Starting phenix.real_space_refine on Thu Mar 13 11:42:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6jt0_9883/03_2025/6jt0_9883.cif Found real_map, /net/cci-nas-00/data/ceres_data/6jt0_9883/03_2025/6jt0_9883.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6jt0_9883/03_2025/6jt0_9883.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6jt0_9883/03_2025/6jt0_9883.map" model { file = "/net/cci-nas-00/data/ceres_data/6jt0_9883/03_2025/6jt0_9883.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6jt0_9883/03_2025/6jt0_9883.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 1 7.16 5 S 59 5.16 5 C 5529 2.51 5 N 1462 2.21 5 O 1551 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8602 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4087 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 542, 4084 Classifications: {'peptide': 542} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 515} Chain breaks: 5 Unresolved non-hydrogen bonds: 217 Unresolved non-hydrogen angles: 267 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 18, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 166 Conformer: "B" Number of residues, atoms: 542, 4084 Classifications: {'peptide': 542} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 515} Chain breaks: 5 Unresolved non-hydrogen bonds: 217 Unresolved non-hydrogen angles: 267 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 18, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 166 bond proxies already assigned to first conformer: 4165 Chain: "B" Number of atoms: 4472 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 576, 4468 Classifications: {'peptide': 576} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 552} Chain breaks: 2 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 114 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 16, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 84 Conformer: "B" Number of residues, atoms: 576, 4468 Classifications: {'peptide': 576} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 552} Chain breaks: 2 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 114 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 16, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 84 bond proxies already assigned to first conformer: 4553 Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N GLU A 147 " occ=0.91 ... (3 atoms not shown) pdb=" CB GLU A 147 " occ=0.91 Time building chain proxies: 10.07, per 1000 atoms: 1.17 Number of scatterers: 8602 At special positions: 0 Unit cell: (148.39, 96.14, 74.195, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 1 26.01 S 59 16.00 O 1551 8.00 N 1462 7.00 C 5529 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: 2.39 Conformation dependent library (CDL) restraints added in 2.1 seconds 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2108 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 10 sheets defined 48.2% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 70 through 83 Processing helix chain 'A' and resid 85 through 101 Processing helix chain 'A' and resid 115 through 126 Processing helix chain 'A' and resid 128 through 149 removed outlier: 3.588A pdb=" N ASP A 148 " --> pdb=" O CYS A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 156 Processing helix chain 'A' and resid 158 through 174 removed outlier: 4.595A pdb=" N SER A 167 " --> pdb=" O LEU A 163 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THR A 168 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 227 Processing helix chain 'A' and resid 237 through 242 removed outlier: 4.090A pdb=" N HIS A 241 " --> pdb=" O PRO A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 286 Processing helix chain 'A' and resid 302 through 309 Processing helix chain 'A' and resid 319 through 323 removed outlier: 3.845A pdb=" N TYR A 323 " --> pdb=" O ASN A 319 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 319 through 323' Processing helix chain 'A' and resid 334 through 341 removed outlier: 4.043A pdb=" N MET A 341 " --> pdb=" O GLY A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 394 removed outlier: 3.925A pdb=" N THR A 394 " --> pdb=" O GLU A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 419 removed outlier: 4.471A pdb=" N GLY A 416 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLU A 417 " --> pdb=" O VAL A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 458 removed outlier: 3.941A pdb=" N GLY A 430 " --> pdb=" O LYS A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 468 removed outlier: 3.621A pdb=" N GLN A 468 " --> pdb=" O GLN A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 496 removed outlier: 3.771A pdb=" N ILE A 493 " --> pdb=" O GLY A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 521 Processing helix chain 'A' and resid 544 through 561 Processing helix chain 'A' and resid 598 through 609 removed outlier: 3.970A pdb=" N THR A 602 " --> pdb=" O GLY A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 627 removed outlier: 3.912A pdb=" N LEU A 625 " --> pdb=" O THR A 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 30 removed outlier: 3.675A pdb=" N ASN B 6 " --> pdb=" O TYR B 2 " (cutoff:3.500A) Proline residue: B 19 - end of helix removed outlier: 3.931A pdb=" N TRP B 22 " --> pdb=" O GLY B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 59 removed outlier: 3.927A pdb=" N THR B 48 " --> pdb=" O ASP B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 81 Processing helix chain 'B' and resid 83 through 90 Processing helix chain 'B' and resid 93 through 100 Processing helix