Starting phenix.real_space_refine on Sat Aug 23 02:54:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8avw_15685/08_2025/8avw_15685.cif Found real_map, /net/cci-nas-00/data/ceres_data/8avw_15685/08_2025/8avw_15685.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8avw_15685/08_2025/8avw_15685.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8avw_15685/08_2025/8avw_15685.map" model { file = "/net/cci-nas-00/data/ceres_data/8avw_15685/08_2025/8avw_15685.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8avw_15685/08_2025/8avw_15685.cif" } resolution = 3.62 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 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: 4 Type Number sf(0) Gaussians S 24 5.16 5 C 5706 2.51 5 N 1602 2.21 5 O 1660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8992 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4448 Classifications: {'peptide': 577} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 531} Chain breaks: 2 Chain: "B" Number of atoms: 4458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4458 Classifications: {'peptide': 579} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 533} Chain breaks: 1 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'LBV': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'LBV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.34, per 1000 atoms: 0.26 Number of scatterers: 8992 At special positions: 0 Unit cell: (93.9253, 98.2338, 174.925, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 24 16.00 O 1660 8.00 N 1602 7.00 C 5706 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=0, symmetry=0 Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 348.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2136 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 8 sheets defined 43.1% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 57 through 63 Processing helix chain 'A' and resid 65 through 70 removed outlier: 3.654A pdb=" N ARG A 70 " --> pdb=" O PRO A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 78 removed outlier: 3.824A pdb=" N LEU A 77 " --> pdb=" O THR A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 removed outlier: 3.764A pdb=" N ALA A 87 " --> pdb=" O PRO A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 148 removed outlier: 3.535A pdb=" N PHE A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 169 Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 257 through 268 removed outlier: 3.713A pdb=" N GLN A 262 " --> pdb=" O PRO A 258 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR A 263 " --> pdb=" O MET A 259 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A 264 " --> pdb=" O HIS A 260 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG A 265 " --> pdb=" O MET A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 331 removed outlier: 4.220A pdb=" N THR A 304 " --> pdb=" O ASP A 300 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A 308 " --> pdb=" O THR A 304 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLN A 317 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL A 318 " --> pdb=" O LEU A 314 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA A 321 " --> pdb=" O GLN A 317 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL A 324 " --> pdb=" O GLU A 320 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN A 329 " --> pdb=" O ALA A 325 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N SER A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 342 removed outlier: 3.673A pdb=" N ARG A 337 " --> pdb=" O GLU A 333 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL A 338 " --> pdb=" O HIS A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 353 removed outlier: 3.837A pdb=" N SER A 353 " --> pdb=" O HIS A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 396 removed outlier: 3.521A pdb=" N VAL A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP A 389 " --> pdb=" O ALA A 385 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA A 393 " --> pdb=" O ASP A 389 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TRP A 394 " --> pdb=" O ALA A 390 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 412 removed outlier: 4.361A pdb=" N LEU A 411 " --> pdb=" O ALA A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 416 removed outlier: 3.661A pdb=" N ALA A 416 " --> pdb=" O PRO A 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 413 through 416' Processing helix chain 'A' and resid 455 through 459 removed outlier: 3.605A pdb=" N ALA A 459 " --> pdb=" O PRO A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 499 removed outlier: 3.679A pdb=" N ILE A 488 " --> pdb=" O HIS A 484 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP A 493 " --> pdb=" O GLU A 489 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP A 496 " --> pdb=" O GLN A 492 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR A 497 " --> pdb=" O ASP A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 543 removed outlier: 3.638A pdb=" N SER A 507 " --> pdb=" O GLY A 503 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL A 508 " --> pdb=" O GLU A 504 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE A 509 " --> pdb=" O ARG A 505 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ASP A 511 " --> pdb=" O SER A 507 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 516 " --> pdb=" O LEU A 512 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR A 517 " --> pdb=" O ASN A 513 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN A 518 " --> pdb=" O ARG A 514 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE A 528 " --> pdb=" O ARG A 524 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N SER A 531 " --> pdb=" O GLY A 527 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN A 535 " --> pdb=" O SER A 531 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLU