Starting phenix.real_space_refine on Sat Dec 28 19:32:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6m4o_30080/12_2024/6m4o_30080.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m4o_30080/12_2024/6m4o_30080.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6m4o_30080/12_2024/6m4o_30080.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m4o_30080/12_2024/6m4o_30080.map" model { file = "/net/cci-nas-00/data/ceres_data/6m4o_30080/12_2024/6m4o_30080.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m4o_30080/12_2024/6m4o_30080.cif" } resolution = 3.4 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 15 atoms to isotropic. 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 1 5.49 5 S 50 5.16 5 C 5746 2.51 5 N 1507 2.21 5 O 1614 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8918 Number of models: 1 Model: "" Number of chains: 6 Chain: "S" Number of atoms: 3258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3258 Classifications: {'peptide': 420} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 398} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "T" Number of atoms: 3887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3887 Classifications: {'peptide': 491} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 473} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1128 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 7, 'TRANS': 131} Chain: "E" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 390 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 47} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'TYR:plan': 2, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 240 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 1, 'TRANS': 26} Chain: "T" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C2 PLP T 601 " occ=0.80 ... (13 atoms not shown) pdb=" P PLP T 601 " occ=0.80 Time building chain proxies: 5.87, per 1000 atoms: 0.66 Number of scatterers: 8918 At special positions: 0 Unit cell: (90.234, 83.55, 119.198, 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 50 16.00 P 1 15.00 O 1614 8.00 N 1507 7.00 C 5746 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.28 Conformation dependent library (CDL) restraints added in 1.1 seconds 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2086 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 6 sheets defined 43.2% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'S' and resid 56 through 61 Processing helix chain 'S' and resid 114 through 123 Processing helix chain 'S' and resid 124 through 129 Processing helix chain 'S' and resid 143 through 156 removed outlier: 3.999A pdb=" N GLU S 149 " --> pdb=" O HIS S 145 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS S 154 " --> pdb=" O ASP S 150 " (cutoff:3.500A) Processing helix chain 'S' and resid 167 through 171 removed outlier: 4.014A pdb=" N THR S 170 " --> pdb=" O GLY S 167 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE S 171 " --> pdb=" O PHE S 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 167 through 171' Processing helix chain 'S' and resid 197 through 202 Processing helix chain 'S' and resid 217 through 229 removed outlier: 3.591A pdb=" N GLN S 224 " --> pdb=" O LEU S 220 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU S 227 " --> pdb=" O GLU S 223 " (cutoff:3.500A) Processing helix chain 'S' and resid 233 through 237 Processing helix chain 'S' and resid 257 through 268 removed outlier: 3.567A pdb=" N LYS S 262 " --> pdb=" O PRO S 258 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU S 263 " --> pdb=" O GLU S 259 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TYR S 265 " --> pdb=" O VAL S 261 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LYS S 266 " --> pdb=" O LYS S 262 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR S 267 " --> pdb=" O LEU S 263 " (cutoff:3.500A) Processing helix chain 'S' and resid 288 through 293 Processing helix chain 'S' and resid 296 through 300 Processing helix chain 'S' and resid 321 through 326 removed outlier: 3.935A pdb=" N ASP S 326 " --> pdb=" O SER S 322 " (cutoff:3.500A) Processing helix chain 'S' and resid 327 through 330 removed outlier: 3.549A pdb=" N LEU S 330 " --> pdb=" O HIS S 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 327 through 330' Processing helix chain 'S' and resid 342 through 359 Processing helix chain 'S' and resid 361 through 374 removed outlier: 3.598A pdb=" N VAL S 365 " --> pdb=" O GLY S 361 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS S 367 " --> pdb=" O PHE S 363 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS S 369 " --> pdb=" O VAL S 365 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN S 372 " --> pdb=" O GLU S 368 " (cutoff:3.500A) Processing helix chain 'S' and resid 404 through 420 removed outlier: 3.588A pdb=" N GLU S 414 " --> pdb=" O ARG S 410 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE S 415 " --> pdb=" O LEU S 411 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL S 416 " --> pdb=" O LEU S 412 " (cutoff:3.500A) Processing helix chain 'S' and resid 421 through 423 No H-bonds generated for 'chain 'S' and resid 421 through 423' Processing helix chain 'S' and resid 453 through 456 Processing helix chain 'S' and resid 457 through 470 removed outlier: 3.505A pdb=" N ILE S 464 " --> pdb=" O ALA S 460 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL S 467 " --> pdb=" O THR S 463 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA S 468 " --> pdb=" O ILE S 464 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN S 469 " --> pdb=" O LYS S 465 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA S 470 " --> pdb=" O GLU S 466 " (cutoff:3.500A) Processing helix chain 'T' and resid 69 through 91 removed outlier: 3.615A pdb=" N LEU T 73 " --> pdb=" O LEU T 69 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N TYR T 75 " --> pdb=" O ALA T 71 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL T 76 " --> pdb=" O VAL T 72 " (cutoff:3.500A) Processing helix chain 'T' and resid 117 through 120 Processing helix chain 'T' and resid 121 through 126 Processing helix chain 'T' and resid 189 through 197 removed outlier: 3.767A pdb=" N ALA T 193 " --> pdb=" O GLN T 189 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS T 194 " --> pdb=" O GLU T 190 