chain 'B' and resid 102 through 112 removed outlier: 3.521A pdb=" N ASP B 106 " --> pdb=" O ASP B 102 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE B 111 " --> pdb=" O HIS B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 157 Processing helix chain 'B' and resid 210 through 217 Processing helix chain 'B' and resid 233 through 240 Processing helix chain 'B' and resid 241 through 244 Processing helix chain 'B' and resid 264 through 271 Processing helix chain 'B' and resid 329 through 337 removed outlier: 3.757A pdb=" N LEU B 333 " --> pdb=" O ASN B 329 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR B 334 " --> pdb=" O LEU B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 354 removed outlier: 4.173A pdb=" N ASP B 351 " --> pdb=" O ASP B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 395 removed outlier: 4.209A pdb=" N TYR B 363 " --> pdb=" O PHE B 359 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU B 378 " --> pdb=" O ASP B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 407 Processing helix chain 'B' and resid 429 through 437 removed outlier: 3.603A pdb=" N HIS B 437 " --> pdb=" O PHE B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 461 removed outlier: 3.709A pdb=" N LYS B 445 " --> pdb=" O GLU B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 508 removed outlier: 4.028A pdb=" N GLY B 508 " --> pdb=" O MET B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 557 removed outlier: 3.986A pdb=" N ASN B 548 " --> pdb=" O GLY B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 573 Processing sheet with id=AA1, first strand: chain 'A' and resid 189 through 193 removed outlier: 4.003A pdb=" N SER A 189 " --> pdb=" O PHE A 205 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 298 through 300 removed outlier: 6.744A pdb=" N MET A 291 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE A 290 " --> pdb=" O PHE A 381 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 475 through 482 removed outlier: 5.484A pdb=" N LYS A 476 " --> pdb=" O ALA A 584 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ALA A 584 " --> pdb=" O LYS A 476 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N SER A 478 " --> pdb=" O VAL A 582 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N VAL A 582 " --> pdb=" O SER A 478 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE A 583 " --> pdb=" O PHE A 597 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 486 through 487 removed outlier: 7.599A pdb=" N MET A 573 " --> pdb=" O LYS A 615 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N ASN A 617 " --> pdb=" O MET A 573 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE A 575 " --> pdb=" O ASN A 617 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ILE A 616 " --> pdb=" O LEU A 657 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 523 through 525 removed outlier: 3.741A pdb=" N TYR A 523 " --> pdb=" O ALA A 535 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N CYS A 533 " --> pdb=" O VAL A 525 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 123 through 124 removed outlier: 6.612A pdb=" N GLN B 178 " --> pdb=" O ILE B 167 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 232 removed outlier: 6.672A pdb=" N ILE B 222 " --> pdb=" O THR B 230 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N CYS B 232 " --> pdb=" O HIS B 220 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N HIS B 220 " --> pdb=" O CYS B 232 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE B 223 " --> pdb=" O ILE B 319 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 470 through 471 removed outlier: 3.737A pdb=" N ASN B 419 " --> pdb=" O GLY B 526 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLY B 526 " --> pdb=" O ASN B 419 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N THR B 421 " --> pdb=" O HIS B 524 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N HIS B 524 " --> pdb=" O THR B 421 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LEU B 423 " --> pdb=" O GLY B 522 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLY B 522 " --> pdb=" O LEU B 423 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL B 529 " --> pdb=" O PHE B 543 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 470 through 471 removed outlier: 3.737A pdb=" N ASN B 419 " --> pdb=" O GLY B 526 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLY B 526 " --> pdb=" O ASN B 419 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N THR B 421 " --> pdb=" O HIS B 524 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N HIS B 524 " --> pdb=" O THR B 421 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LEU B 423 " --> pdb=" O GLY B 522 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLY B 522 " --> pdb=" O LEU B 423 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE B 521 " --> pdb=" O ASN B 563 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N SER B 565 " --> pdb=" O ILE B 521 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ILE B 523 " --> pdb=" O SER B 565 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ILE B 562 " --> pdb=" O LEU B 604 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL B 601 " --> pdb=" O GLY B 588 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLY B 588 " --> pdb=" O VAL B 601 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N PHE B 603 " --> pdb=" O HIS B 586 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N HIS B 586 " --> pdb=" O PHE B 603 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N SER B 605 " --> pdb=" O LEU B 584 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N LEU B 584 " --> pdb=" O SER B 605 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 511 through 512 457 hydrogen bonds defined for protein. 