A 536 " --> pdb=" O HIS A 532 " (cutoff:3.500A) Proline residue: A 537 - end of helix Processing helix chain 'A' and resid 546 through 551 Processing helix chain 'A' and resid 563 through 591 removed outlier: 3.827A pdb=" N ARG A 573 " --> pdb=" O GLY A 569 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU A 574 " --> pdb=" O PHE A 570 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N HIS A 586 " --> pdb=" O THR A 582 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR A 587 " --> pdb=" O GLN A 583 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR A 589 " --> pdb=" O LEU A 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 63 Processing helix chain 'B' and resid 65 through 70 removed outlier: 3.654A pdb=" N ARG B 70 " --> pdb=" O PRO B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 78 removed outlier: 3.827A pdb=" N LEU B 77 " --> pdb=" O THR B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 removed outlier: 3.766A pdb=" N ALA B 87 " --> pdb=" O PRO B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 148 removed outlier: 3.544A pdb=" N PHE B 145 " --> pdb=" O ARG B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 169 Processing helix chain 'B' and resid 209 through 216 Processing helix chain 'B' and resid 257 through 268 removed outlier: 3.713A pdb=" N GLN B 262 " --> pdb=" O PRO B 258 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR B 263 " --> pdb=" O MET B 259 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 264 " --> pdb=" O HIS B 260 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG B 265 " --> pdb=" O MET B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 331 removed outlier: 4.199A pdb=" N THR B 304 " --> pdb=" O ASP B 300 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B 308 " --> pdb=" O THR B 304 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLN B 317 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL B 318 " --> pdb=" O LEU B 314 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA B 321 " --> pdb=" O GLN B 317 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL B 324 " --> pdb=" O GLU B 320 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLN B 329 " --> pdb=" O ALA B 325 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER B 330 " --> pdb=" O ALA B 326 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU B 331 " --> pdb=" O PHE B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 342 removed outlier: 3.687A pdb=" N ARG B 337 " --> pdb=" O GLU B 333 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL B 338 " --> pdb=" O HIS B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 353 removed outlier: 3.837A pdb=" N SER B 353 " --> pdb=" O HIS B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 396 removed outlier: 3.524A pdb=" N VAL B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP B 389 " --> pdb=" O ALA B 385 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA B 393 " --> pdb=" O ASP B 389 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TRP B 394 " --> pdb=" O ALA B 390 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU B 396 " --> pdb=" O LEU B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 412 removed outlier: 4.371A pdb=" N LEU B 411 " --> pdb=" O ALA B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 416 removed outlier: 3.659A pdb=" N ALA B 416 " --> pdb=" O PRO B 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 413 through 416' Processing helix chain 'B' and resid 455 through 459 removed outlier: 3.605A pdb=" N ALA B 459 " --> pdb=" O PRO B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 499 removed outlier: 3.678A pdb=" N ILE B 488 " --> pdb=" O HIS B 484 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP B 493 " --> pdb=" O GLU B 489 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP B 496 " --> pdb=" O GLN B 492 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR B 497 " --> pdb=" O ASP B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 543 removed outlier: 3.507A pdb=" N ARG B 505 " --> pdb=" O ALA B 501 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER B 507 " --> pdb=" O GLY B 503 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL B 508 " --> pdb=" O GLU B 504 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ILE B 509 " --> pdb=" O ARG B 505 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP B 511 " --> pdb=" O SER B 507 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU B 516 " --> pdb=" O LEU B 512 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR B 517 " --> pdb=" O ASN B 513 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN B 518 " --> pdb=" O ARG B 514 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER B 519 " --> pdb=" O ALA B 515 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE B 528 " --> pdb=" O ARG B 524 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N SER B 531 " --> pdb=" O GLY B 527 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN B 535 " --> pdb=" O SER B 531 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU B 536 " --> pdb=" O HIS B 532 " (cutoff:3.500A) Proline residue: B 537 - end of helix Processing helix chain 'B' and resid 546 through 551 Processing helix chain 'B' and resid 563 through 591 removed outlier: 3.833A pdb=" N ARG B 573 " --> pdb=" O GLY B 569 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU B 574 " --> pdb=" O PHE B 570 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N HIS B 586 " --> pdb=" O THR B 582 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR B 587 " --> pdb=" O GLN B 583 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR B 589 " --> pdb=" O LEU B 585 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 35 removed outlier: 6.676A pdb=" N THR A 43 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N MET A 54 