Starting phenix.real_space_refine on Wed Nov 20 01:15:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iaj_35304/11_2024/8iaj_35304.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iaj_35304/11_2024/8iaj_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iaj_35304/11_2024/8iaj_35304.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iaj_35304/11_2024/8iaj_35304.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iaj_35304/11_2024/8iaj_35304.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iaj_35304/11_2024/8iaj_35304.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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: 11.34, per 1000 atoms: 0.55 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: 4.78 Conformation dependent library (CDL) restraints added in 2.8 seconds 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: 2.21 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: 6.57 Time building geometry restraints manager: 5.58 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } 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: 0.880 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: 0.680 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 43.730 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.100 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.280 ------------------------------------------------------------------------------- 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 : 0.006 0.197 21232 Z= 0.395 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (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 TRP 0.010 0.001 TRP D 106 HIS 0.004 0.001 HIS G 45 PHE 0.036 0.002 PHE C 62 TYR 0.022 0.002 TYR F 533 ARG 0.007 0.001 ARG D 42 *********************** 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 : 2.384 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: 0.3325 time to fit residues: 139.5208 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 : 2.510 ------------------------------------------------------------------------------- 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 216 optimal weight: 5.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.0570 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 10.0000 chunk 149 optimal weight: 1.9990 chunk 232 optimal weight: 0.8980 overall best weight: 0.9300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 237 GLN ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 HIS B 145 ASN ** D 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 GLN E 237 GLN ** E 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 HIS F 145 ASN ** H 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21232 Z= 0.177 Angle : 0.575 6.590 28772 Z= 0.306 Chirality : 0.043 0.184 3256 Planarity : 0.005 0.044 3652 Dihedral : 7.384 99.312 2933 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.83 % Allowed : 6.00 % Favored : 93.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.17), residues: 2582 helix: 1.85 (0.15), residues: 1230 sheet: 0.13 (0.31), residues: 280 loop : -2.07 (0.17), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 142 HIS 0.003 0.001 HIS C 45 PHE 0.013 0.001 PHE C 62 TYR 0.014 0.001 TYR B 510 ARG 0.003 0.000 ARG H 174 *********************** 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 283 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 264 time to evaluate : 2.400 Fit side-chains REVERT: A 94 ASP cc_start: 0.8402 (m-30) cc_final: 0.7982 (m-30) REVERT: A 341 MET cc_start: 0.8237 (mtt) cc_final: 0.8000 (mtp) REVERT: B 466 MET cc_start: 0.8065 (ttp) cc_final: 0.7761 (ttp) REVERT: D 39 THR cc_start: 0.8435 (p) cc_final: 0.8139 (p) REVERT: D 73 THR cc_start: 0.9175 (m) cc_final: 0.8906 (p) REVERT: C 59 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8724 (tp) REVERT: E 94 ASP cc_start: 0.8385 (m-30) cc_final: 0.7954 (m-30) REVERT: E 341 MET cc_start: 0.8248 (mtt) cc_final: 0.8006 (mtp) REVERT: F 466 MET cc_start: 0.8218 (ttp) cc_final: 0.7905 (ttp) REVERT: H 39 THR cc_start: 0.8444 (p) cc_final: 0.8150 (p) REVERT: H 73 THR cc_start: 0.9169 (m) cc_final: 0.8900 (p) REVERT: G 59 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8666 (tp) outliers start: 19 outliers final: 11 residues processed: 275 average time/residue: 0.3224 time to fit residues: 139.9999 Evaluate side-chains 231 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 218 time to evaluate : 2.