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL T 195 " --> pdb=" O ALA T 191 " (cutoff:3.500A) Processing helix chain 'T' and resid 213 through 228 removed outlier: 3.685A pdb=" N GLU T 217 " --> pdb=" O LEU T 213 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA T 224 " --> pdb=" O GLU T 220 " (cutoff:3.500A) Processing helix chain 'T' and resid 238 through 243 removed outlier: 3.742A pdb=" N ASN T 242 " --> pdb=" O GLY T 238 " (cutoff:3.500A) Processing helix chain 'T' and resid 245 through 250 Processing helix chain 'T' and resid 263 through 273 removed outlier: 3.597A pdb=" N VAL T 267 " --> pdb=" O HIS T 263 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA T 270 " --> pdb=" O LEU T 266 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER T 273 " --> pdb=" O GLY T 269 " (cutoff:3.500A) Processing helix chain 'T' and resid 284 through 297 removed outlier: 3.580A pdb=" N LEU T 291 " --> pdb=" O SER T 287 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE T 296 " --> pdb=" O LEU T 292 " (cutoff:3.500A) Processing helix chain 'T' and resid 327 through 335 removed outlier: 4.450A pdb=" N LEU T 333 " --> pdb=" O GLU T 329 " (cutoff:3.500A) Processing helix chain 'T' and resid 358 through 363 removed outlier: 3.642A pdb=" N TYR T 362 " --> pdb=" O GLY T 358 " (cutoff:3.500A) Processing helix chain 'T' and resid 366 through 370 removed outlier: 3.635A pdb=" N ASP T 369 " --> pdb=" O ASP T 366 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL T 370 " --> pdb=" O PRO T 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 366 through 370' Processing helix chain 'T' and resid 391 through 396 Processing helix chain 'T' and resid 412 through 428 removed outlier: 3.698A pdb=" N GLU T 417 " --> pdb=" O PRO T 413 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE T 419 " --> pdb=" O VAL T 415 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N CYS T 425 " --> pdb=" O THR T 421 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE T 426 " --> pdb=" O SER T 422 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET T 427 " --> pdb=" O MET T 423 " (cutoff:3.500A) Processing helix chain 'T' and resid 438 through 455 removed outlier: 3.676A pdb=" N ARG T 447 " --> pdb=" O ALA T 443 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG T 450 " --> pdb=" O THR T 446 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG T 451 " --> pdb=" O ARG T 447 " (cutoff:3.500A) Processing helix chain 'T' and resid 478 through 489 removed outlier: 3.790A pdb=" N ARG T 484 " --> pdb=" O GLY T 480 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU T 487 " --> pdb=" O GLY T 483 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS T 488 " --> pdb=" O ARG T 484 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG T 489 " --> pdb=" O GLU T 485 " (cutoff:3.500A) Processing helix chain 'T' and resid 517 through 535 removed outlier: 3.619A pdb=" N ALA T 524 " --> pdb=" O ILE T 520 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL T 531 " --> pdb=" O GLU T 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 39 removed outlier: 3.514A pdb=" N LEU A 28 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ALA A 29 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE A 30 " --> pdb=" O TYR A 26 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL A 36 " --> pdb=" O LEU A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 50 removed outlier: 3.698A pdb=" N TRP A 49 " --> pdb=" O VAL A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 63 removed outlier: 3.563A pdb=" N LEU A 54 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N HIS A 56 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR A 61 " --> pdb=" O ASN A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 116 Proline residue: A 106 - end of helix removed outlier: 3.533A pdb=" N LEU A 112 " --> pdb=" O VAL A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 119 No H-bonds generated for 'chain 'A' and resid 117 through 119' Processing helix chain 'A' and resid 121 through 129 removed outlier: 3.676A pdb=" N VAL A 129 " --> pdb=" O VAL A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 136 removed outlier: 3.551A pdb=" N LEU A 135 " --> pdb=" O LEU A 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 23 removed outlier: 3.583A pdb=" N MET E 13 " --> pdb=" O ALA E 9 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE E 16 " --> pdb=" O GLN E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 26 No H-bonds generated for 'chain 'E' and resid 24 through 26' Processing helix chain 'E' and resid 33 through 46 removed outlier: 3.756A pdb=" N PHE E 37 " --> pdb=" O GLU E 33 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE E 44 " --> pdb=" O MET E 40 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL E 45 " --> pdb=" O LEU E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 55 removed outlier: 3.587A pdb=" N TYR E 50 " --> pdb=" O GLY E 46 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY E 52 " --> pdb=" O ALA E 48 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL E 54 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 40 removed outlier: 3.597A pdb=" N LEU B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE B 36 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG B 37 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE B 40 " --> pdb=" O ILE B 36 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'S' and resid 92 through 94 Processing sheet with id=AA2, first strand: chain 'S' and resid 160 through 164 removed outlier: 3.512A pdb=" N ILE S 162 " --> pdb=" O CYS S 318 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS S 318 " --> pdb=" O ILE S 162 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'S' and resid 205 through 208 removed outlier: 6.302A pdb=" N VAL S 185 " --> pdb=" O LYS S 207 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ILE S 184 " --> pdb=" O PHE S 241 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N VAL S 243 " --> pdb=" O ILE S 184 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N PHE S 186 " --> pdb=" O VAL S 243 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ILE S 242 " --> pdb=" O PHE S 272 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'T' and resid 145 through 152 removed outlier: 5.705A pdb=" N VAL T 146 " --> pdb=" O GLY T 169 