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU A 41 " --> pdb=" O MET A 54 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU A 111 " --> pdb=" O LEU A 103 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.881A pdb=" N LEU A 175 " --> pdb=" O ILE A 187 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N GLU A 189 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL A 173 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N TRP A 284 " --> pdb=" O PHE A 178 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL A 277 " --> pdb=" O TRP A 284 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LEU A 286 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL A 275 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ALA A 288 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LEU A 273 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N HIS A 290 " --> pdb=" O SER A 271 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N SER A 271 " --> pdb=" O HIS A 290 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG A 222 " --> pdb=" O SER A 274 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 375 through 380 removed outlier: 4.101A pdb=" N PHE A 372 " --> pdb=" O ARG A 375 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLU A 436 " --> pdb=" O VAL A 430 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 447 through 452 removed outlier: 4.010A pdb=" N LEU A 447 " --> pdb=" O LYS A 476 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 34 through 35 removed outlier: 6.668A pdb=" N THR B 43 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N MET B 54 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LEU B 41 " --> pdb=" O MET B 54 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU B 111 " --> pdb=" O LEU B 103 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 202 through 203 removed outlier: 6.881A pdb=" N LEU B 175 " --> pdb=" O ILE B 187 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N GLU B 189 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N VAL B 173 " --> pdb=" O GLU B 189 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N TRP B 284 " --> pdb=" O PHE B 178 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL B 277 " --> pdb=" O TRP B 284 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LEU B 286 " --> pdb=" O VAL B 275 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL B 275 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ALA B 288 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU B 273 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N HIS B 290 " --> pdb=" O SER B 271 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N SER B 271 " --> pdb=" O HIS B 290 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG B 222 " --> pdb=" O SER B 274 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 375 through 380 removed outlier: 4.102A pdb=" N PHE B 372 " --> pdb=" O ARG B 375 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLU B 436 " --> pdb=" O VAL B 430 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 445 through 452 removed outlier: 7.252A pdb=" N LEU B 445 " --> pdb=" O GLY B 478 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N GLY B 478 " --> pdb=" O LEU B 445 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU B 447 " --> pdb=" O LYS B 476 " (cutoff:3.500A) 376 hydrogen bonds defined for protein. 1068 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: 1.24 Time building geometry restraints manager: 1.02 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: 1910 1.34 - 1.46: 3087 1.46 - 1.58: 4186 1.58 - 1.70: 0 1.70 - 1.82: 40 Bond restraints: 9223 Sorted by residual: bond pdb=" C2D LBV A1000 " pdb=" C3D LBV A1000 " ideal model delta sigma weight residual 1.358 1.432 -0.074 2.00e-02 2.50e+03 1.35e+01 bond pdb=" C2D LBV B1000 " pdb=" C3D LBV B1000 " ideal model delta sigma weight residual 1.358 1.430 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" C4C LBV A1000 " pdb=" CHD LBV A1000 " ideal model delta sigma weight residual 1.428 1.357 0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" C4C LBV B1000 " pdb=" CHD LBV B1000 " ideal model delta sigma weight residual 1.428 1.359 0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C SER B 558 " pdb=" N PRO B 559 " ideal model delta sigma weight residual 1.334 1.362 -0.028 8.40e-03 1.42e+04 1.12e+01 ... (remaining 9218 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 8965 1.36 - 2.72: 2797 2.72 - 4.07: 757 4.07 - 5.43: 83 5.43 - 6.79: 9 Bond angle restraints: 12611 Sorted by residual: angle pdb=" N GLN A 329 " pdb=" CA GLN A 329 " pdb=" C GLN A 329 " ideal model delta sigma weight residual 114.04 108.55 5.49 1.24e+00 6.50e-01 1.96e+01 angle pdb=" N GLN B 329 " pdb=" CA GLN B 329 " pdb=" C GLN B 329 " ideal model delta sigma weight residual 114.04 108.56 5.48 1.24e+00 6.50e-01 1.95e+01 angle pdb=" N LEU B 360 " pdb=" CA LEU B 360 " pdb=" C LEU B 360 " ideal model delta sigma weight residual 114.56 109.47 5.09 1.27e+00 6.20e-01 1.61e+01 angle pdb=" N LEU A 360 " pdb=" CA LEU A 360 " pdb=" C LEU A 360 " ideal model delta sigma weight residual 114.56 109.55 5.01 1.27e+00 6.20e-01 1.55e+01 angle pdb=" C LEU B 297 " pdb=" N PRO B 298 " pdb=" CA PRO B 298 " ideal model delta sigma weight residual 119.66 122.52 -2.86 7.30e-01 1.88e+00 1.54e+01 ... (remaining 12606 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.85: 4637 15.85 - 31.71: 575 31.71 - 47.56: 176 47.56 - 63.41: 99 63.41 - 79.27: 32 Dihedral angle restraints: 5519 sinusoidal: 2210 harmonic: 3309 Sorted by residual: dihedral pdb=" CA HIS B 219 " pdb=" C HIS B 219 " pdb=" N LEU B 220 " pdb=" CA LEU B 220 " ideal model delta harmonic sigma weight residual -180.00 -157.34 -22.66 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA HIS A 219 " pdb=" C HIS A 219 " pdb=" N LEU A 220 " pdb=" CA LEU A 220 " ideal model delta harmonic sigma weight residual -180.00 -157.70 -22.30 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" C ASN A 243 " pdb=" N ASN A 243 " pdb=" CA ASN A 243 " pdb=" CB ASN A 243 " ideal model delta harmonic sigma weight residual -122.60 -131.77 9.17 0 2.50e+00 1.60e-01 1.35e+01 ... (remaining 5516 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 771 0.058 - 0.116: 394 0.116 - 0.175: 186 0.175 - 0.233: 48 0.233 - 0.291: 13 Chirality restraints: 1412 Sorted by residual: chirality pdb=" CA ASN A 243 " pdb=" N ASN A 243 " pdb=" C ASN A 243 " pdb=" CB ASN A 243 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CA GLN B 551 " pdb=" N GLN B 551 " pdb=" C GLN B 551 " pdb=" CB GLN B 551 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CA ASN B 243 " pdb=" N ASN B 243 " pdb=" C ASN B 243 " pdb=" CB ASN B 243 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 1409 not shown) Planarity restraints: 1657 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C LBV A1000 " 0.063 2.00e-02 2.50e+03 2.16e-01 1.05e+03 pdb=" C2C LBV A1000 " -0.100 2.00e-02 2.50e+03 pdb=" C3C LBV A1000 " 0.083 2.00e-02 2.50e+03 pdb=" C4C LBV A1000 " -0.068 2.00e-02 2.50e+03 pdb=" CAC LBV A1000 " -0.376 2.00e-02 2.50e+03 pdb=" CHC LBV A1000 " 0.254 2.00e-02 2.50e+03 pdb=" CHD LBV A1000 " -0.218 2.00e-02 2.50e+03 pdb=" CMC LBV A1000 " 0.377 2.00e-02 2.50e+03 pdb=" N_C LBV A1000 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C LBV B1000 " 0.052 2.00e-02 2.50e+03 1.63e-01 5.97e+02 pdb=" C2C LBV B1000 " -0.073 2.00e-02 2.50e+03 pdb=" C3C LBV B1000 " 0.063 2.00e-02 2.50e+03 pdb=" C4C LBV B1000 " -0.054 2.00e-02 2.50e+03 pdb=" CAC LBV B1000 " -0.282 2.00e-02 2.50e+03 pdb=" CHC LBV B1000 " 0.173 2.00e-02 2.50e+03 pdb=" CHD LBV B1000 " -0.181 2.00e-02 2.50e+03 pdb=" CMC LBV B1000 " 0.286 2.00e-02 2.50e+03 pdb=" N_C LBV B1000 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D LBV B1000 " -0.010 2.00e-02 2.50e+03 1.47e-01 4.89e+02 pdb=" C2D LBV B1000 " -0.044 2.00e-02 2.50e+03 pdb=" C3D LBV B1000 " 0.014 2.00e-02 2.50e+03 pdb=" C4D LBV B1000 " -0.035 2.00e-02 2.50e+03 pdb=" CAD LBV B1000 " 0.102 2.00e-02 2.50e+03 pdb=" CHD LBV B1000 " 0.257 2.00e-02 2.50e+03 pdb=" CMD LBV B1000 " -0.102 2.00e-02 2.50e+03 pdb=" N_D LBV B1000 " -0.301 2.00e-02 2.50e+03 pdb=" O_D LBV B1000 " 0.121 2.00e-02 2.50e+03 ... (remaining 1654 not shown) Histogram of nonbonded interaction distances: 2.60 - 3.06: 4021 3.06 - 3.52: 9099 3.52 - 3.98: 13399 3.98 - 4.44: 15372 4.44 - 4.90: 25170 Nonbonded interactions: 67061 Sorted by model distance: nonbonded pdb=" O GLY A 527 " pdb=" OG1 THR B 589 " model vdw 2.602 3.040 nonbonded pdb=" N ALA B 356 " pdb=" N LEU B 357 " model vdw 2.606 2.560 nonbonded pdb=" N ALA A 356 " pdb=" N LEU A 357 " model vdw 2.607 2.560 nonbonded pdb=" N GLY A 270 " pdb=" O HIS A 291 " model vdw 2.610 3.120 nonbonded pdb=" N GLY B 270 " pdb=" O HIS B 291 " model vdw 2.611 3.120 ... (remaining 67056 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 'B' and (resid 7 through 106 or resid 109 through 1000)) } 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 group one per residue 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: 6.900 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: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.310 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.074 9223 Z= 0.504 Angle : 1.383 6.790 12611 Z= 0.934 Chirality : 0.084 0.291 1412 Planarity : 0.010 0.216 1657 Dihedral : 18.216 79.266 3383 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.71 % Favored : 95.11 % Rotamer: Outliers : 3.45 % Allowed : 12.18 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.09 (0.19), residues: 1146 helix: -4.02 (0.14), residues: 436 sheet: 0.01 (0.35), residues: 178 loop : -2.44 (0.21), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 141 TYR 0.017 0.002 TYR A 588 PHE 0.014 0.002 PHE A 145 TRP 0.009 0.002 TRP A 284 HIS 0.008 0.001 HIS B 335 Details of bonding type rmsd covalent geometry : bond 0.00758 ( 9223) covalent geometry : angle 1.38312 (12611) hydrogen bonds : bond 0.33024 ( 376) hydrogen bonds : angle 10.23071 ( 1068) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 124 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ILE cc_start: 0.8239 (mm) cc_final: 0.7799 (mm) REVERT: A 45 ASP cc_start: 0.8033 (t70) cc_final: 0.7510 (t0) REVERT: A 222 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.8065 (pmm150) REVERT: A 444 GLU cc_start: 0.8985 (OUTLIER) cc_final: 0.8187 (tp30) REVERT: A 476 LYS cc_start: 0.7886 (mttt) cc_final: 0.7002 (mttp) REVERT: A 479 TYR cc_start: 0.8608 (m-80) cc_final: 0.7193 (m-80) REVERT: A 489 GLU cc_start: 0.9119 (tt0) cc_final: 0.8716 (tp30) REVERT: A 522 GLU cc_start: 0.8782 (mm-30) cc_final: 0.8374 (tm-30) REVERT: A 526 TYR cc_start: 0.7969 (OUTLIER) cc_final: 0.7124 (t80) REVERT: A 588 TYR cc_start: 0.7104 (m-80) cc_final: 0.6670 (m-80) REVERT: B 24 CYS cc_start: 0.8689 (p) cc_final: 0.8338 (p) REVERT: B 381 GLU cc_start: 0.8767 (mm-30) cc_final: 0.8510 (mp0) REVERT: B 477 ARG cc_start: 0.8057 (mtt180) cc_final: 0.7820 (ptp90) REVERT: B 512 LEU cc_start: 0.8810 (mt) cc_final: 0.8524 (tp) REVERT: B 524 ARG cc_start: 0.9127 (mtt180) cc_final: 0.8756 (tpp-160) REVERT: B 526 TYR cc_start: 0.8189 (OUTLIER) cc_final: 0.7776 (t80) outliers start: 32 outliers final: 5 residues processed: 150 average time/residue: 0.1148 time to fit residues: 22.6893 Evaluate side-chains 80 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 444 GLU Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 526 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 113 optimal weight: 0.1980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 HIS B 72 GLN B 290 HIS B 525 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.125324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.096426 restraints weight = 20726.