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 G residue 59 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 129 optimal weight: 10.0000 chunk 72 optimal weight: 0.8980 chunk 193 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 232 optimal weight: 0.9980 chunk 251 optimal weight: 3.9990 chunk 207 optimal weight: 5.9990 chunk 230 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 186 optimal weight: 0.0050 overall best weight: 1.1196 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21232 Z= 0.172 Angle : 0.543 7.124 28772 Z= 0.288 Chirality : 0.042 0.182 3256 Planarity : 0.005 0.049 3652 Dihedral : 7.109 96.551 2927 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.09 % Allowed : 8.78 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.17), residues: 2582 helix: 2.03 (0.15), residues: 1218 sheet: 0.30 (0.32), residues: 280 loop : -1.92 (0.17), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 142 HIS 0.002 0.001 HIS C 45 PHE 0.015 0.001 PHE E 256 TYR 0.014 0.001 TYR B 510 ARG 0.002 0.000 ARG D 174 *********************** 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 261 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 236 time to evaluate : 2.419 Fit side-chains REVERT: A 85 LYS cc_start: 0.8342 (tppt) cc_final: 0.8022 (mmtp) REVERT: A 98 ASP cc_start: 0.7957 (m-30) cc_final: 0.7727 (m-30) REVERT: D 39 THR cc_start: 0.8381 (p) cc_final: 0.8072 (p) REVERT: D 42 ARG cc_start: 0.7694 (ttm110) cc_final: 0.7301 (mtm180) REVERT: C 59 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8784 (tp) REVERT: E 85 LYS cc_start: 0.8349 (tppt) cc_final: 0.8017 (mmtp) REVERT: E 98 ASP cc_start: 0.7955 (m-30) cc_final: 0.7716 (m-30) REVERT: E 308 LYS cc_start: 0.8360 (ttmt) cc_final: 0.8026 (ttmm) REVERT: F 466 MET cc_start: 0.8217 (ttp) cc_final: 0.7766 (ttp) REVERT: F 483 VAL cc_start: 0.8442 (m) cc_final: 0.8141 (t) REVERT: H 39 THR cc_start: 0.8393 (p) cc_final: 0.8084 (p) REVERT: H 42 ARG cc_start: 0.7702 (ttm110) cc_final: 0.7287 (mtm180) REVERT: G 59 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8771 (tp) outliers start: 25 outliers final: 19 residues processed: 251 average time/residue: 0.3369 time to fit residues: 132.5989 Evaluate side-chains 247 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 226 time to evaluate : 2.362 ------------------------------------------------------------------------------- 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 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 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 230 optimal weight: 0.0000 chunk 175 optimal weight: 2.9990 chunk 120 optimal weight: 0.6980 chunk 25 optimal weight: 6.9990 chunk 111 optimal weight: 9.9990 chunk 156 optimal weight: 8.9990 chunk 233 optimal weight: 7.9990 chunk 247 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 221 optimal weight: 0.0000 chunk 66 optimal weight: 1.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- 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 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 171 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 21232 Z= 0.145 Angle : 0.510 6.359 28772 Z= 0.270 Chirality : 0.041 0.182 3256 Planarity : 0.004 0.049 3652 Dihedral : 6.962 94.293 2927 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.43 % Allowed : 9.78 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.17), residues: 2582 helix: 2.15 (0.15), residues: 1220 sheet: 0.51 (0.33), residues: 266 loop : -1.69 (0.18), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 100 HIS 0.003 0.001 HIS C 45 PHE 0.014 0.001 PHE C 62 TYR 0.013 0.001 TYR B 510 ARG 0.002 0.000 ARG H 174 *********************** 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 270 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 237 time to evaluate : 2.188 Fit side-chains REVERT: A 94 ASP cc_start: 0.8126 (m-30) cc_final: 0.7902 (m-30) REVERT: A 98 ASP cc_start: 0.7974 (m-30) cc_final: 0.7642 (m-30) REVERT: D 39 THR cc_start: 0.8464 (p) cc_final: 0.8143 (p) REVERT: D 42 ARG cc_start: 0.7576 (ttm110) cc_final: 0.7315 (mtm180) REVERT: C 59 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8874 (tp) REVERT: E 94 ASP cc_start: 0.8168 (m-30) cc_final: 0.7910 (m-30) REVERT: E 98 ASP cc_start: 0.7980 (m-30) cc_final: 0.7649 (m-30) REVERT: F 116 MET cc_start: 0.7523 (mmm) cc_final: 0.7161 (mmm) REVERT: F 466 MET cc_start: 0.8208 (ttp) cc_final: 0.7878 (ttp) REVERT: F 483 VAL cc_start: 0.8271 (m) cc_final: 0.8065 (t) REVERT: H 39 THR cc_start: 0.8477 (p) cc_final: 0.8159 (p) REVERT: H 42 ARG cc_start: 0.7631 (ttm110) cc_final: 0.7332 (mtm180) REVERT: G 59 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8862 (tp) outliers start: 33 outliers final: 24 residues processed: 257 average time/residue: 0.3255 time to fit residues: 132.9483 Evaluate side-chains 249 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 223 time to evaluate : 2.