1298 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.80 Time building geometry restraints manager: 2.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.38: 3085 1.38 - 1.55: 5579 1.55 - 1.71: 26 1.71 - 1.88: 90 1.88 - 2.05: 4 Bond restraints: 8784 Sorted by residual: bond pdb=" C ASP B 106 " pdb=" O ASP B 106 " ideal model delta sigma weight residual 1.237 1.266 -0.029 1.17e-02 7.31e+03 6.10e+00 bond pdb=" C ALA B 103 " pdb=" O ALA B 103 " ideal model delta sigma weight residual 1.237 1.263 -0.026 1.17e-02 7.31e+03 4.90e+00 bond pdb=" CA ALA B 103 " pdb=" C ALA B 103 " ideal model delta sigma weight residual 1.523 1.552 -0.028 1.30e-02 5.92e+03 4.74e+00 bond pdb=" CA GLU A 230 " pdb=" CB GLU A 230 " ideal model delta sigma weight residual 1.524 1.551 -0.026 1.22e-02 6.72e+03 4.62e+00 bond pdb=" CA THR B 110 " pdb=" C THR B 110 " ideal model delta sigma weight residual 1.523 1.551 -0.028 1.30e-02 5.92e+03 4.59e+00 ... (remaining 8779 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 11684 2.05 - 4.09: 207 4.09 - 6.14: 33 6.14 - 8.18: 9 8.18 - 10.23: 2 Bond angle restraints: 11935 Sorted by residual: angle pdb=" C THR B 110 " pdb=" N ILE B 111 " pdb=" CA ILE B 111 " ideal model delta sigma weight residual 120.56 130.79 -10.23 1.28e+00 6.10e-01 6.38e+01 angle pdb=" N VAL A 231 " pdb=" CA VAL A 231 " pdb=" C VAL A 231 " ideal model delta sigma weight residual 108.17 115.21 -7.04 1.46e+00 4.69e-01 2.33e+01 angle pdb=" C LEU B 338 " pdb=" N TYR B 339 " pdb=" CA TYR B 339 " ideal model delta sigma weight residual 121.54 128.89 -7.35 1.91e+00 2.74e-01 1.48e+01 angle pdb=" C LEU B 108 " pdb=" N ALA B 109 " pdb=" CA ALA B 109 " ideal model delta sigma weight residual 120.28 125.10 -4.82 1.34e+00 5.57e-01 1.29e+01 angle pdb=" N TYR B 395 " pdb=" CA TYR B 395 " pdb=" C TYR B 395 " ideal model delta sigma weight residual 110.06 115.00 -4.94 1.43e+00 4.89e-01 1.19e+01 ... (remaining 11930 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 4896 17.53 - 35.05: 289 35.05 - 52.58: 48 52.58 - 70.10: 12 70.10 - 87.63: 7 Dihedral angle restraints: 5252 sinusoidal: 1996 harmonic: 3256 Sorted by residual: dihedral pdb=" CA LEU A 398 " pdb=" C LEU A 398 " pdb=" N TYR A 399 " pdb=" CA TYR A 399 " ideal model delta harmonic sigma weight residual 180.00 151.13 28.87 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA ASP B 262 " pdb=" C ASP B 262 " pdb=" N ILE B 263 " pdb=" CA ILE B 263 " ideal model delta harmonic sigma weight residual -180.00 -155.07 -24.93 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA HIS A 655 " pdb=" C HIS A 655 " pdb=" N PHE A 656 " pdb=" CA PHE A 656 " ideal model delta harmonic sigma weight residual 180.00 155.11 24.89 0 5.00e+00 4.00e-02 2.48e+01 ... (remaining 5249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1037 0.044 - 0.088: 264 0.088 - 0.132: 82 0.132 - 0.176: 6 0.176 - 0.220: 1 Chirality restraints: 1390 Sorted by residual: chirality pdb=" CG LEU B 9 " pdb=" CB LEU B 9 " pdb=" CD1 LEU B 9 " pdb=" CD2 LEU B 9 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA PRO B 210 " pdb=" N PRO B 210 " pdb=" C PRO B 210 " pdb=" CB PRO B 210 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.65e-01 chirality pdb=" CA VAL B 564 " pdb=" N VAL B 564 " pdb=" C VAL B 564 " pdb=" CB VAL B 564 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.02e-01 ... (remaining 1387 not shown) Planarity restraints: 1515 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 250 " -0.037 5.00e-02 4.00e+02 5.65e-02 5.11e+00 pdb=" N PRO A 251 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 251 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 251 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 112 " -0.028 5.00e-02 4.00e+02 4.30e-02 2.96e+00 pdb=" N PRO B 113 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 113 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 113 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 328 " 0.025 5.00e-02 4.00e+02 3.82e-02 2.34e+00 pdb=" N PRO A 329 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 329 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 329 " 0.020 5.00e-02 4.00e+02 ... (remaining 1512 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1258 2.76 - 3.29: 8396 3.29 - 3.83: 13964 3.83 - 4.36: 15931 4.36 - 4.90: 27305 Nonbonded interactions: 66854 Sorted by model distance: nonbonded pdb=" NH2 ARG A 410 " pdb=" OD1 ASN B 100 " model vdw 2.225 3.120 nonbonded pdb=" O THR B 392 " pdb=" OG SER B 396 " model vdw 2.267 3.040 nonbonded pdb=" O SER A 581 " pdb=" ND2 ASN A 600 " model vdw 2.295 3.120 nonbonded pdb=" O LEU A 74 " pdb=" OG SER A 77 " model vdw 2.309 3.040 nonbonded pdb=" ND1 HIS B 524 " pdb=" OG SER B 565 " model vdw 2.335 3.120 ... (remaining 66849 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.30 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: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 30.290 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 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 : 0.004 0.100 8784 Z= 0.231 Angle : 0.710 10.228 11935 Z= 0.391 Chirality : 0.043 0.220 1390 Planarity : 0.004 0.057 1515 Dihedral : 12.208 87.630 3144 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.73 % Favored : 93.91 % Rotamer: Outliers : 4.73 % Allowed : 6.59 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.22), residues: 1101 helix: -1.01 (0.20), residues: 505 