Starting phenix.real_space_refine on Tue Mar 3 21:44:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6jt0_9883/03_2026/6jt0_9883.cif Found real_map, /net/cci-nas-00/data/ceres_data/6jt0_9883/03_2026/6jt0_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 { model { file = "/net/cci-nas-00/data/ceres_data/6jt0_9883/03_2026/6jt0_9883.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6jt0_9883/03_2026/6jt0_9883.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6jt0_9883/03_2026/6jt0_9883.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6jt0_9883/03_2026/6jt0_9883.map" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: {'GLU:plan': 18, 'PHE:plan': 3, 'GLN:plan1': 6, 'ASP:plan': 8, 'HIS:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 4} 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: {'GLU:plan': 18, 'PHE:plan': 3, 'GLN:plan1': 6, 'ASP:plan': 8, 'HIS:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 4} 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: {'GLU:plan': 16, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'ARG:plan': 1} 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: {'GLU:plan': 16, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'ARG:plan': 1} 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: 3.64, per 1000 atoms: 0.42 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: 0.80 Conformation dependent library (CDL) restraints added in 804.8 milliseconds 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: 0.24 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: 1.44 Time building geometry restraints manager: 1.04 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: 1.600 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 12.040 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.440 ------------------------------------------------------------------------------- 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= 0.174 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.003 0.000 ARG B 360 TYR 0.016 0.002 TYR B 339 PHE 0.023 0.002 PHE A 458 TRP 0.004 0.001 TRP B 602 HIS 0.004 0.001 HIS B 176 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 8784) covalent geometry : angle 0.71044 (11935) hydrogen bonds : bond 0.12713 ( 445) hydrogen bonds : angle 6.04783 ( 1298) *********************** 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 : 0.275 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: 0.9187 (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: 0.8503 (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: 0.9060 (tp30) REVERT: B 69 MET cc_start: 0.9468 (mtm) cc_final: 0.9099 (ptm) REVERT: B 162 ILE cc_start: 0.9430 (pt) cc_final: 0.8937 (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: 0.8582 (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: 0.9034 (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: 12 residues processed: 211 average time/residue: 0.0755 time to fit residues: 22.6868 Evaluate side-chains 118 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 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 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 108 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 7.9990 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 9.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.054900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.043527 restraints weight = 71328.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.045459 restraints weight = 33685.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.046781 restraints weight = 20635.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.047721 restraints weight = 14509.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.048407 restraints weight = 11147.504| |-----------------------------------------------------------------------------| r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2919 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 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 = 0.2915 r_free = 0.2915 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.2915 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 8784 Z= 0.217 Angle : 0.793 12.814 11935 Z= 0.389 Chirality : 0.045 0.226 1390 Planarity : 0.005 0.110 1515 Dihedral : 7.733 82.974 1233 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.09 % Favored : 94.64 % Rotamer: Outliers : 4.62 % Allowed : 14.18 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.24), residues: 1101 helix: 0.11 (0.22), residues: 521 sheet: -1.41 (0.33), residues: 211 loop : -2.32 (0.29), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 464 TYR 0.023 0.002 TYR B 569 PHE 0.024 0.002 PHE A 141 TRP 0.006 0.001 TRP B 602 HIS 0.005 0.001 HIS B 498 Details of bonding type rmsd covalent geometry : bond 0.00490 ( 8784) covalent geometry : angle 0.79320 (11935) hydrogen bonds : bond 0.04533 ( 445) hydrogen bonds : angle 5.04870 ( 1298) *********************** 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 141 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 99 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.9473 (pp) cc_final: 0.9034 (tt) REVERT: A 236 MET cc_start: 0.8441 (mmm) cc_final: 0.8176 (mmm) REVERT: A 256 SER cc_start: 0.8885 (t) cc_final: 0.8450 (p) REVERT: A 344 MET cc_start: 0.8442 (mtm) cc_final: 0.8233 (mtp) REVERT: A 483 LEU cc_start: 0.9363 (tp) cc_final: 0.9026 (tt) REVERT: A 520 