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLY T 169 " --> pdb=" O VAL T 146 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU T 150 " --> pdb=" O ASN T 165 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ASN T 165 " --> pdb=" O GLU T 150 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N GLN T 152 " --> pdb=" O THR T 163 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR T 163 " --> pdb=" O GLN T 152 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N GLY T 492 " --> pdb=" O GLY T 169 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE T 171 " --> pdb=" O GLY T 492 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'T' and resid 231 through 235 removed outlier: 3.588A pdb=" N GLY T 386 " --> pdb=" O TYR T 235 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY T 389 " --> pdb=" O MET T 373 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL T 372 " --> pdb=" O LEU T 341 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ILE T 310 " --> pdb=" O TYR T 340 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N TYR T 342 " --> pdb=" O ILE T 310 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE T 312 " --> pdb=" O TYR T 342 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N ASP T 344 " --> pdb=" O ILE T 312 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N VAL T 314 " --> pdb=" O ASP T 344 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'T' and resid 468 through 471 removed outlier: 3.837A pdb=" N VAL T 494 " --> pdb=" O ARG T 509 " (cutoff:3.500A) 254 hydrogen bonds defined for protein. 729 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: 2.34 Time building geometry restraints manager: 2.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2619 1.33 - 1.45: 1432 1.45 - 1.57: 4977 1.57 - 1.69: 2 1.69 - 1.81: 82 Bond restraints: 9112 Sorted by residual: bond pdb=" CA LEU T 261 " pdb=" CB LEU T 261 " ideal model delta sigma weight residual 1.527 1.589 -0.062 1.75e-02 3.27e+03 1.27e+01 bond pdb=" CG1 ILE S 162 " pdb=" CD1 ILE S 162 " ideal model delta sigma weight residual 1.513 1.443 0.070 3.90e-02 6.57e+02 3.26e+00 bond pdb=" N SER T 540 " pdb=" CA SER T 540 " ideal model delta sigma weight residual 1.453 1.475 -0.022 1.31e-02 5.83e+03 2.70e+00 bond pdb=" C GLU E 30 " pdb=" N PRO E 31 " ideal model delta sigma weight residual 1.334 1.372 -0.038 2.34e-02 1.83e+03 2.65e+00 bond pdb=" CA ILE T 246 " pdb=" C ILE T 246 " ideal model delta sigma weight residual 1.520 1.533 -0.013 8.80e-03 1.29e+04 2.33e+00 ... (remaining 9107 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 11852 2.55 - 5.10: 392 5.10 - 7.64: 60 7.64 - 10.19: 20 10.19 - 12.74: 4 Bond angle restraints: 12328 Sorted by residual: angle pdb=" C TYR A 116 " pdb=" N THR A 117 " pdb=" CA THR A 117 " ideal model delta sigma weight residual 121.54 130.39 -8.85 1.91e+00 2.74e-01 2.15e+01 angle pdb=" C THR S 453 " pdb=" N GLU S 454 " pdb=" CA GLU S 454 " ideal model delta sigma weight residual 121.54 129.88 -8.34 1.91e+00 2.74e-01 1.91e+01 angle pdb=" N VAL S 73 " pdb=" CA VAL S 73 " pdb=" C VAL S 73 " ideal model delta sigma weight residual 108.88 118.22 -9.34 2.16e+00 2.14e-01 1.87e+01 angle pdb=" C LYS T 109 " pdb=" N ASP T 110 " pdb=" CA ASP T 110 " ideal model delta sigma weight residual 121.54 129.59 -8.05 1.91e+00 2.74e-01 1.78e+01 angle pdb=" CA ARG S 239 " pdb=" CB ARG S 239 " pdb=" CG ARG S 239 " ideal model delta sigma weight residual 114.10 122.32 -8.22 2.00e+00 2.50e-01 1.69e+01 ... (remaining 12323 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.46: 5039 15.46 - 30.92: 309 30.92 - 46.38: 85 46.38 - 61.85: 6 61.85 - 77.31: 8 Dihedral angle restraints: 5447 sinusoidal: 2189 harmonic: 3258 Sorted by residual: dihedral pdb=" CA VAL T 48 " pdb=" C VAL T 48 " pdb=" N THR T 49 " pdb=" CA THR T 49 " ideal model delta harmonic sigma weight residual -180.00 -144.44 -35.56 0 5.00e+00 4.00e-02 5.06e+01 dihedral pdb=" CA VAL S 281 " pdb=" C VAL S 281 " pdb=" N LEU S 282 " pdb=" CA LEU S 282 " ideal model delta harmonic sigma weight residual 180.00 148.93 31.07 0 5.00e+00 4.00e-02 3.86e+01 dihedral pdb=" CA PHE S 394 " pdb=" C PHE S 394 " pdb=" N HIS S 395 " pdb=" CA HIS S 395 " ideal model delta harmonic sigma weight residual 180.00 150.38 29.62 0 5.00e+00 4.00e-02 3.51e+01 ... (remaining 5444 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 930 0.057 - 0.113: 355 0.113 - 0.170: 81 0.170 - 0.226: 10 0.226 - 0.283: 4 Chirality restraints: 1380 Sorted by residual: chirality pdb=" CB ILE T 459 " pdb=" CA ILE T 459 " pdb=" CG1 ILE T 459 " pdb=" CG2 ILE T 459 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CB ILE T 171 " pdb=" CA ILE T 171 " pdb=" CG1 ILE T 171 " pdb=" CG2 ILE T 171 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CB VAL S 237 " pdb=" CA VAL S 237 " pdb=" CG1 VAL S 237 " pdb=" CG2 VAL S 237 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 1377 not shown) Planarity restraints: 1562 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR T 501 " -0.051 5.00e-02 4.00e+02 7.68e-02 9.43e+00 pdb=" N PRO T 502 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO T 502 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO T 502 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER T 402 " -0.013 2.00e-02 2.50e+03 2.53e-02 6.42e+00 pdb=" C SER T 402 " 0.044 2.00e-02 2.50e+03 pdb=" O SER T 402 " -0.016 2.00e-02 2.50e+03 pdb=" N HIS T 403 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR T 103 " 0.012 2.00e-02 2.50e+03 2.37e-02 5.60e+00 pdb=" C THR T 103 " -0.041 2.00e-02 2.50e+03 pdb=" O THR T 103 " 0.015 2.00e-02 2.50e+03 pdb=" N GLU T 104 " 0.014 2.00e-02 2.50e+03 ... (remaining 1559 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1010 2.74 - 3.28: 8210 3.28 - 3.82: 14181 3.82 - 4.36: 17142 4.36 - 4.90: 29531 Nonbonded interactions: 70074 Sorted by model distance: nonbonded pdb=" OD2 ASP S 188 " pdb=" OH TYR S 248 " model vdw 2.203 3.040 nonbonded pdb=" OH TYR S 178 " pdb=" O VAL S 324 " model vdw 2.228 3.040 nonbonded pdb=" OG1 THR S 427 " pdb=" OE1 GLU T 209 " model vdw 2.250 3.040 nonbonded pdb=" OH TYR A 110 " pdb=" OG1 THR A 128 " model vdw 2.260 3.040 nonbonded pdb=" OH TYR T 448 " pdb=" OD1 ASP T 522 " model vdw 2.323 3.040 ... (remaining 70069 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.80 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: 1.