sheet: -2.10 (0.31), residues: 211 loop : -2.74 (0.27), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 602 HIS 0.004 0.001 HIS B 176 PHE 0.023 0.002 PHE A 458 TYR 0.016 0.002 TYR B 339 ARG 0.003 0.000 ARG B 360 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 178 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.9551 (pp) cc_final: 0.9186 (tt) REVERT: A 256 SER cc_start: 0.8985 (t) cc_final: 0.8331 (p) REVERT: A 309 MET cc_start: 0.8928 (ttm) cc_final: 0.8504 (tmm) REVERT: A 341 MET cc_start: 0.9062 (mmt) cc_final: 0.8707 (mmm) REVERT: A 384 SER cc_start: 0.9182 (m) cc_final: 0.8978 (p) REVERT: A 503 ILE cc_start: 0.9734 (mm) cc_final: 0.9468 (tt) REVERT: A 520 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8777 (tt) REVERT: A 557 MET cc_start: 0.9490 (mmt) cc_final: 0.9003 (tmm) REVERT: B 65 GLU cc_start: 0.9303 (mm-30) cc_final: 0.9073 (tp30) REVERT: B 69 MET cc_start: 0.9468 (mtm) cc_final: 0.9091 (ptm) REVERT: B 162 ILE cc_start: 0.9430 (pt) cc_final: 0.8938 (mm) REVERT: B 164 MET cc_start: 0.9129 (ttm) cc_final: 0.8891 (ttm) REVERT: B 243 LEU cc_start: 0.8978 (tt) cc_final: 0.8581 (pp) REVERT: B 338 LEU cc_start: 0.9191 (mt) cc_final: 0.8910 (mt) REVERT: B 373 THR cc_start: 0.9292 (m) cc_final: 0.9035 (p) REVERT: B 388 LYS cc_start: 0.8934 (ttmt) cc_final: 0.8615 (tppt) REVERT: B 423 LEU cc_start: 0.9667 (tt) cc_final: 0.9438 (tp) REVERT: B 424 PHE cc_start: 0.9273 (m-80) cc_final: 0.8741 (m-10) REVERT: B 478 LYS cc_start: 0.9289 (mttm) cc_final: 0.8762 (mmtm) REVERT: B 499 LEU cc_start: 0.9494 (tp) cc_final: 0.9061 (tp) REVERT: B 503 MET cc_start: 0.9462 (mtp) cc_final: 0.9098 (mtm) REVERT: B 505 GLU cc_start: 0.9620 (OUTLIER) cc_final: 0.9385 (mt-10) REVERT: B 537 MET cc_start: 0.8906 (mmm) cc_final: 0.8503 (tmm) REVERT: B 541 CYS cc_start: 0.9380 (m) cc_final: 0.8863 (m) REVERT: B 572 LEU cc_start: 0.9692 (mm) cc_final: 0.9441 (mm) REVERT: B 573 MET cc_start: 0.9467 (mmp) cc_final: 0.9226 (mmp) outliers start: 43 outliers final: 11 residues processed: 211 average time/residue: 0.1822 time to fit residues: 54.4402 Evaluate side-chains 116 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 505 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 0.0970 chunk 44 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 chunk 64 optimal weight: 0.6980 chunk 100 optimal weight: 0.5980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 HIS B 367 GLN ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 GLN B 563 ASN B 581 GLN ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.057161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.045141 restraints weight = 85814.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.047289 restraints weight = 37338.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.048763 restraints weight = 22038.395| |-----------------------------------------------------------------------------| r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2921 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2921 r_free = 0.2921 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.2919 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8784 Z= 0.207 Angle : 0.779 14.871 11935 Z= 0.369 Chirality : 0.045 0.195 1390 Planarity : 0.005 0.094 1515 Dihedral : 7.608 86.395 1231 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.09 % Favored : 95.64 % Rotamer: Outliers : 3.52 % Allowed : 14.84 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.24), residues: 1101 helix: 0.00 (0.21), residues: 520 sheet: -1.29 (0.32), residues: 217 loop : -2.41 (0.29), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 602 HIS 0.005 0.001 HIS B 498 PHE 0.030 0.002 PHE A 646 TYR 0.026 0.002 TYR B 569 ARG 0.007 0.000 ARG B 464 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 108 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.9463 (pp) cc_final: 0.9074 (tt) REVERT: A 236 MET cc_start: 0.8330 (mmm) cc_final: 0.8038 (mmm) REVERT: A 256 SER cc_start: 0.8874 (t) cc_final: 0.8375 (p) REVERT: A 384 SER cc_start: 0.8961 (m) cc_final: 0.8702 (p) REVERT: A 520 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8839 (tt) REVERT: A 556 MET cc_start: 0.9496 (ttm) cc_final: 0.9215 (mpp) REVERT: A 573 MET cc_start: 0.8909 (mmm) cc_final: 0.8426 (mmm) REVERT: B 1 MET cc_start: 0.9227 (tpp) cc_final: 0.8832 (tpp) REVERT: B 11 LEU cc_start: 0.9521 (tp) cc_final: 0.9274 (tp) REVERT: B 69 MET cc_start: 0.9161 (mtm) cc_final: 0.8530 (ptm) REVERT: B 320 LEU cc_start: 0.9312 (tp) cc_final: 0.9005 (tt) REVERT: B 478 LYS cc_start: 0.9360 (mttm) cc_final: 0.8903 (mmtm) REVERT: B 503 MET cc_start: 0.9322 (mtp) cc_final: 0.8997 (mtm) REVERT: B 541 CYS cc_start: 0.8383 (m) cc_final: 0.7936 (m) REVERT: B 572 LEU cc_start: 0.9394 (mm) cc_final: 0.9057 (mm) outliers start: 32 outliers final: 16 residues processed: 135 average time/residue: 0.1852 time to fit residues: 36.2730 Evaluate side-chains 104 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 563 ASN Chi-restraints excluded: chain B residue 568 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 40 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 44 optimal weight: 10.0000 chunk 46 optimal weight: 7.9990 chunk 13 optimal weight: 7.9990 chunk 82 optimal weight: 1.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 GLN ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.054167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.043284 restraints weight = 60466.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.045056 restraints weight = 31183.