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 508 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 375 ILE 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 130 GLN Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 508 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 206 optimal weight: 7.9990 chunk 140 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 184 optimal weight: 9.9990 chunk 102 optimal weight: 0.0060 chunk 211 optimal weight: 0.9980 chunk 171 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 126 optimal weight: 4.9990 chunk 222 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 overall best weight: 1.6000 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21232 Z= 0.203 Angle : 0.548 7.258 28772 Z= 0.289 Chirality : 0.042 0.174 3256 Planarity : 0.005 0.052 3652 Dihedral : 6.978 94.264 2926 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.39 % Allowed : 10.96 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.17), residues: 2582 helix: 2.07 (0.15), residues: 1234 sheet: 0.54 (0.33), residues: 256 loop : -1.69 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 142 HIS 0.003 0.001 HIS E 374 PHE 0.019 0.001 PHE C 62 TYR 0.017 0.001 TYR B 510 ARG 0.002 0.000 ARG D 174 *********************** 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 252 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 220 time to evaluate : 2.464 Fit side-chains REVERT: A 85 LYS cc_start: 0.8364 (tppt) cc_final: 0.8069 (mmtp) REVERT: B 116 MET cc_start: 0.7426 (mmm) cc_final: 0.7223 (mmp) REVERT: D 39 THR cc_start: 0.8491 (p) cc_final: 0.8179 (p) REVERT: C 59 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8912 (tp) REVERT: E 85 LYS cc_start: 0.8302 (tppt) cc_final: 0.7975 (tppt) REVERT: F 116 MET cc_start: 0.7506 (mmm) cc_final: 0.7107 (mmm) REVERT: F 239 LYS cc_start: 0.8434 (ptmm) cc_final: 0.8153 (tttm) REVERT: F 466 MET cc_start: 0.8284 (ttp) cc_final: 0.8030 (ttp) REVERT: H 39 THR cc_start: 0.8506 (p) cc_final: 0.8196 (p) REVERT: G 59 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8903 (tp) outliers start: 32 outliers final: 27 residues processed: 240 average time/residue: 0.3202 time to fit residues: 122.6319 Evaluate side-chains 244 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 215 time to evaluate : 2.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 127 MET 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 375 ILE 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 127 MET 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 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 83 optimal weight: 7.9990 chunk 222 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 chunk 145 optimal weight: 0.9980 chunk 61 optimal weight: 0.4980 chunk 247 optimal weight: 0.9990 chunk 205 optimal weight: 0.8980 chunk 114 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 130 optimal weight: 7.9990 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** ** E 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 171 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21232 Z= 0.161 Angle : 0.527 10.475 28772 Z= 0.275 Chirality : 0.041 0.178 3256 Planarity : 0.005 0.054 3652 Dihedral : 6.893 93.671 2926 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.65 % Allowed : 11.30 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.17), residues: 2582 helix: 2.16 (0.15), residues: 1234 sheet: 0.57 (0.33), residues: 256 loop : -1.63 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 142 HIS 0.003 0.001 HIS A 374 PHE 0.018 0.001 PHE C 62 TYR 0.028 0.001 TYR A 460 ARG 0.002 0.000 ARG H 42 *********************** 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: 38 poor density : 229 time to evaluate : 2.401 Fit side-chains REVERT: B 116 MET cc_start: 0.7338 (mmm) cc_final: 0.7075 (mmm) REVERT: B 239 LYS cc_start: 0.8345 (ptmm) cc_final: 0.8065 (tttm) REVERT: D 39 THR cc_start: 0.8466 (p) cc_final: 