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.098050 restraints weight = 12558.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.098362 restraints weight = 10421.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.098999 restraints weight = 7272.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.101616 restraints weight = 6403.807| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9223 Z= 0.145 Angle : 0.663 8.943 12611 Z= 0.337 Chirality : 0.042 0.131 1412 Planarity : 0.004 0.032 1657 Dihedral : 7.403 67.183 1322 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.18 % Favored : 97.64 % Rotamer: Outliers : 2.05 % Allowed : 16.92 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.32 (0.22), residues: 1146 helix: -2.12 (0.20), residues: 450 sheet: 0.69 (0.39), residues: 164 loop : -1.65 (0.24), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 566 TYR 0.019 0.002 TYR B 263 PHE 0.014 0.001 PHE B 528 TRP 0.023 0.002 TRP B 523 HIS 0.010 0.001 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 9223) covalent geometry : angle 0.66269 (12611) hydrogen bonds : bond 0.06204 ( 376) hydrogen bonds : angle 6.02625 ( 1068) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 MET cc_start: 0.8060 (ptp) cc_final: 0.7838 (ptt) REVERT: A 476 LYS cc_start: 0.8183 (mttt) cc_final: 0.7418 (mttp) REVERT: A 479 TYR cc_start: 0.8059 (m-80) cc_final: 0.7608 (m-80) REVERT: A 526 TYR cc_start: 0.7077 (OUTLIER) cc_final: 0.6538 (t80) REVERT: A 588 TYR cc_start: 0.7069 (m-80) cc_final: 0.5965 (m-80) REVERT: B 256 THR cc_start: 0.8760 (m) cc_final: 0.8367 (p) REVERT: B 526 TYR cc_start: 0.8208 (OUTLIER) cc_final: 0.7702 (t80) outliers start: 19 outliers final: 7 residues processed: 90 average time/residue: 0.0999 time to fit residues: 12.5623 Evaluate side-chains 68 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 526 TYR Chi-restraints excluded: chain B residue 588 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 3 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 chunk 109 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 HIS ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 291 HIS B 532 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.122276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.094112 restraints weight = 21061.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.096719 restraints weight = 13583.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.096516 restraints weight = 10577.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.096909 restraints weight = 7224.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.097364 restraints weight = 6355.078| |-----------------------------------------------------------------------------| r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9223 Z= 0.196 Angle : 0.649 8.791 12611 Z= 0.327 Chirality : 0.044 0.151 1412 Planarity : 0.005 0.062 1657 Dihedral : 6.681 64.075 1309 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.14 % Favored : 96.68 % Rotamer: Outliers : 2.37 % Allowed : 16.70 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.45 (0.23), residues: 1146 helix: -1.17 (0.22), residues: 448 sheet: 0.85 (0.40), residues: 165 loop : -1.28 (0.25), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 510 TYR 0.025 0.002 TYR B 176 PHE 0.015 0.002 PHE A 544 TRP 0.013 0.002 TRP A 434 HIS 0.006 0.001 HIS B 38 Details of bonding type rmsd covalent geometry : bond 0.00463 ( 9223) covalent geometry : angle 0.64867 (12611) hydrogen bonds : bond 0.05570 ( 376) hydrogen bonds : angle 5.60819 ( 1068) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 66 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 476 LYS cc_start: 0.8109 (mttt) cc_final: 0.7642 (mttp) REVERT: A 512 LEU cc_start: 0.8224 (mp) cc_final: 0.7972 (tp) REVERT: A 526 TYR cc_start: 0.7104 (OUTLIER) cc_final: 0.6430 (t80) REVERT: A 560 ASP cc_start: 0.6715 (OUTLIER) cc_final: 0.6510 (m-30) REVERT: A 588 TYR cc_start: 0.6924 (m-80) cc_final: 0.6336 (m-80) REVERT: B 526 TYR cc_start: 0.8299 (OUTLIER) cc_final: 0.7616 (t80) REVERT: B 534 MET cc_start: 0.9117 (tpp) cc_final: 0.8555 (tpp) outliers start: 22 outliers final: 8 residues processed: 84 average time/residue: 0.1165 time to fit residues: 13.6912 Evaluate side-chains 71 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 560 ASP Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 526 TYR Chi-restraints excluded: chain B residue 588 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 55 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 57 optimal weight: 10.0000 chunk 107 optimal weight: 0.2980 chunk 67 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS B 262 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.123218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.090785 restraints weight = 21058.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.091301 restraints weight = 11787.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.093952 restraints weight = 8059.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.093578 restraints weight = 6389.