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8862 (tt) REVERT: A 573 MET cc_start: 0.8802 (mmm) cc_final: 0.8529 (mmm) REVERT: A 607 PHE cc_start: 0.8983 (m-80) cc_final: 0.8759 (t80) REVERT: B 1 MET cc_start: 0.9234 (tpp) cc_final: 0.8302 (mmm) REVERT: B 11 LEU cc_start: 0.9537 (tp) cc_final: 0.9311 (tp) REVERT: B 66 ILE cc_start: 0.9417 (OUTLIER) cc_final: 0.9197 (pt) REVERT: B 69 MET cc_start: 0.9140 (mtm) cc_final: 0.8589 (ptm) REVERT: B 115 MET cc_start: 0.9302 (ptm) cc_final: 0.9052 (ptm) REVERT: B 164 MET cc_start: 0.8507 (ttm) cc_final: 0.8214 (ttm) REVERT: B 478 LYS cc_start: 0.9445 (mttm) cc_final: 0.8886 (mmtm) REVERT: B 503 MET cc_start: 0.9262 (mtp) cc_final: 0.9013 (mtm) REVERT: B 541 CYS cc_start: 0.8382 (m) cc_final: 0.7959 (m) REVERT: B 572 LEU cc_start: 0.9367 (mm) cc_final: 0.9023 (mm) outliers start: 42 outliers final: 21 residues processed: 134 average time/residue: 0.0731 time to fit residues: 14.3546 Evaluate side-chains 107 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.218 ------------------------------------------------------------------------------- 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 398 LEU Chi-restraints excluded: chain A residue 409 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 13 VAL Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 66 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 393 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 553 THR 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 102 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 33 optimal weight: 0.9990 chunk 42 optimal weight: 0.2980 chunk 54 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 93 optimal weight: 1.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 GLN ** 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 = 0.3110 r_free = 0.3110 target = 0.054485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.042827 restraints weight = 78121.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.044780 restraints weight = 36286.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.046135 restraints weight = 22196.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.047030 restraints weight = 15620.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.047729 restraints weight = 12166.714| |-----------------------------------------------------------------------------| r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2894 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.2890 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 8784 Z= 0.204 Angle : 0.777 12.619 11935 Z= 0.376 Chirality : 0.045 0.185 1390 Planarity : 0.005 0.059 1515 Dihedral : 7.107 86.610 1225 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.18 % Favored : 94.55 % Rotamer: Outliers : 3.74 % Allowed : 16.04 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.25), residues: 1101 helix: 0.69 (0.22), residues: 519 sheet: -1.25 (0.33), residues: 221 loop : -1.96 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 570 TYR 0.026 0.002 TYR B 569 PHE 0.026 0.002 PHE A 141 TRP 0.008 0.001 TRP B 602 HIS 0.005 0.001 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00463 ( 8784) covalent geometry : angle 0.77717 (11935) hydrogen bonds : bond 0.04406 ( 445) hydrogen bonds : angle 4.87699 ( 1298) *********************** 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 125 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 91 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.9497 (pp) cc_final: 0.9123 (tt) REVERT: A 236 MET cc_start: 0.8582 (mmm) cc_final: 0.8267 (mmm) REVERT: A 256 SER cc_start: 0.8961 (t) cc_final: 0.8419 (p) REVERT: A 301 PHE cc_start: 0.8561 (OUTLIER) cc_final: 0.7678 (m-80) REVERT: A 520 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8845 (tt) REVERT: A 556 MET cc_start: 0.9242 (mtt) cc_final: 0.8624 (tmm) REVERT: B 1 MET cc_start: 0.9165 (tpp) cc_final: 0.8282 (mmm) REVERT: B 11 LEU cc_start: 0.9556 (tp) cc_final: 0.9266 (tp) REVERT: B 164 MET cc_start: 0.8470 (ttm) cc_final: 0.8160 (ttm) REVERT: B 351 ASP cc_start: 0.8880 (m-30) cc_final: 0.8643 (t0) REVERT: B 478 LYS cc_start: 0.9504 (mttm) cc_final: 0.8980 (mmtm) REVERT: B 541 CYS cc_start: 0.8343 (m) cc_final: 0.7947 (m) REVERT: B 572 LEU cc_start: 0.9378 (mm) cc_final: 0.9144 (mm) REVERT: B 592 MET cc_start: 0.7673 (mmm) cc_final: 0.7221 (mmm) outliers start: 34 outliers final: 21 residues processed: 117 average time/residue: 0.0725 time to fit residues: 12.7270 Evaluate side-chains 106 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 83 time to evaluate : 0.336 ------------------------------------------------------------------------------- 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 347 VAL 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 409 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 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 389 LYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 563 ASN Chi-restraints excluded: chain B residue 568 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 45 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 72 optimal weight: 0.2980 chunk 80 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 86 optimal weight: 0.8980 chunk 4 optimal weight: 7.9990 chunk 49 optimal weight: 7.9990 chunk 21 optimal weight: 0.6980 chunk 96 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 563 ASN ** 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 = 0.3165 r_free = 0.3165 target = 0.056049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.043539 restraints weight = 112372.