0.8134 (p) REVERT: D 42 ARG cc_start: 0.7611 (ttm110) cc_final: 0.7271 (mtm180) REVERT: C 59 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8865 (tp) REVERT: E 125 MET cc_start: 0.7432 (mtm) cc_final: 0.7136 (mtm) REVERT: F 116 MET cc_start: 0.7455 (mmm) cc_final: 0.7240 (mmp) REVERT: F 239 LYS cc_start: 0.8338 (ptmm) cc_final: 0.8065 (tttm) REVERT: F 466 MET cc_start: 0.8244 (ttp) cc_final: 0.7799 (ttp) REVERT: H 39 THR cc_start: 0.8478 (p) cc_final: 0.8144 (p) REVERT: H 42 ARG cc_start: 0.7634 (ttm110) cc_final: 0.7281 (mtm180) REVERT: G 59 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8893 (tp) outliers start: 38 outliers final: 26 residues processed: 255 average time/residue: 0.3295 time to fit residues: 133.0165 Evaluate side-chains 246 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 218 time to evaluate : 2.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 375 ILE 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 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 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 238 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 141 optimal weight: 0.8980 chunk 180 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 208 optimal weight: 0.8980 chunk 138 optimal weight: 0.6980 chunk 246 optimal weight: 8.9990 chunk 154 optimal weight: 0.8980 chunk 150 optimal weight: 1.9990 chunk 113 optimal weight: 0.0770 overall best weight: 0.6938 ------------------------------------------------------------------------------- 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 D 171 GLN ** E 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 477 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 21232 Z= 0.136 Angle : 0.507 9.514 28772 Z= 0.265 Chirality : 0.041 0.179 3256 Planarity : 0.004 0.052 3652 Dihedral : 6.772 92.997 2926 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.83 % Allowed : 11.78 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.17), residues: 2582 helix: 2.24 (0.15), residues: 1242 sheet: 0.78 (0.34), residues: 246 loop : -1.43 (0.18), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 106 HIS 0.002 0.000 HIS G 45 PHE 0.020 0.001 PHE C 62 TYR 0.014 0.001 TYR B 510 ARG 0.002 0.000 ARG B 496 *********************** 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: 42 poor density : 225 time to evaluate : 2.654 Fit side-chains REVERT: A 85 LYS cc_start: 0.8392 (tppt) cc_final: 0.8116 (tppt) REVERT: B 116 MET cc_start: 0.7346 (mmm) cc_final: 0.7117 (mmm) REVERT: B 181 GLU cc_start: 0.7497 (mm-30) cc_final: 0.7260 (mm-30) REVERT: B 239 LYS cc_start: 0.8226 (ptmm) cc_final: 0.7976 (tttm) REVERT: B 548 ARG cc_start: 0.7797 (OUTLIER) cc_final: 0.6790 (ttp-110) REVERT: D 39 THR cc_start: 0.8409 (p) cc_final: 0.8075 (p) REVERT: D 42 ARG cc_start: 0.7491 (ttm110) cc_final: 0.7169 (mtm180) REVERT: C 59 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8834 (tp) REVERT: E 85 LYS cc_start: 0.8315 (tppt) cc_final: 0.8025 (tppt) REVERT: E 125 MET cc_start: 0.7427 (mtm) cc_final: 0.7083 (mtm) REVERT: F 119 ASP cc_start: 0.8168 (OUTLIER) cc_final: 0.7945 (m-30) REVERT: F 181 GLU cc_start: 0.7495 (mm-30) cc_final: 0.7266 (mm-30) REVERT: F 239 LYS cc_start: 0.8206 (ptmm) cc_final: 0.7969 (tttm) REVERT: F 466 MET cc_start: 0.8198 (ttp) cc_final: 0.7877 (ttp) REVERT: F 548 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.6882 (ttp-110) REVERT: H 39 THR cc_start: 0.8418 (p) cc_final: 0.8081 (p) REVERT: H 42 ARG cc_start: 0.7630 (ttm110) cc_final: 0.7277 (mtm180) REVERT: G 59 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8825 (tp) outliers start: 42 outliers final: 26 residues processed: 254 average time/residue: 0.3381 time to fit residues: 134.1745 Evaluate side-chains 240 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 209 time to evaluate : 2.