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.046249 restraints weight = 19750.547| |-----------------------------------------------------------------------------| r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2851 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2851 r_free = 0.2851 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.2846 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 8784 Z= 0.352 Angle : 0.811 12.256 11935 Z= 0.397 Chirality : 0.046 0.189 1390 Planarity : 0.005 0.065 1515 Dihedral : 7.104 81.533 1225 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.36 % Favored : 94.36 % Rotamer: Outliers : 3.41 % Allowed : 15.93 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.25), residues: 1101 helix: 0.70 (0.22), residues: 516 sheet: -1.18 (0.33), residues: 221 loop : -1.94 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 602 HIS 0.006 0.001 HIS B 266 PHE 0.028 0.002 PHE A 141 TYR 0.021 0.002 TYR A 399 ARG 0.006 0.001 ARG B 570 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 92 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.9508 (pp) cc_final: 0.9133 (tt) REVERT: A 236 MET cc_start: 0.8582 (mmm) cc_final: 0.8263 (mmm) REVERT: A 256 SER cc_start: 0.8997 (t) cc_final: 0.8459 (p) REVERT: A 520 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8865 (tt) REVERT: B 1 MET cc_start: 0.9194 (tpp) cc_final: 0.8252 (mmm) REVERT: B 11 LEU cc_start: 0.9549 (tp) cc_final: 0.9244 (tp) REVERT: B 164 MET cc_start: 0.8695 (ttm) cc_final: 0.8320 (ttm) REVERT: B 351 ASP cc_start: 0.8963 (m-30) cc_final: 0.8714 (t70) REVERT: B 478 LYS cc_start: 0.9478 (mttm) cc_final: 0.8940 (mmtm) REVERT: B 503 MET cc_start: 0.9302 (mtp) cc_final: 0.9097 (mtm) REVERT: B 541 CYS cc_start: 0.8378 (m) cc_final: 0.8002 (m) REVERT: B 572 LEU cc_start: 0.9436 (mm) cc_final: 0.9196 (mm) REVERT: B 592 MET cc_start: 0.7780 (mmm) cc_final: 0.7327 (mmm) outliers start: 31 outliers final: 21 residues processed: 119 average time/residue: 0.1739 time to fit residues: 30.8108 Evaluate side-chains 106 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 637 ARG Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 563 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 73 optimal weight: 0.7980 chunk 45 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 chunk 22 optimal weight: 0.4980 chunk 106 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 56 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 563 ASN ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.056207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.045171 restraints weight = 60100.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.047059 restraints weight = 30022.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.048321 restraints weight = 18723.282| |-----------------------------------------------------------------------------| r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2920 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2920 r_free = 0.2920 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2920 r_free = 0.2920 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.2920 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8784 Z= 0.193 Angle : 0.748 12.911 11935 Z= 0.349 Chirality : 0.043 0.188 1390 Planarity : 0.004 0.050 1515 Dihedral : 6.526 83.519 1225 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.09 % Favored : 95.73 % Rotamer: Outliers : 2.86 % Allowed : 17.91 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.25), residues: 1101 helix: 1.12 (0.23), residues: 513 sheet: -0.93 (0.34), residues: 221 loop : -1.66 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 22 HIS 0.004 0.001 HIS B 498 PHE 0.028 0.002 PHE A 141 TYR 0.017 0.002 TYR A 399 ARG 0.003 0.000 ARG B 464 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 94 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.9496 (pp) cc_final: 0.9130 (tt) REVERT: A 236 MET cc_start: 0.8651 (mmm) cc_final: 0.8368 (mmm) REVERT: A 256 SER cc_start: 0.9029 (t) cc_final: 0.8495 (p) REVERT: A 301 PHE cc_start: 0.8442 (OUTLIER) cc_final: 0.7228 (m-80) REVERT: A 483 LEU cc_start: 0.9402 (tt) cc_final: 0.8556 (tt) REVERT: A 520 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8823 (tt) REVERT: A 557 MET cc_start: 0.8712 (tpp) cc_final: 0.8423 (tpp) REVERT: B 1 MET cc_start: 0.9171 (tpp) cc_final: 0.8809 (tpp) REVERT: B 11 LEU cc_start: 0.9565 (tp) cc_final: 0.9221 (tp) REVERT: B 503 MET cc_start: 0.9237 (mtp) cc_final: 0.8974 (mtm) REVERT: B 541 CYS cc_start: 0.8398 (m) cc_final: 0.8014 (m) REVERT: B 572 LEU cc_start: 0.9328 (mm) cc_final: 0.9100 (mm) REVERT: B 592 MET cc_start: 0.7587 (mmm) cc_final: 0.7130 (mmm) outliers start: 26 outliers final: 19 residues processed: 117 average time/residue: 0.1809 time to fit residues: 31.3150 Evaluate side-chains 110 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 637 ARG Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 563 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 79 optimal weight: 0.7980 chunk 99 optimal weight: 6.9990 chunk 32 optimal weight: 0.8980 chunk 86 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 10 optimal weight: 0.0020 chunk 82 optimal weight: 0.1980 chunk 36 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 ASN ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.056157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.045105 restraints weight = 59013.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.046974 restraints weight = 29957.