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.093671 restraints weight = 6028.997| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9223 Z= 0.142 Angle : 0.577 9.234 12611 Z= 0.286 Chirality : 0.041 0.128 1412 Planarity : 0.004 0.051 1657 Dihedral : 6.456 64.335 1309 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.01 % Favored : 97.91 % Rotamer: Outliers : 2.80 % Allowed : 17.13 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.24), residues: 1146 helix: -0.53 (0.23), residues: 456 sheet: 1.07 (0.40), residues: 163 loop : -1.05 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 222 TYR 0.018 0.002 TYR B 176 PHE 0.013 0.001 PHE A 544 TRP 0.010 0.001 TRP A 284 HIS 0.005 0.001 HIS B 38 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 9223) covalent geometry : angle 0.57656 (12611) hydrogen bonds : bond 0.04561 ( 376) hydrogen bonds : angle 5.28353 ( 1068) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 65 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.6660 (pmm150) REVERT: A 512 LEU cc_start: 0.8083 (mp) cc_final: 0.7864 (tp) REVERT: A 526 TYR cc_start: 0.7176 (OUTLIER) cc_final: 0.6497 (t80) REVERT: A 588 TYR cc_start: 0.6982 (m-80) cc_final: 0.6266 (m-80) REVERT: B 526 TYR cc_start: 0.8372 (OUTLIER) cc_final: 0.7628 (t80) outliers start: 26 outliers final: 13 residues processed: 87 average time/residue: 0.1006 time to fit residues: 12.3229 Evaluate side-chains 77 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 526 TYR Chi-restraints excluded: chain B residue 588 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 84 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 97 optimal weight: 0.2980 chunk 106 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 chunk 108 optimal weight: 8.9990 chunk 1 optimal weight: 0.8980 chunk 38 optimal weight: 0.0980 chunk 76 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.124191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.091330 restraints weight = 20876.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.093407 restraints weight = 11171.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.095016 restraints weight = 7364.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.094782 restraints weight = 6505.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.094939 restraints weight = 5948.906| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9223 Z= 0.111 Angle : 0.559 9.585 12611 Z= 0.272 Chirality : 0.040 0.126 1412 Planarity : 0.004 0.049 1657 Dihedral : 6.179 64.761 1309 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.16 % Allowed : 17.78 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.24), residues: 1146 helix: -0.14 (0.23), residues: 465 sheet: 0.91 (0.38), residues: 183 loop : -0.78 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 310 TYR 0.016 0.002 TYR A 479 PHE 0.014 0.001 PHE A 544 TRP 0.009 0.001 TRP B 523 HIS 0.003 0.001 HIS A 334 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 9223) covalent geometry : angle 0.55881 (12611) hydrogen bonds : bond 0.04012 ( 376) hydrogen bonds : angle 5.05128 ( 1068) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 62 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.6574 (pmm150) REVERT: A 512 LEU cc_start: 0.8123 (mp) cc_final: 0.7889 (tt) REVERT: A 526 TYR cc_start: 0.7268 (OUTLIER) cc_final: 0.6284 (t80) REVERT: A 588 TYR cc_start: 0.7025 (m-80) cc_final: 0.6371 (m-80) REVERT: B 189 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7268 (tt0) REVERT: B 520 ASN cc_start: 0.4775 (OUTLIER) cc_final: 0.4482 (t0) REVERT: B 523 TRP cc_start: 0.7819 (t60) cc_final: 0.7605 (t60) REVERT: B 526 TYR cc_start: 0.8435 (OUTLIER) cc_final: 0.7821 (t80) REVERT: B 534 MET cc_start: 0.9107 (tpp) cc_final: 0.8705 (tpp) outliers start: 20 outliers final: 11 residues processed: 78 average time/residue: 0.1002 time to fit residues: 11.1966 Evaluate side-chains 75 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 520 ASN Chi-restraints excluded: chain B residue 526 TYR Chi-restraints excluded: chain B residue 588 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 77 optimal weight: 0.9990 chunk 60 optimal weight: 0.3980 chunk 51 optimal weight: 10.0000 chunk 3 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 54 optimal weight: 0.0980 chunk 63 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.124653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.097198 restraints weight = 20954.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.098628 restraints weight = 13367.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.098868 restraints weight = 11449.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.099941 restraints weight = 7787.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.100150 restraints weight = 6742.706| |-----------------------------------------------------------------------------| r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9223 Z= 0.105 Angle : 0.536 10.064 12611 Z= 0.260 Chirality : 0.040 0.126 1412 Planarity : 0.004 0.046 1657 Dihedral : 5.909 65.362 1309 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.48 % Allowed : 17.46 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.24), residues: 1146 helix: 0.22 (0.23), residues: 466 sheet: 0.97 (0.38), residues: 183 loop : -0.62 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 310 TYR 0.014 0.002 TYR A 479 PHE 0.015 0.001 PHE A 544 TRP 0.009 0.001 TRP B 523 HIS 0.003 0.001 HIS B 334 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 9223) covalent geometry : angle 0.53638 (12611) hydrogen bonds : bond 0.03681 ( 376) hydrogen bonds : angle 4.85637 ( 1068) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 58 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 222 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.6126 (pmm150) REVERT: A 526 TYR cc_start: 0.7005 (OUTLIER) cc_final: 0.6136 (t80) REVERT: A 588 TYR cc_start: 0.6944 (m-80) cc_final: 0.6268 (m-80) REVERT: B 189 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7400 (tt0) REVERT: B 520 ASN cc_start: 0.4991 (OUTLIER) cc_final: 0.4690 (t0) REVERT: B 526 TYR cc_start: 0.8399 (OUTLIER) cc_final: 0.7771 (t80) REVERT: B 534 MET cc_start: 0.9184 (tpp) cc_final: 0.8789 (tpp) outliers start: 23 outliers final: 13 residues processed: 78 average time/residue: 0.0972 time to fit residues: 10.9021 Evaluate side-chains 72 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 54 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 520 ASN Chi-restraints excluded: chain B residue 526 TYR Chi-restraints excluded: chain B residue 588 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 79 optimal weight: 0.5980 chunk 18 optimal weight: 5.9990 chunk 85 optimal weight: 0.0000 chunk 101 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 69 optimal weight: 0.0670 chunk 73 optimal weight: 0.8980 overall best weight: 0.4722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.125031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.093912 restraints weight = 20992.