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain B residue 91 LEU 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 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 C residue 59 LEU Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 508 THR Chi-restraints excluded: chain E residue 514 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 119 ASP 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 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 59 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 152 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 48 optimal weight: 7.9990 chunk 47 optimal weight: 0.9980 chunk 156 optimal weight: 4.9990 chunk 168 optimal weight: 7.9990 chunk 121 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 193 optimal weight: 0.0270 overall best weight: 1.8042 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21232 Z= 0.217 Angle : 0.566 12.455 28772 Z= 0.296 Chirality : 0.043 0.171 3256 Planarity : 0.005 0.059 3652 Dihedral : 6.931 94.052 2926 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.70 % Allowed : 11.87 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.17), residues: 2582 helix: 2.20 (0.15), residues: 1238 sheet: 0.61 (0.33), residues: 254 loop : -1.59 (0.18), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 142 HIS 0.004 0.001 HIS C 45 PHE 0.024 0.001 PHE C 62 TYR 0.018 0.001 TYR B 510 ARG 0.002 0.000 ARG B 437 *********************** 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 247 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 208 time to evaluate : 2.659 Fit side-chains REVERT: A 261 MET cc_start: 0.7674 (mmt) cc_final: 0.6778 (mmt) REVERT: B 116 MET cc_start: 0.7384 (mmm) cc_final: 0.7116 (mmm) REVERT: B 181 GLU cc_start: 0.7503 (mm-30) cc_final: 0.7273 (mm-30) REVERT: B 520 ASP cc_start: 0.7411 (m-30) cc_final: 0.7149 (m-30) REVERT: D 39 THR cc_start: 0.8476 (p) cc_final: 0.8176 (p) REVERT: C 14 THR cc_start: 0.7586 (p) cc_final: 0.7270 (p) REVERT: C 59 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8833 (tp) REVERT: E 125 MET cc_start: 0.7591 (mtm) cc_final: 0.7325 (mtm) REVERT: F 181 GLU cc_start: 0.7503 (mm-30) cc_final: 0.7275 (mm-30) REVERT: F 466 MET cc_start: 0.8294 (ttp) cc_final: 0.8056 (ttp) REVERT: H 39 THR cc_start: 0.8481 (p) cc_final: 0.8178 (p) REVERT: G 14 THR cc_start: 0.7588 (p) cc_final: 0.7276 (p) REVERT: G 59 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8826 (tp) outliers start: 39 outliers final: 29 residues processed: 236 average time/residue: 0.3503 time to fit residues: 131.1528 Evaluate side-chains 234 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 203 time to evaluate : 2.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 91 LEU 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 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 59 LEU 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 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 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 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 224 optimal weight: 0.9990 chunk 236 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 229 optimal weight: 9.9990 chunk 138 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 180 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 207 optimal weight: 4.9990 chunk 217 optimal weight: 5.9990 chunk 150 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21232 Z= 0.215 Angle : 0.562 10.964 28772 Z= 0.294 Chirality : 0.043 0.173 3256 Planarity : 0.005 0.056 3652 Dihedral : 6.962 93.902 2926 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.74 % Allowed : 11.78 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.17), residues: 2582 helix: 2.16 (0.15), residues: 1234 sheet: 0.65 (0.33), residues: 254 loop : -1.59 (0.18), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 142 HIS 0.004 0.001 HIS A 374 PHE 0.024 0.001 PHE C 62 TYR 0.017 0.001 TYR B 510 ARG 0.002 0.000 ARG H 42 *********************** 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 243 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 203 time to evaluate : 2.491 Fit side-chains REVERT: A 85 LYS cc_start: 0.8449 (tppt) cc_final: 0.8234 (tppt) REVERT: B 116 MET cc_start: 0.7441 (mmm) cc_final: 0.7163 (mmm) REVERT: B 548 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.6786 (ttp-110) REVERT: D 39 THR cc_start: 0.8374 (p) cc_final: 0.8073 (p) REVERT: C 14 THR cc_start: 0.7556 (p) cc_final: 0.7236 (p) REVERT: C 59 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8815 (tp) REVERT: E 85 LYS cc_start: 0.8457 (tppt) cc_final: 0.8243 (tppt) REVERT: E 533 MET cc_start: 0.7906 (OUTLIER) cc_final: 0.7581 (mtm) REVERT: F 466 MET cc_start: 0.8302 (ttp) cc_final: 0.8077 (ttp) REVERT: F 548 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.6784 (ttp-110) REVERT: H 39 THR cc_start: 0.8384 (p) cc_final: 0.8077 (p) REVERT: G 59 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8822 (tp) outliers start: 40 outliers final: 26 residues processed: 231 average time/residue: 0.3381 time to fit residues: 123.2049 Evaluate side-chains 229 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 198 time to evaluate : 2.