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 22.590 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 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 : 0.007 0.073 9112 Z= 0.466 Angle : 1.144 12.740 12328 Z= 0.613 Chirality : 0.062 0.283 1380 Planarity : 0.008 0.077 1562 Dihedral : 11.527 77.308 3361 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.41 % Favored : 88.41 % Rotamer: Outliers : 1.15 % Allowed : 7.23 % Favored : 91.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -5.81 (0.17), residues: 1113 helix: -4.55 (0.10), residues: 459 sheet: -3.66 (0.42), residues: 101 loop : -3.22 (0.22), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP T 134 HIS 0.010 0.002 HIS T 347 PHE 0.030 0.003 PHE S 209 TYR 0.034 0.003 TYR S 166 ARG 0.011 0.002 ARG S 405 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 268 time to evaluate : 1.061 Fit side-chains revert: symmetry clash REVERT: S 95 VAL cc_start: 0.9104 (t) cc_final: 0.8815 (p) REVERT: S 107 ASN cc_start: 0.8117 (p0) cc_final: 0.7890 (p0) REVERT: S 146 LEU cc_start: 0.8843 (mm) cc_final: 0.8335 (mm) REVERT: S 345 LEU cc_start: 0.8823 (mm) cc_final: 0.8433 (mt) REVERT: T 82 THR cc_start: 0.9049 (t) cc_final: 0.8631 (p) REVERT: T 86 TYR cc_start: 0.8506 (m-80) cc_final: 0.7581 (m-80) REVERT: T 155 ASP cc_start: 0.7079 (t0) cc_final: 0.6842 (t70) REVERT: T 177 ASN cc_start: 0.8167 (t0) cc_final: 0.7582 (t0) REVERT: T 304 ARG cc_start: 0.7976 (mmt90) cc_final: 0.7012 (ttp-170) REVERT: T 537 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8514 (pp) REVERT: A 116 TYR cc_start: 0.7117 (m-80) cc_final: 0.6867 (m-80) REVERT: E 13 MET cc_start: 0.8130 (tpt) cc_final: 0.7665 (tpt) outliers start: 11 outliers final: 2 residues processed: 275 average time/residue: 0.2614 time to fit residues: 93.8791 Evaluate side-chains 142 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 139 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 327 LEU Chi-restraints excluded: chain T residue 372 VAL Chi-restraints excluded: chain T residue 537 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 0.4980 chunk 86 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 81 ASN S 114 ASN S 211 HIS S 231 ASN S 428 GLN ** T 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 50 GLN T 116 GLN T 212 ASN T 216 HIS T 242 ASN T 284 ASN T 490 ASN T 516 HIS B 24 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9112 Z= 0.257 Angle : 0.734 9.137 12328 Z= 0.378 Chirality : 0.048 0.229 1380 Planarity : 0.006 0.084 1562 Dihedral : 6.731 52.047 1238 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 3.87 % Allowed : 13.30 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.32 (0.20), residues: 1113 helix: -2.78 (0.19), residues: 463 sheet: -3.30 (0.42), residues: 106 loop : -2.81 (0.23), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP T 134 HIS 0.004 0.001 HIS S 395 PHE 0.020 0.002 PHE T 449 TYR 0.016 0.002 TYR S 166 ARG 0.009 0.001 ARG T 57 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 157 time to evaluate : 0.989 Fit side-chains revert: symmetry clash REVERT: S 107 ASN cc_start: 0.8029 (p0) cc_final: 0.7813 (p0) REVERT: S 428 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.8045 (tm130) REVERT: T 86 TYR cc_start: 0.8568 (m-80) cc_final: 0.7572 (m-80) REVERT: T 126 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8648 (tt) REVERT: T 155 ASP cc_start: 0.7196 (t0) cc_final: 0.6849 (t0) REVERT: T 177 ASN cc_start: 0.8232 (t0) cc_final: 0.7617 (t0) REVERT: T 183 ARG cc_start: 0.8141 (pmm-80) cc_final: 0.7338 (ptp90) REVERT: T 304 ARG cc_start: 0.7967 (mmt90) cc_final: 0.7179 (ttp-110) outliers start: 37 outliers final: 23 residues processed: 183 average time/residue: 0.2396 time to fit residues: 58.9479 Evaluate side-chains 159 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 170 THR Chi-restraints excluded: chain S residue 184 ILE Chi-restraints excluded: chain S residue 278 SER Chi-restraints excluded: chain S residue 282 LEU Chi-restraints excluded: chain S residue 330 LEU Chi-restraints excluded: chain S residue 368 GLU Chi-restraints excluded: chain S residue 419 CYS Chi-restraints excluded: chain S residue 428 GLN Chi-restraints excluded: chain S residue 434 LYS Chi-restraints excluded: chain T residue 48 VAL Chi-restraints excluded: chain T residue 126 LEU Chi-restraints excluded: chain T residue 171 ILE Chi-restraints excluded: chain T residue 327 LEU Chi-restraints excluded: chain T residue 372 VAL Chi-restraints excluded: chain T residue 378 THR Chi-restraints excluded: chain T residue 380 SER Chi-restraints excluded: chain T residue 533 ASP Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain E residue 12 GLN Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 32 TRP Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain B residue 30 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 0.4980 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 89 optimal weight: 0.5980 chunk 99 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 80 optimal weight: 0.1980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 445 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9112 Z= 0.197 Angle : 0.669 8.160 12328 Z= 0.337 Chirality : 0.046 0.183 1380 Planarity : 0.005 0.070 1562 Dihedral : 6.007 35.514 1236 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 4.19 % Allowed : 14.24 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.37 (0.23), residues: 1113 helix: -1.74 (0.22), residues: 458 sheet: -3.07 (0.44), residues: 104 loop : -2.48 (0.24), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP T 134 HIS 0.002 0.001 HIS T 263 PHE 0.014 0.001 PHE A 124 TYR 0.017 0.001 TYR E 18 ARG 0.008 0.001 ARG T 541 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 153 time to evaluate : 1.099 Fit side-chains revert: symmetry clash REVERT: S 61 ILE cc_start: 0.8178 (mm) cc_final: 0.7942 (mt) REVERT: S 274 GLU cc_start: 0.8443 (tm-30) cc_final: 0.8198 (tm-30) REVERT: S 428 GLN cc_start: 0.8872 (OUTLIER) cc_final: 0.8133 (tp-100) REVERT: S 465 LYS cc_start: 0.8347 (tmtt) cc_final: 0.7919 (tttm) REVERT: T 86 TYR cc_start: 0.8483 (m-80) cc_final: 0.7514 (m-80) REVERT: T 87 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8738 (tt) REVERT: T 126 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8697 (tt) REVERT: T 