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.095075 restraints weight = 11874.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.095665 restraints weight = 8021.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.096367 restraints weight = 7449.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.096507 restraints weight = 6740.907| |-----------------------------------------------------------------------------| r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9223 Z= 0.101 Angle : 0.538 10.801 12611 Z= 0.258 Chirality : 0.040 0.166 1412 Planarity : 0.004 0.043 1657 Dihedral : 5.700 65.065 1309 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.26 % Allowed : 18.00 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.24), residues: 1146 helix: 0.46 (0.23), residues: 466 sheet: 1.03 (0.39), residues: 183 loop : -0.52 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 524 TYR 0.013 0.002 TYR B 472 PHE 0.029 0.001 PHE A 570 TRP 0.019 0.001 TRP B 523 HIS 0.004 0.001 HIS A 334 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 9223) covalent geometry : angle 0.53758 (12611) hydrogen bonds : bond 0.03551 ( 376) hydrogen bonds : angle 4.75786 ( 1068) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 55 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 ILE cc_start: 0.8291 (mm) cc_final: 0.7980 (mm) REVERT: A 222 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.6264 (pmm150) REVERT: A 479 TYR cc_start: 0.8107 (m-80) cc_final: 0.7820 (m-10) REVERT: B 189 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7363 (tt0) REVERT: B 222 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.7987 (pmm150) REVERT: B 526 TYR cc_start: 0.8455 (OUTLIER) cc_final: 0.7985 (t80) REVERT: B 534 MET cc_start: 0.9221 (tpp) cc_final: 0.8847 (tpp) outliers start: 21 outliers final: 13 residues processed: 73 average time/residue: 0.1014 time to fit residues: 10.6177 Evaluate side-chains 72 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 55 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 526 TYR Chi-restraints excluded: chain B residue 588 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 92 optimal weight: 2.9990 chunk 90 optimal weight: 0.2980 chunk 112 optimal weight: 0.0040 chunk 16 optimal weight: 0.6980 chunk 24 optimal weight: 5.9990 chunk 1 optimal weight: 0.2980 chunk 81 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 96 optimal weight: 0.1980 overall best weight: 0.2992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 HIS B 520 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.126171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.098606 restraints weight = 20859.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.100545 restraints weight = 12735.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.100803 restraints weight = 9848.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.101430 restraints weight = 7330.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.103109 restraints weight = 6386.780| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9223 Z= 0.091 Angle : 0.532 10.857 12611 Z= 0.252 Chirality : 0.040 0.124 1412 Planarity : 0.004 0.042 1657 Dihedral : 5.377 65.045 1307 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.72 % Allowed : 19.07 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.25), residues: 1146 helix: 0.77 (0.24), residues: 467 sheet: 1.21 (0.39), residues: 182 loop : -0.46 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 477 TYR 0.012 0.002 TYR B 472 PHE 0.017 0.001 PHE A 570 TRP 0.027 0.001 TRP B 523 HIS 0.003 0.001 HIS B 334 Details of bonding type rmsd covalent geometry : bond 0.00205 ( 9223) covalent geometry : angle 0.53225 (12611) hydrogen bonds : bond 0.03120 ( 376) hydrogen bonds : angle 4.57811 ( 1068) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: A 19 ILE cc_start: 0.8300 (mm) cc_final: 0.7993 (mm) REVERT: A 411 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8726 (tp) REVERT: A 479 TYR cc_start: 0.8025 (m-80) cc_final: 0.7815 (m-10) REVERT: A 588 TYR cc_start: 0.7225 (m-80) cc_final: 0.6797 (t80) REVERT: B 526 TYR cc_start: 0.8438 (OUTLIER) cc_final: 0.7959 (t80) REVERT: B 534 MET cc_start: 0.9175 (tpp) cc_final: 0.8820 (tpp) REVERT: B 588 TYR cc_start: 0.6771 (OUTLIER) cc_final: 0.5442 (t80) outliers start: 16 outliers final: 13 residues processed: 72 average time/residue: 0.0993 time to fit residues: 10.3823 Evaluate side-chains 69 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 53 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 526 TYR Chi-restraints excluded: chain B residue 588 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 30 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 7 optimal weight: 0.0770 chunk 12 optimal weight: 0.3980 chunk 46 optimal weight: 0.6980 chunk 69 optimal weight: 0.0870 chunk 78 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.126078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.098835 restraints weight = 20826.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.100844 restraints weight = 12933.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.100964 restraints weight = 10324.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.101554 restraints weight = 7382.