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.048216 restraints weight = 18782.608| |-----------------------------------------------------------------------------| r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2917 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.2917 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8784 Z= 0.188 Angle : 0.726 12.152 11935 Z= 0.340 Chirality : 0.043 0.190 1390 Planarity : 0.004 0.049 1515 Dihedral : 6.318 81.702 1225 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.27 % Favored : 95.55 % Rotamer: Outliers : 3.41 % Allowed : 17.80 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.26), residues: 1101 helix: 1.33 (0.23), residues: 513 sheet: -0.76 (0.34), residues: 221 loop : -1.56 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 22 HIS 0.002 0.001 HIS A 578 PHE 0.025 0.002 PHE A 141 TYR 0.022 0.001 TYR B 569 ARG 0.003 0.000 ARG B 464 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 93 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.9498 (pp) cc_final: 0.9134 (tt) REVERT: A 236 MET cc_start: 0.8652 (mmm) cc_final: 0.8358 (mmm) REVERT: A 256 SER cc_start: 0.9083 (t) cc_final: 0.8629 (p) REVERT: A 301 PHE cc_start: 0.8421 (OUTLIER) cc_final: 0.7421 (m-80) REVERT: A 399 TYR cc_start: 0.8647 (OUTLIER) cc_final: 0.8368 (m-10) REVERT: A 520 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8674 (tt) REVERT: A 556 MET cc_start: 0.9407 (ttm) cc_final: 0.8608 (tmm) REVERT: A 573 MET cc_start: 0.8556 (mmm) cc_final: 0.8044 (mmm) REVERT: B 11 LEU cc_start: 0.9584 (tp) cc_final: 0.9251 (tp) REVERT: B 320 LEU cc_start: 0.9407 (tp) cc_final: 0.9129 (tt) REVERT: B 351 ASP cc_start: 0.8883 (m-30) cc_final: 0.8449 (t70) REVERT: B 478 LYS cc_start: 0.9509 (mttm) cc_final: 0.8977 (mmtm) REVERT: B 541 CYS cc_start: 0.8395 (m) cc_final: 0.8032 (m) REVERT: B 569 TYR cc_start: 0.9134 (t80) cc_final: 0.8754 (t80) REVERT: B 572 LEU cc_start: 0.9312 (mm) cc_final: 0.9107 (mm) REVERT: B 592 MET cc_start: 0.7578 (mmm) cc_final: 0.7178 (mmm) outliers start: 31 outliers final: 19 residues processed: 119 average time/residue: 0.1729 time to fit residues: 30.3709 Evaluate side-chains 111 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 399 TYR Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 637 ARG Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 563 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 43 optimal weight: 1.9990 chunk 25 optimal weight: 9.9990 chunk 27 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 79 optimal weight: 0.0870 chunk 102 optimal weight: 9.9990 chunk 105 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 overall best weight: 2.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.054864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.043634 restraints weight = 66719.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.045507 restraints weight = 32686.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.046811 restraints weight = 20392.436| |-----------------------------------------------------------------------------| r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2882 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.2882 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 8784 Z= 0.274 Angle : 0.760 12.205 11935 Z= 0.358 Chirality : 0.045 0.187 1390 Planarity : 0.004 0.048 1515 Dihedral : 6.072 84.075 1220 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.82 % Favored : 95.00 % Rotamer: Outliers : 3.30 % Allowed : 18.35 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.26), residues: 1101 helix: 1.37 (0.23), residues: 519 sheet: -0.75 (0.34), residues: 221 loop : -1.52 (0.33), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 602 HIS 0.004 0.001 HIS B 266 PHE 0.024 0.002 PHE A 141 TYR 0.019 0.002 TYR A 399 ARG 0.003 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 84 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.9520 (pp) cc_final: 0.9163 (tt) REVERT: A 236 MET cc_start: 0.8612 (mmm) cc_final: 0.8337 (mmm) REVERT: A 256 SER cc_start: 0.9155 (t) cc_final: 0.8679 (p) REVERT: A 301 PHE cc_start: 0.8549 (OUTLIER) cc_final: 0.7351 (m-80) REVERT: A 556 MET cc_start: 0.9435 (ttm) cc_final: 0.8676 (tmm) REVERT: A 573 MET cc_start: 0.8524 (mmm) cc_final: 0.8171 (mmm) REVERT: B 1 MET cc_start: 0.9153 (tpp) cc_final: 0.8393 (mmm) REVERT: B 11 LEU cc_start: 0.9588 (tp) cc_final: 0.9269 (tp) REVERT: B 541 CYS cc_start: 0.8328 (m) cc_final: 0.7964 (m) REVERT: B 569 TYR cc_start: 0.9139 (t80) cc_final: 0.8870 (t80) REVERT: B 592 MET cc_start: 0.7597 (mmm) cc_final: 0.7186 (mmm) outliers start: 30 outliers final: 23 residues processed: 109 average time/residue: 0.1756 time to fit residues: 28.4873 Evaluate side-chains 109 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain A residue 637 ARG Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 563 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 13 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 chunk 102 optimal weight: 7.9990 chunk 57 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 ASN ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.055930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.044266 restraints weight = 76884.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.046300 restraints weight = 35490.