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 188 ILE 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 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 C residue 59 LEU 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 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 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 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 243 optimal weight: 5.9990 chunk 148 optimal weight: 6.9990 chunk 115 optimal weight: 4.9990 chunk 169 optimal weight: 1.9990 chunk 255 optimal weight: 2.9990 chunk 234 optimal weight: 1.9990 chunk 203 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 156 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 161 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21232 Z= 0.252 Angle : 0.587 10.325 28772 Z= 0.308 Chirality : 0.044 0.171 3256 Planarity : 0.005 0.055 3652 Dihedral : 7.054 94.066 2926 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 1.61 % Allowed : 12.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.17), residues: 2582 helix: 2.12 (0.15), residues: 1226 sheet: 0.59 (0.33), residues: 254 loop : -1.60 (0.18), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 142 HIS 0.005 0.001 HIS E 374 PHE 0.026 0.002 PHE C 62 TYR 0.030 0.002 TYR A 460 ARG 0.002 0.000 ARG H 42 ********************** 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 244 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 207 time to evaluate : 2.425 Fit side-chains REVERT: B 116 MET cc_start: 0.7443 (mmm) cc_final: 0.7161 (mmm) REVERT: B 520 ASP cc_start: 0.7514 (m-30) cc_final: 0.7288 (m-30) REVERT: B 548 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.6791 (ttp-110) REVERT: D 39 THR cc_start: 0.8395 (p) cc_final: 0.8077 (p) REVERT: C 14 THR cc_start: 0.7593 (p) cc_final: 0.7273 (p) REVERT: C 59 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8815 (tp) REVERT: E 533 MET cc_start: 0.7933 (OUTLIER) cc_final: 0.7730 (mtm) REVERT: F 466 MET cc_start: 0.8341 (ttp) cc_final: 0.7895 (ttp) REVERT: F 520 ASP cc_start: 0.7519 (m-30) cc_final: 0.7268 (m-30) REVERT: F 548 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.6787 (ttp-110) REVERT: H 39 THR cc_start: 0.8405 (p) cc_final: 0.8083 (p) REVERT: G 14 THR cc_start: 0.7583 (p) cc_final: 0.7261 (p) REVERT: G 59 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8805 (tp) outliers start: 37 outliers final: 27 residues processed: 234 average time/residue: 0.3443 time to fit residues: 125.3532 Evaluate side-chains 232 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 200 time to evaluate : 2.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 533 MET 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 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 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 216 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 187 optimal weight: 0.2980 chunk 29 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 203 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 208 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 178 optimal weight: 5.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- 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 D 171 GLN ** E 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 171 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.124226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.096613 restraints weight = 28233.517| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 1.78 r_work: 0.2915 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21232 Z= 0.223 Angle : 0.568 10.006 28772 Z= 0.298 Chirality : 0.043 0.173 3256 Planarity : 0.005 0.053 3652 Dihedral : 7.033 93.918 2926 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.65 % Allowed : 12.00 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.17), residues: 2582 helix: 2.11 (0.15), residues: 1234 sheet: 0.59 (0.33), residues: 254 loop : -1.60 (0.18), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 142 HIS 0.004 0.001 HIS A 374 PHE 0.023 0.001 PHE C 62 TYR 0.029 0.001 TYR E 460 ARG 0.002 0.000 ARG A 456 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4098.25 seconds wall clock time: 76 minutes 22.94 seconds (4582.94 seconds total)