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.103831 restraints weight = 6480.110| |-----------------------------------------------------------------------------| r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9223 Z= 0.097 Angle : 0.537 11.599 12611 Z= 0.256 Chirality : 0.040 0.147 1412 Planarity : 0.004 0.038 1657 Dihedral : 5.351 65.155 1307 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.05 % Allowed : 19.40 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.25), residues: 1146 helix: 0.88 (0.24), residues: 468 sheet: 1.25 (0.39), residues: 182 loop : -0.44 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 328 TYR 0.012 0.002 TYR B 472 PHE 0.015 0.001 PHE A 570 TRP 0.019 0.001 TRP B 523 HIS 0.004 0.001 HIS A 334 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 9223) covalent geometry : angle 0.53669 (12611) hydrogen bonds : bond 0.03124 ( 376) hydrogen bonds : angle 4.52737 ( 1068) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 59 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: A 19 ILE cc_start: 0.8312 (mm) cc_final: 0.7975 (mm) REVERT: A 411 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8715 (tp) REVERT: A 588 TYR cc_start: 0.7257 (m-80) cc_final: 0.6856 (t80) REVERT: B 189 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7343 (tt0) REVERT: B 526 TYR cc_start: 0.8411 (OUTLIER) cc_final: 0.7924 (t80) REVERT: B 534 MET cc_start: 0.9160 (tpp) cc_final: 0.8919 (tpp) REVERT: B 588 TYR cc_start: 0.6865 (OUTLIER) cc_final: 0.5500 (t80) outliers start: 19 outliers final: 12 residues processed: 74 average time/residue: 0.0974 time to fit residues: 10.5080 Evaluate side-chains 69 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 53 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 526 TYR Chi-restraints excluded: chain B residue 588 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 50 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 36 optimal weight: 0.0770 chunk 107 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 112 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 96 optimal weight: 0.1980 chunk 12 optimal weight: 2.9990 chunk 13 optimal weight: 0.3980 chunk 102 optimal weight: 0.2980 overall best weight: 0.3138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.126562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.099485 restraints weight = 20788.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.100702 restraints weight = 13225.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.101283 restraints weight = 10518.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.101937 restraints weight = 7719.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.102537 restraints weight = 6810.752| |-----------------------------------------------------------------------------| r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.4169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9223 Z= 0.095 Angle : 0.541 12.315 12611 Z= 0.258 Chirality : 0.040 0.122 1412 Planarity : 0.004 0.038 1657 Dihedral : 5.298 64.898 1307 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.62 % Allowed : 20.15 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.25), residues: 1146 helix: 1.04 (0.24), residues: 467 sheet: 1.30 (0.38), residues: 183 loop : -0.33 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 310 TYR 0.012 0.002 TYR B 472 PHE 0.014 0.001 PHE A 570 TRP 0.019 0.001 TRP B 523 HIS 0.003 0.001 HIS A 334 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 9223) covalent geometry : angle 0.54127 (12611) hydrogen bonds : bond 0.03042 ( 376) hydrogen bonds : angle 4.45898 ( 1068) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: A 19 ILE cc_start: 0.8259 (mm) cc_final: 0.7942 (mm) REVERT: A 588 TYR cc_start: 0.7246 (m-80) cc_final: 0.6899 (t80) REVERT: B 189 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7282 (tt0) REVERT: B 523 TRP cc_start: 0.7946 (t60) cc_final: 0.7378 (t60) REVERT: B 588 TYR cc_start: 0.6813 (OUTLIER) cc_final: 0.5822 (t80) outliers start: 15 outliers final: 12 residues processed: 66 average time/residue: 0.0959 time to fit residues: 9.3269 Evaluate side-chains 66 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 588 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 87 optimal weight: 0.5980 chunk 32 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 80 optimal weight: 0.0000 chunk 71 optimal weight: 0.8980 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.125307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.098408 restraints weight = 20576.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.099327 restraints weight = 13483.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.099902 restraints weight = 11108.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.100634 restraints weight = 7825.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.101060 restraints weight = 6915.545| |-----------------------------------------------------------------------------| r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.4227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9223 Z= 0.116 Angle : 0.568 12.575 12611 Z= 0.269 Chirality : 0.040 0.127 1412 Planarity : 0.004 0.038 1657 Dihedral : 5.261 65.324 1305 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.94 % Allowed : 20.26 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.25), residues: 1146 helix: 1.07 (0.24), residues: 473 sheet: 1.19 (0.38), residues: 183 loop : -0.29 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 310 TYR 0.014 0.002 TYR B 176 PHE 0.014 0.001 PHE A 570 TRP 0.016 0.001 TRP B 523 HIS 0.004 0.001 HIS B 533 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 9223) covalent geometry : angle 0.56754 (12611) hydrogen bonds : bond 0.03344 ( 376) hydrogen bonds : angle 4.49754 ( 1068) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1653.44 seconds wall clock time: 29 minutes 20.93 seconds (1760.93 seconds total)