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.047670 restraints weight = 21441.143| |-----------------------------------------------------------------------------| r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2904 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.2904 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8784 Z= 0.194 Angle : 0.745 12.515 11935 Z= 0.341 Chirality : 0.044 0.212 1390 Planarity : 0.004 0.046 1515 Dihedral : 5.848 89.795 1218 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.82 % Favored : 96.00 % Rotamer: Outliers : 3.52 % Allowed : 18.35 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.26), residues: 1101 helix: 1.47 (0.23), residues: 514 sheet: -0.60 (0.34), residues: 221 loop : -1.38 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 22 HIS 0.002 0.001 HIS B 105 PHE 0.025 0.002 PHE A 141 TYR 0.021 0.002 TYR A 399 ARG 0.003 0.000 ARG B 464 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 93 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.9506 (pp) cc_final: 0.9186 (tt) REVERT: A 236 MET cc_start: 0.8643 (mmm) cc_final: 0.8358 (mmm) REVERT: A 256 SER cc_start: 0.9127 (t) cc_final: 0.8660 (p) REVERT: A 301 PHE cc_start: 0.8432 (OUTLIER) cc_final: 0.7487 (m-80) REVERT: A 384 SER cc_start: 0.8982 (m) cc_final: 0.8739 (p) REVERT: A 482 MET cc_start: 0.8503 (tpp) cc_final: 0.8004 (tpp) REVERT: A 556 MET cc_start: 0.9445 (ttm) cc_final: 0.8694 (tmm) REVERT: B 1 MET cc_start: 0.9115 (tpp) cc_final: 0.8367 (mmm) REVERT: B 11 LEU cc_start: 0.9588 (tp) cc_final: 0.9286 (tp) REVERT: B 164 MET cc_start: 0.8538 (ttm) cc_final: 0.8337 (ttm) REVERT: B 424 PHE cc_start: 0.8996 (m-80) cc_final: 0.8588 (m-10) REVERT: B 541 CYS cc_start: 0.8252 (m) cc_final: 0.7908 (m) REVERT: B 569 TYR cc_start: 0.9088 (t80) cc_final: 0.8884 (t80) REVERT: B 592 MET cc_start: 0.7561 (mmm) cc_final: 0.7134 (mmm) outliers start: 32 outliers final: 23 residues processed: 117 average time/residue: 0.1697 time to fit residues: 29.4310 Evaluate side-chains 110 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 86 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain A residue 637 ARG Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 563 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 92 optimal weight: 7.9990 chunk 74 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.056150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.044872 restraints weight = 65910.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.046741 restraints weight = 32813.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.048041 restraints weight = 20654.998| |-----------------------------------------------------------------------------| r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2913 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.2913 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.4151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8784 Z= 0.187 Angle : 0.773 12.838 11935 Z= 0.350 Chirality : 0.044 0.384 1390 Planarity : 0.004 0.042 1515 Dihedral : 5.775 86.872 1218 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.73 % Favored : 96.09 % Rotamer: Outliers : 2.75 % Allowed : 19.34 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.27), residues: 1101 helix: 1.54 (0.24), residues: 518 sheet: -0.45 (0.35), residues: 221 loop : -1.22 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 22 HIS 0.003 0.001 HIS B 105 PHE 0.024 0.001 PHE A 141 TYR 0.020 0.001 TYR A 399 ARG 0.007 0.000 ARG B 552 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 86 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.9486 (pp) cc_final: 0.9162 (tt) REVERT: A 236 MET cc_start: 0.8665 (mmm) cc_final: 0.8366 (mmm) REVERT: A 256 SER cc_start: 0.9121 (t) cc_final: 0.8600 (p) REVERT: A 301 PHE cc_start: 0.8359 (OUTLIER) cc_final: 0.7560 (m-80) REVERT: A 384 SER cc_start: 0.8959 (m) cc_final: 0.8681 (p) REVERT: A 482 MET cc_start: 0.8484 (tpp) cc_final: 0.8020 (tpp) REVERT: A 483 LEU cc_start: 0.9150 (tt) cc_final: 0.8752 (tp) REVERT: A 556 MET cc_start: 0.9417 (ttm) cc_final: 0.8858 (tmm) REVERT: B 1 MET cc_start: 0.9077 (tpp) cc_final: 0.8378 (mmm) REVERT: B 69 MET cc_start: 0.9144 (ptp) cc_final: 0.8816 (ptp) REVERT: B 424 PHE cc_start: 0.8986 (m-80) cc_final: 0.8605 (m-10) REVERT: B 541 CYS cc_start: 0.8143 (m) cc_final: 0.7846 (m) REVERT: B 592 MET cc_start: 0.7594 (mmm) cc_final: 0.7167 (mmm) outliers start: 25 outliers final: 23 residues processed: 107 average time/residue: 0.1769 time to fit residues: 28.1555 Evaluate side-chains 107 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 83 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain A residue 637 ARG Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 542 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 38 optimal weight: 0.0570 chunk 26 optimal weight: 0.8980 chunk 67 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 14 optimal weight: 0.0570 chunk 7 optimal weight: 0.0370 chunk 47 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.3694 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.057174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.045357 restraints weight = 76987.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.047457 restraints weight = 35410.