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 1.78 r_work: 0.2999 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 21234 Z= 0.093 Angle : 0.496 8.275 28772 Z= 0.259 Chirality : 0.040 0.181 3256 Planarity : 0.004 0.051 3652 Dihedral : 6.694 91.600 2926 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.61 % Allowed : 12.70 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.17), residues: 2582 helix: 2.34 (0.15), residues: 1242 sheet: 0.84 (0.34), residues: 246 loop : -1.34 (0.19), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 456 TYR 0.013 0.001 TYR B 147 PHE 0.019 0.001 PHE C 62 TRP 0.008 0.001 TRP B 294 HIS 0.002 0.000 HIS F 514 Details of bonding type rmsd covalent geometry : bond 0.00193 (21232) covalent geometry : angle 0.49569 (28772) hydrogen bonds : bond 0.03181 ( 985) hydrogen bonds : angle 4.05688 ( 2889) Misc. bond : bond 0.00043 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4574.48 seconds wall clock time: 79 minutes 6.95 seconds (4746.95 seconds total)