155 ASP cc_start: 0.7368 (t0) cc_final: 0.7001 (t0) REVERT: T 177 ASN cc_start: 0.8231 (t0) cc_final: 0.7599 (t0) REVERT: T 304 ARG cc_start: 0.8007 (mmt90) cc_final: 0.7015 (ttp-170) REVERT: T 317 ILE cc_start: 0.8653 (mp) cc_final: 0.8400 (mt) REVERT: E 13 MET cc_start: 0.8258 (tpt) cc_final: 0.7562 (tpt) outliers start: 40 outliers final: 20 residues processed: 177 average time/residue: 0.2250 time to fit residues: 54.7416 Evaluate side-chains 157 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 170 THR Chi-restraints excluded: chain S residue 184 ILE Chi-restraints excluded: chain S residue 278 SER Chi-restraints excluded: chain S residue 282 LEU Chi-restraints excluded: chain S residue 307 MET Chi-restraints excluded: chain S residue 419 CYS Chi-restraints excluded: chain S residue 428 GLN Chi-restraints excluded: chain S residue 434 LYS Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain T residue 126 LEU Chi-restraints excluded: chain T residue 171 ILE Chi-restraints excluded: chain T residue 327 LEU Chi-restraints excluded: chain T residue 372 VAL Chi-restraints excluded: chain T residue 380 SER Chi-restraints excluded: chain T residue 533 ASP Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain E residue 12 GLN Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 32 TRP Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain B residue 31 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 51 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 47 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 428 GLN ** T 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 154 HIS T 242 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 9112 Z= 0.388 Angle : 0.750 9.652 12328 Z= 0.379 Chirality : 0.050 0.257 1380 Planarity : 0.006 0.070 1562 Dihedral : 6.220 43.902 1236 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.60 % Favored : 89.40 % Rotamer: Outliers : 5.13 % Allowed : 14.87 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.03 (0.24), residues: 1113 helix: -1.35 (0.23), residues: 471 sheet: -3.11 (0.42), residues: 113 loop : -2.33 (0.25), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP T 134 HIS 0.004 0.001 HIS T 101 PHE 0.020 0.002 PHE B 40 TYR 0.017 0.002 TYR B 23 ARG 0.011 0.001 ARG T 57 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 137 time to evaluate : 0.835 Fit side-chains revert: symmetry clash REVERT: S 274 GLU cc_start: 0.8490 (tm-30) cc_final: 0.8211 (tm-30) REVERT: T 86 TYR cc_start: 0.8586 (m-80) cc_final: 0.7546 (m-80) REVERT: T 126 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8684 (tt) REVERT: T 155 ASP cc_start: 0.7289 (t0) cc_final: 0.6911 (t0) REVERT: T 177 ASN cc_start: 0.8267 (t0) cc_final: 0.7805 (t0) REVERT: T 317 ILE cc_start: 0.8870 (mp) cc_final: 0.8626 (mt) REVERT: A 113 THR cc_start: 0.7370 (p) cc_final: 0.7125 (t) REVERT: A 121 GLN cc_start: 0.7281 (tt0) cc_final: 0.7051 (tt0) REVERT: A 150 ILE cc_start: 0.6883 (OUTLIER) cc_final: 0.6512 (tt) REVERT: E 13 MET cc_start: 0.8157 (tpt) cc_final: 0.7523 (tpt) REVERT: E 26 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8721 (mm) outliers start: 49 outliers final: 27 residues processed: 173 average time/residue: 0.2039 time to fit residues: 50.1711 Evaluate side-chains 154 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 170 THR Chi-restraints excluded: chain S residue 184 ILE Chi-restraints excluded: chain S residue 278 SER Chi-restraints excluded: chain S residue 282 LEU Chi-restraints excluded: chain S residue 344 LEU Chi-restraints excluded: chain S residue 419 CYS Chi-restraints excluded: chain S residue 428 GLN Chi-restraints excluded: chain S residue 434 LYS Chi-restraints excluded: chain T residue 48 VAL Chi-restraints excluded: chain T residue 126 LEU Chi-restraints excluded: chain T residue 171 ILE Chi-restraints excluded: chain T residue 210 ILE Chi-restraints excluded: chain T residue 327 LEU Chi-restraints excluded: chain T residue 372 VAL Chi-restraints excluded: chain T residue 378 THR Chi-restraints excluded: chain T residue 380 SER Chi-restraints excluded: chain T residue 388 ILE Chi-restraints excluded: chain T residue 491 ILE Chi-restraints excluded: chain T residue 520 ILE Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain E residue 12 GLN Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 32 TRP Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 31 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 73 optimal weight: 0.5980 chunk 0 optimal weight: 0.6980 chunk 54 optimal weight: 5.9990 chunk 95 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 428 GLN T 47 HIS T 135 ASN ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9112 Z= 0.192 Angle : 0.660 11.333 12328 Z= 0.330 Chirality : 0.045 0.168 1380 Planarity : 0.005 0.062 1562 Dihedral : 5.791 40.597 1236 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer: Outliers : 3.98 % Allowed : 16.75 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.24), residues: 1113 helix: -0.87 (0.24), residues: 460 sheet: -2.88 (0.45), residues: 106 loop : -2.17 (0.26), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP T 134 HIS 0.003 0.001 HIS B 24 PHE 0.021 0.001 PHE A 95 TYR 0.010 0.001 TYR S 82 ARG 0.007 0.000 ARG T 57 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 135 time to evaluate : 1.020 Fit side-chains revert: symmetry clash REVERT: S 61 ILE cc_start: 0.8205 (mm) cc_final: 0.7972 (mt) REVERT: S 274 GLU cc_start: 0.8402 (tm-30) cc_final: 0.8106 (tm-30) REVERT: S 395 HIS cc_start: 0.8508 (m-70) cc_final: 0.7994 (m-70) REVERT: S 428 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.8139 (tp-100) REVERT: T 86 TYR cc_start: 0.8500 (m-80) cc_final: 0.7470 (m-80) REVERT: T 126 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8661 (tt) REVERT: T 155 ASP cc_start: 0.7481 (t0) cc_final: 0.7110 (t0) REVERT: T 177 ASN cc_start: 0.8159 (t0) cc_final: 0.7734 (t0) REVERT: T 183 ARG cc_start: 0.8106 (pmm-80) cc_final: 0.7653 (ptt180) REVERT: T 317 ILE cc_start: 0.8803 (mp) cc_final: 0.8550 (mt) REVERT: T 537 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8306 (pp) REVERT: A 121 GLN cc_start: 0.7267 (tt0) cc_final: 0.6968 (tt0) REVERT: E 13 MET cc_start: 0.8128 (tpt) cc_final: 0.7539 (tpt) REVERT: E 26 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8649 (mm) outliers