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.048864 restraints weight = 21256.596| |-----------------------------------------------------------------------------| r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2941 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.2941 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8784 Z= 0.171 Angle : 0.781 19.481 11935 Z= 0.346 Chirality : 0.044 0.383 1390 Planarity : 0.004 0.037 1515 Dihedral : 5.642 84.776 1218 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.55 % Favored : 96.36 % Rotamer: Outliers : 2.20 % Allowed : 20.66 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.27), residues: 1101 helix: 1.50 (0.24), residues: 515 sheet: -0.19 (0.36), residues: 220 loop : -1.27 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 602 HIS 0.002 0.000 HIS A 100 PHE 0.024 0.001 PHE A 141 TYR 0.016 0.001 TYR A 399 ARG 0.007 0.000 ARG B 552 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.9450 (pp) cc_final: 0.9159 (tt) REVERT: A 191 LEU cc_start: 0.9358 (tt) cc_final: 0.8910 (mm) REVERT: A 236 MET cc_start: 0.8735 (mmm) cc_final: 0.8387 (mmm) REVERT: A 256 SER cc_start: 0.9125 (t) cc_final: 0.8794 (p) REVERT: A 301 PHE cc_start: 0.8207 (OUTLIER) cc_final: 0.7724 (m-80) REVERT: A 384 SER cc_start: 0.8923 (m) cc_final: 0.8607 (p) REVERT: A 482 MET cc_start: 0.8524 (tpp) cc_final: 0.7983 (tpp) REVERT: A 483 LEU cc_start: 0.9085 (tt) cc_final: 0.8694 (tp) REVERT: A 556 MET cc_start: 0.9431 (ttm) cc_final: 0.8861 (tmm) REVERT: B 1 MET cc_start: 0.9102 (tpp) cc_final: 0.8755 (tpp) REVERT: B 69 MET cc_start: 0.9147 (ptp) cc_final: 0.8829 (ptp) REVERT: B 541 CYS cc_start: 0.8075 (m) cc_final: 0.7794 (m) REVERT: B 592 MET cc_start: 0.7639 (mmm) cc_final: 0.7223 (mmm) outliers start: 20 outliers final: 15 residues processed: 103 average time/residue: 0.1717 time to fit residues: 26.6028 Evaluate side-chains 101 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain A residue 637 ARG Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 542 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 79 optimal weight: 0.2980 chunk 58 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 55 optimal weight: 0.4980 chunk 101 optimal weight: 0.4980 chunk 94 optimal weight: 0.0870 chunk 54 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.057432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.045543 restraints weight = 77241.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.047617 restraints weight = 35915.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.049015 restraints weight = 21806.379| |-----------------------------------------------------------------------------| r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2941 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.2941 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.4451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8784 Z= 0.172 Angle : 0.772 13.174 11935 Z= 0.344 Chirality : 0.043 0.201 1390 Planarity : 0.004 0.037 1515 Dihedral : 5.531 80.407 1213 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.98 % Allowed : 20.88 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.27), residues: 1101 helix: 1.53 (0.23), residues: 517 sheet: -0.11 (0.36), residues: 220 loop : -1.27 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 22 HIS 0.002 0.001 HIS B 498 PHE 0.024 0.001 PHE A 141 TYR 0.022 0.001 TYR B 363 ARG 0.007 0.000 ARG B 552 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.9396 (pp) cc_final: 0.9139 (tt) REVERT: A 191 LEU cc_start: 0.9351 (tt) cc_final: 0.8923 (mm) REVERT: A 236 MET cc_start: 0.8725 (mmm) cc_final: 0.8371 (mmm) REVERT: A 256 SER cc_start: 0.9120 (t) cc_final: 0.8777 (p) REVERT: A 301 PHE cc_start: 0.8173 (OUTLIER) cc_final: 0.7808 (m-80) REVERT: A 384 SER cc_start: 0.8918 (m) cc_final: 0.8607 (p) REVERT: A 483 LEU cc_start: 0.9038 (tt) cc_final: 0.8803 (tp) REVERT: A 556 MET cc_start: 0.9396 (ttm) cc_final: 0.8883 (tmm) REVERT: B 1 MET cc_start: 0.9051 (tpp) cc_final: 0.8792 (tpp) REVERT: B 69 MET cc_start: 0.9147 (ptp) cc_final: 0.8823 (ptp) REVERT: B 424 PHE cc_start: 0.8979 (OUTLIER) cc_final: 0.8438 (m-10) REVERT: B 541 CYS cc_start: 0.8111 (m) cc_final: 0.7791 (m) REVERT: B 592 MET cc_start: 0.7513 (mmm) cc_final: 0.7131 (mmm) outliers start: 18 outliers final: 16 residues processed: 103 average time/residue: 0.1631 time to fit residues: 25.3065 Evaluate side-chains 106 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain A residue 637 ARG Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 424 PHE Chi-restraints excluded: chain B residue 542 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 16 optimal weight: 0.0270 chunk 70 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 0.0000 chunk 21 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 63 optimal weight: 0.4980 chunk 81 optimal weight: 9.9990 overall best weight: 0.9044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.056972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.045397 restraints weight = 71395.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.047380 restraints weight = 33936.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.048738 restraints weight = 20793.984| |-----------------------------------------------------------------------------| r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2934 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.2934 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.4522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8784 Z= 0.190 Angle : 0.805 20.966 11935 Z= 0.356 Chirality : 0.044 0.245 1390 Planarity : 0.004 0.037 1515 Dihedral : 5.542 81.139 1213 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.42 % Allowed : 20.55 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.27), residues: 1101 helix: 1.57 (0.23), residues: 521 sheet: -0.09 (0.36), residues: 220 loop : -1.17 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 467 HIS 0.002 0.001 HIS B 266 PHE 0.023 0.001 PHE A 141 TYR 0.016 0.001 TYR A 399 ARG 0.007 0.000 ARG B 552 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2949.02 seconds wall clock time: 51 minutes 47.62 seconds (3107.62 seconds total)