start: 38 outliers final: 23 residues processed: 161 average time/residue: 0.2036 time to fit residues: 46.6241 Evaluate side-chains 151 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 124 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 170 THR Chi-restraints excluded: chain S residue 184 ILE Chi-restraints excluded: chain S residue 278 SER Chi-restraints excluded: chain S residue 282 LEU Chi-restraints excluded: chain S residue 330 LEU Chi-restraints excluded: chain S residue 344 LEU Chi-restraints excluded: chain S residue 419 CYS Chi-restraints excluded: chain S residue 428 GLN Chi-restraints excluded: chain S residue 434 LYS Chi-restraints excluded: chain T residue 66 THR Chi-restraints excluded: chain T residue 126 LEU Chi-restraints excluded: chain T residue 130 ILE Chi-restraints excluded: chain T residue 171 ILE Chi-restraints excluded: chain T residue 327 LEU Chi-restraints excluded: chain T residue 372 VAL Chi-restraints excluded: chain T residue 378 THR Chi-restraints excluded: chain T residue 380 SER Chi-restraints excluded: chain T residue 388 ILE Chi-restraints excluded: chain T residue 537 LEU Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain E residue 12 GLN Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 32 TRP Chi-restraints excluded: chain B residue 31 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 102 optimal weight: 0.8980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 428 GLN T 135 ASN ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9112 Z= 0.248 Angle : 0.679 10.937 12328 Z= 0.338 Chirality : 0.047 0.223 1380 Planarity : 0.005 0.061 1562 Dihedral : 5.747 42.475 1236 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.42 % Favored : 89.58 % Rotamer: Outliers : 4.71 % Allowed : 17.28 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.25), residues: 1113 helix: -0.76 (0.25), residues: 467 sheet: -2.83 (0.45), residues: 105 loop : -2.12 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP T 134 HIS 0.003 0.001 HIS B 24 PHE 0.018 0.001 PHE A 95 TYR 0.012 0.001 TYR T 362 ARG 0.009 0.000 ARG T 57 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 126 time to evaluate : 0.917 Fit side-chains revert: symmetry clash REVERT: S 183 ASP cc_start: 0.7633 (m-30) cc_final: 0.7331 (m-30) REVERT: S 189 ARG cc_start: 0.7340 (OUTLIER) cc_final: 0.6882 (ttt90) REVERT: S 274 GLU cc_start: 0.8410 (tm-30) cc_final: 0.8134 (tm-30) REVERT: S 359 ASN cc_start: 0.8296 (t0) cc_final: 0.7319 (m-40) REVERT: S 395 HIS cc_start: 0.8517 (m-70) cc_final: 0.8020 (m-70) REVERT: S 428 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8280 (tp-100) REVERT: T 86 TYR cc_start: 0.8509 (m-80) cc_final: 0.7525 (m-80) REVERT: T 126 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8692 (tt) REVERT: T 177 ASN cc_start: 0.8239 (t0) cc_final: 0.7781 (t0) REVERT: T 183 ARG cc_start: 0.8143 (pmm-80) cc_final: 0.7686 (ptt180) REVERT: T 261 LEU cc_start: 0.7389 (pt) cc_final: 0.7131 (pp) REVERT: T 317 ILE cc_start: 0.8804 (mp) cc_final: 0.8559 (mt) REVERT: T 537 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8348 (pp) REVERT: A 20 ARG cc_start: 0.8485 (tmt-80) cc_final: 0.8185 (tpt170) REVERT: A 121 GLN cc_start: 0.7320 (tt0) cc_final: 0.7036 (tt0) REVERT: E 13 MET cc_start: 0.8116 (tpt) cc_final: 0.7516 (tpt) outliers start: 45 outliers final: 31 residues processed: 160 average time/residue: 0.2051 time to fit residues: 46.1832 Evaluate side-chains 156 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 121 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 170 THR Chi-restraints excluded: chain S residue 184 ILE Chi-restraints excluded: chain S residue 189 ARG Chi-restraints excluded: chain S residue 278 SER Chi-restraints excluded: chain S residue 282 LEU Chi-restraints excluded: chain S residue 330 LEU Chi-restraints excluded: chain S residue 344 LEU Chi-restraints excluded: chain S residue 419 CYS Chi-restraints excluded: chain S residue 428 GLN Chi-restraints excluded: chain S residue 434 LYS Chi-restraints excluded: chain T residue 66 THR Chi-restraints excluded: chain T residue 126 LEU Chi-restraints excluded: chain T residue 130 ILE Chi-restraints excluded: chain T residue 171 ILE Chi-restraints excluded: chain T residue 250 VAL Chi-restraints excluded: chain T residue 327 LEU Chi-restraints excluded: chain T residue 372 VAL Chi-restraints excluded: chain T residue 378 THR Chi-restraints excluded: chain T residue 380 SER Chi-restraints excluded: chain T residue 388 ILE Chi-restraints excluded: chain T residue 491 ILE Chi-restraints excluded: chain T residue 520 ILE Chi-restraints excluded: chain T residue 537 LEU Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain E residue 12 GLN Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 32 TRP Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 31 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 42 optimal weight: 8.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 428 GLN T 135 ASN ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9112 Z= 0.341 Angle : 0.725 10.633 12328 Z= 0.362 Chirality : 0.049 0.167 1380 Planarity : 0.005 0.065 1562 Dihedral : 5.931 45.484 1236 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.69 % Favored : 89.31 % Rotamer: Outliers : 5.03 % Allowed : 16.65 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.25), residues: 1113 helix: -0.75 (0.24), residues: 476 sheet: -2.91 (0.44), residues: 112 loop : -2.04 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP T 134 HIS 0.004 0.001 HIS B 24 PHE 0.017 0.002 PHE A 95 TYR 0.017 0.002 TYR E 18 ARG 0.008 0.001 ARG T 57 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 125 time to evaluate : 0.984 Fit side-chains revert: symmetry clash REVERT: S 107 ASN cc_start: 0.8129 (p0) cc_final: 0.7924 (p0) REVERT: S 183 ASP cc_start: 0.7715 (m-30) cc_final: 0.7393 (m-30) REVERT: S 189 ARG cc_start: 0.7407 (OUTLIER) cc_final: 0.6840 (ttt90) REVERT: S 274 GLU cc_start: 0.8396 (tm-30) cc_final: 0.8122 (tm-30) REVERT: S 359 ASN cc_start: 0.8344 (t0) cc_final: 0.7337 (m-40) REVERT: S 465 LYS cc_start: 0.8036 (tmtt) cc_final: 0.7714 (tttm) REVERT: T 86 TYR cc_start: 0.8562 (m-80) cc_final: 0.7477 (m-80) REVERT: T 126 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8722 (tt) REVERT: T 183 ARG cc_start: 0.8165 (pmm-80) cc_final: 0.7723 (ptt180) REVERT: T 317 ILE cc_start: 0.8873 (mp) cc_final: 0.8631 (mt) REVERT: A 121 GLN cc_start: 0.7428 (tt0) cc_final: 0.7123 (tt0) REVERT: E 13 MET cc_start: 0.8066 (tpt) cc_final: 0.7472 (tpt) outliers start: 48 outliers final: 35 residues processed: 160 average time/residue: 0.2092 time to fit residues: 47.3816 Evaluate side-chains 151 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 114 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 170 THR Chi-restraints excluded: chain S residue 184 ILE Chi-restraints excluded: chain S residue 189 ARG Chi-restraints excluded: chain S residue 210 LYS Chi-restraints excluded: chain S residue 278 SER Chi-restraints excluded: chain S residue 282 LEU Chi-restraints excluded: chain S residue 330 LEU Chi-restraints excluded: chain S residue 344 LEU Chi-restraints excluded: chain S residue 419 CYS Chi-restraints excluded: chain S residue 428 GLN Chi-restraints excluded: chain S residue 434 LYS Chi-restraints excluded: chain S residue 466 GLU Chi-restraints excluded: chain T residue 48 VAL Chi-restraints excluded: chain T residue 66 THR Chi-restraints excluded: chain T residue 126 LEU Chi-restraints excluded: chain T residue 130 ILE Chi-restraints excluded: chain T residue 171 ILE Chi-restraints excluded: chain T residue 203 VAL Chi-restraints excluded: chain T residue 250 VAL Chi-restraints excluded: chain T residue 327 LEU Chi-restraints excluded: chain T residue 372 VAL Chi-restraints excluded: chain T residue 378 THR Chi-restraints excluded: chain T residue 380 SER Chi-restraints excluded: chain T residue 388 ILE Chi-restraints excluded: chain T residue 491 ILE Chi-restraints excluded: chain T residue 520 ILE Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain E residue 12 GLN Chi-restraints excluded: chain E residue 32 TRP Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 31 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 67 optimal weight: 0.0670 chunk 72 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 83 optimal weight: 0.7980 chunk 96 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 428 GLN T 135 ASN ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9112 Z= 0.163 Angle : 0.662 10.532 12328 Z= 0.325 Chirality : 0.045 0.160 1380 Planarity : 0.005 0.061 1562 Dihedral : 5.540 41.827 1236 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 3.35 % Allowed : 18.53 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.25), residues: 1113 helix: -0.36 (0.25), residues: 463 sheet: -3.19 (0.47), residues: 94 loop : -1.97 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP T 134 HIS 0.003 0.001 HIS B 24 PHE 0.015 0.001 PHE A 95 TYR 0.011 0.001 TYR S 335 ARG 0.008 0.000 ARG T 57 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 129 time to evaluate : 1.220 Fit side-chains REVERT: S 107 ASN cc_start: 0.8138 (p0) cc_final: 0.7877 (p0) REVERT: S 183 ASP cc_start: 0.7578 (m-30) cc_final: 0.7255 (m-30) REVERT: S 189 ARG cc_start: 0.7309 (OUTLIER) cc_final: 0.6899 (ttt90) REVERT: S 274 GLU cc_start: 0.8380 (tm-30) cc_final: 0.8127 (tm-30) REVERT: S 359 ASN cc_start: 0.8283 (t0) cc_final: 0.7256 (m-40) REVERT: S 395 HIS cc_start: 0.8445 (m-70) cc_final: 0.8000 (m-70) REVERT: S 465 LYS cc_start: 0.8023 (tmtt) cc_final: 0.7810 (tttm) REVERT: T 86 TYR cc_start: 0.8479 (m-80) cc_final: 0.7447 (m-80) REVERT: T 93 TYR cc_start: 0.7363 (OUTLIER) cc_final: 0.6918 (m-10) REVERT: T 126 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8618 (tt) REVERT: T 177 ASN cc_start: 0.8185 (t0) cc_final: 0.7773 (t0) REVERT: T 183 ARG cc_start: 0.8100 (pmm-80) cc_final: 0.7684 (ptt180) REVERT: T 317 ILE cc_start: 0.8740 (mp) cc_final: 0.8504 (mt) REVERT: A 20 ARG cc_start: 0.8504 (tmt-80) cc_final: 0.8290 (tpt170) REVERT: E 13 MET cc_start: 0.7996 (tpt) cc_final: 0.7377 (tpt) REVERT: E 26 LEU cc_start: 0.8906 (mm) cc_final: 0.8637 (mm) outliers start: 32 outliers final: 20 residues processed: 156 average time/residue: 0.2429 time to fit residues: 54.1591 Evaluate side-chains 143 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 184 ILE Chi-restraints excluded: chain S residue 189 ARG Chi-restraints excluded: chain S residue 278 SER Chi-restraints excluded: chain S residue 282 LEU Chi-restraints excluded: chain S residue 428 GLN Chi-restraints excluded: chain S residue 434 LYS Chi-restraints excluded: chain T residue 66 THR Chi-restraints excluded: chain T residue 93 TYR Chi-restraints excluded: chain T residue 126 LEU Chi-restraints excluded: chain T residue 130 ILE Chi-restraints excluded: chain T residue 171 ILE Chi-restraints excluded: chain T residue 203 VAL Chi-restraints excluded: chain T residue 327 LEU Chi-restraints excluded: chain T residue 372 VAL Chi-restraints excluded: chain T residue 378 THR Chi-restraints excluded: chain T residue 380 SER Chi-restraints excluded: chain T residue 388 ILE Chi-restraints excluded: chain T residue 491 ILE Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain E residue 32 TRP Chi-restraints excluded: chain B residue 31 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 chunk 93 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 104 optimal weight: 7.9990 chunk 63 optimal weight: 0.7980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 428 GLN T 135 ASN ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9112 Z= 0.247 Angle : 0.697 9.920 12328 Z= 0.341 Chirality : 0.047 0.164 1380 Planarity : 0.005 0.064 1562 Dihedral : 5.602 43.895 1236 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.33 % Favored : 89.67 % Rotamer: Outliers : 3.77 % Allowed : 18.64 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.25), residues: 1113 helix: -0.29 (0.25), residues: 465 sheet: -3.10 (0.48), residues: 94 loop : -1.95 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP T 134 HIS 0.003 0.001 HIS B 24 PHE 0.016 0.001 PHE B 40 TYR 0.015 0.001 TYR T 461 ARG 0.010 0.000 ARG T 57 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 122 time to evaluate : 1.029 Fit side-chains revert: symmetry clash REVERT: S 107 ASN cc_start: 0.8272 (p0) cc_final: 0.8037 (p0) REVERT: S 183 ASP cc_start: 0.7603 (m-30) cc_final: 0.7262 (m-30) REVERT: S 189 ARG cc_start: 0.7336 (OUTLIER) cc_final: 0.6836 (ttt90) REVERT: S 274 GLU cc_start: 0.8402 (tm-30) cc_final: 0.8168 (tm-30) REVERT: S 359 ASN cc_start: 0.8269 (t0) cc_final: 0.7255 (m-40) REVERT: S 428 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.8324 (tp-100) REVERT: S 465 LYS cc_start: 0.8020 (tmtt) cc_final: 0.7798 (tttm) REVERT: T 86 TYR cc_start: 0.8505 (m-80) cc_final: 0.7443 (m-80) REVERT: T 93 TYR cc_start: 0.7375 (OUTLIER) cc_final: 0.6957 (m-10) REVERT: T 126 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8708 (tt) REVERT: T 177 ASN cc_start: 0.8235 (t0) cc_final: 0.7772 (t0) REVERT: T 183 ARG cc_start: 0.8121 (pmm-80) cc_final: 0.7696 (ptt180) REVERT: T 317 ILE cc_start: 0.8762 (mp) cc_final: 0.8519 (mt) REVERT: E 26 LEU cc_start: 0.8989 (mm) cc_final: 0.8698 (mm) outliers start: 36 outliers final: 26 residues processed: 153 average time/residue: 0.2055 time to fit residues: 43.9678 Evaluate side-chains 149 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 119 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 184 ILE Chi-restraints excluded: chain S residue 189 ARG Chi-restraints excluded: chain S residue 278 SER Chi-restraints excluded: chain S residue 282 LEU Chi-restraints excluded: chain S residue 330 LEU Chi-restraints excluded: chain S residue 419 CYS Chi-restraints excluded: chain S residue 428 GLN Chi-restraints excluded: chain S residue 434 LYS Chi-restraints excluded: chain T residue 48 VAL Chi-restraints excluded: chain T residue 66 THR Chi-restraints excluded: chain T residue 93 TYR Chi-restraints excluded: chain T residue 126 LEU Chi-restraints excluded: chain T residue 130 ILE Chi-restraints excluded: chain T residue 171 ILE Chi-restraints excluded: chain T residue 203 VAL Chi-restraints excluded: chain T residue 250 VAL Chi-restraints excluded: chain T residue 327 LEU Chi-restraints excluded: chain T residue 372 VAL Chi-restraints excluded: chain T residue 378 THR Chi-restraints excluded: chain T residue 380 SER Chi-restraints excluded: chain T residue 388 ILE Chi-restraints excluded: chain T residue 491 ILE Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain E residue 32 TRP Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain B residue 31 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 87 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 53 optimal weight: 7.9990 chunk 69 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 428 GLN T 135 ASN ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9112 Z= 0.185 Angle : 0.675 9.790 12328 Z= 0.329 Chirality : 0.045 0.163 1380 Planarity : 0.005 0.064 1562 Dihedral : 5.474 42.929 1236 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 2.83 % Allowed : 19.90 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.25), residues: 1113 helix: -0.19 (0.25), residues: 465 sheet: -3.00 (0.48), residues: 94 loop : -1.88 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP T 134 HIS 0.003 0.001 HIS B 24 PHE 0.015 0.001 PHE B 40 TYR 0.019 0.001 TYR E 18 ARG 0.007 0.000 ARG T 57 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 1.105 Fit side-chains REVERT: S 107 ASN cc_start: 0.8274 (p0) cc_final: 0.8049 (p0) REVERT: S 183 ASP cc_start: 0.7611 (m-30) cc_final: 0.7263 (m-30) REVERT: S 189 ARG cc_start: 0.7307 (OUTLIER) cc_final: 0.6903 (ttt90) REVERT: S 274 GLU cc_start: 0.8379 (tm-30) cc_final: 0.8157 (tm-30) REVERT: S 359 ASN cc_start: 0.8276 (t0) cc_final: 0.7255 (m-40) REVERT: S 395 HIS cc_start: 0.8428 (m-70) cc_final: 0.7977 (m-70) REVERT: T 86 TYR cc_start: 0.8470 (m-80) cc_final: 0.7424 (m-80) REVERT: T 93 TYR cc_start: 0.7370 (OUTLIER) cc_final: 0.6977 (m-10) REVERT: T 126 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8638 (tt) REVERT: T 177 ASN cc_start: 0.8194 (t0) cc_final: 0.7774 (t0) REVERT: T 183 ARG cc_start: 0.8094 (pmm-80) cc_final: 0.7645 (ptt180) REVERT: T 261 LEU cc_start: 0.7417 (pt) cc_final: 0.7187 (pp) REVERT: T 317 ILE cc_start: 0.8701 (mp) cc_final: 0.8480 (mt) REVERT: E 26 LEU cc_start: 0.8937 (mm) cc_final: 0.8640 (mm) outliers start: 27 outliers final: 21 residues processed: 147 average time/residue: 0.2340 time to fit residues: 48.8737 Evaluate side-chains 142 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 184 ILE Chi-restraints excluded: chain S residue 189 ARG Chi-restraints excluded: chain S residue 282 LEU Chi-restraints excluded: chain S residue 330 LEU Chi-restraints excluded: chain S residue 434 LYS Chi-restraints excluded: chain T residue 48 VAL Chi-restraints excluded: chain T residue 66 THR Chi-restraints excluded: chain T residue 93 TYR Chi-restraints excluded: chain T residue 126 LEU Chi-restraints excluded: chain T residue 130 ILE Chi-restraints excluded: chain T residue 171 ILE Chi-restraints excluded: chain T residue 203 VAL Chi-restraints excluded: chain T residue 250 VAL Chi-restraints excluded: chain T residue 327 LEU Chi-restraints excluded: chain T residue 372 VAL Chi-restraints excluded: chain T residue 378 THR Chi-restraints excluded: chain T residue 380 SER Chi-restraints excluded: chain T residue 388 ILE Chi-restraints excluded: chain T residue 491 ILE Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain E residue 32 TRP Chi-restraints excluded: chain B residue 31 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 87 optimal weight: 0.0670 chunk 36 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 91 HIS T 135 ASN ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.125860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.109461 restraints weight = 15765.023| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.33 r_work: 0.3342 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3353 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3353 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9112 Z= 0.163 Angle : 0.663 9.337 12328 Z= 0.321 Chirality : 0.045 0.165 1380 Planarity : 0.004 0.061 1562 Dihedral : 5.307 42.073 1236 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 3.14 % Allowed : 19.06 % Favored : 77.80 % 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: -1.76 (0.25), residues: 1113 helix: -0.06 (0.25), residues: 465 sheet: -2.76 (0.47), residues: 101 loop : -1.83 (0.26), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP T 134 HIS 0.003 0.001 HIS B 24 PHE 0.015 0.001 PHE B 40 TYR 0.012 0.001 TYR T 461 ARG 0.006 0.000 ARG T 57 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2121.04 seconds wall clock time: 39 minutes 36.78 seconds (2376.78 seconds total)