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.045826 restraints weight = 43399.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.047420 restraints weight = 24542.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.048528 restraints weight = 16340.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.049305 restraints weight = 12145.921| |-----------------------------------------------------------------------------| r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2956 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2956 r_free = 0.2956 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2956 r_free = 0.2956 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.2956 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3345 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= 0.122 Angle : 0.741 12.615 11935 Z= 0.347 Chirality : 0.043 0.189 1390 Planarity : 0.004 0.048 1515 Dihedral : 6.513 88.402 1225 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.18 % Favored : 95.64 % Rotamer: Outliers : 3.19 % Allowed : 17.91 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.26), residues: 1101 helix: 1.15 (0.23), residues: 513 sheet: -0.86 (0.34), residues: 218 loop : -1.74 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 464 TYR 0.023 0.002 TYR B 569 PHE 0.027 0.002 PHE A 141 TRP 0.007 0.001 TRP B 22 HIS 0.004 0.001 HIS B 498 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 8784) covalent geometry : angle 0.74083 (11935) hydrogen bonds : bond 0.03828 ( 445) hydrogen bonds : angle 4.56209 ( 1298) *********************** 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 126 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 97 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.9474 (pp) cc_final: 0.9088 (tt) REVERT: A 236 MET cc_start: 0.8655 (mmm) cc_final: 0.8369 (mmm) REVERT: A 256 SER cc_start: 0.9065 (t) cc_final: 0.8595 (p) REVERT: A 301 PHE cc_start: 0.8387 (OUTLIER) cc_final: 0.7322 (m-80) REVERT: A 520 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8676 (tt) REVERT: B 1 MET cc_start: 0.9139 (tpp) cc_final: 0.8803 (tpp) REVERT: B 11 LEU cc_start: 0.9576 (tp) cc_final: 0.9242 (tp) REVERT: B 478 LYS cc_start: 0.9541 (mttm) cc_final: 0.8965 (mmtm) REVERT: B 541 CYS cc_start: 0.8456 (m) cc_final: 0.7999 (m) REVERT: B 569 TYR cc_start: 0.9098 (t80) cc_final: 0.8897 (t80) REVERT: B 592 MET cc_start: 0.7463 (mmm) cc_final: 0.7126 (mmm) outliers start: 29 outliers final: 19 residues processed: 123 average time/residue: 0.0731 time to fit residues: 13.4149 Evaluate side-chains 107 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 0.329 ------------------------------------------------------------------------------- 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 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 472 VAL 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 274 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 31 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 19 optimal weight: 0.3980 chunk 52 optimal weight: 0.4980 chunk 87 optimal weight: 0.8980 chunk 3 optimal weight: 9.9990 chunk 54 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN 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 = 0.3166 r_free = 0.3166 target = 0.056066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.044261 restraints weight = 81436.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.046340 restraints weight = 36257.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.047782 restraints weight = 21778.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.048809 restraints weight = 14946.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.049536 restraints weight = 11282.841| |-----------------------------------------------------------------------------| r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2966 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2966 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3621 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= 0.123 Angle : 0.730 12.169 11935 Z= 0.342 Chirality : 0.044 0.219 1390 Planarity : 0.004 0.046 1515 Dihedral : 6.317 88.674 1223 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.18 % Favored : 95.64 % Rotamer: Outliers : 3.63 % Allowed : 18.46 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.26), residues: 1101 helix: 1.34 (0.23), residues: 513 sheet: -0.64 (0.35), residues: 219 loop : -1.56 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 464 TYR 0.017 0.001 TYR B 569 PHE 0.025 0.002 PHE A 141 TRP 0.003 0.001 TRP B 22 HIS 0.003 0.001 HIS A 578 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 8784) covalent geometry : angle 0.72998 (11935) hydrogen bonds : bond 0.03684 ( 445) hydrogen bonds : angle 4.37701 ( 1298) *********************** 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 123 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 90 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.9472 (pp) cc_final: 0.9092 (tt) REVERT: A 236 MET cc_start: 0.8637 (mmm) cc_final: 0.8343 (mmm) REVERT: A 256 SER cc_start: 0.9066 (t) cc_final: 0.8591 (p) REVERT: A 301 PHE cc_start: 0.8333 (OUTLIER) cc_final: 0.7445 (m-80) REVERT: A 399 TYR cc_start: 0.8660 (OUTLIER) cc_final: 0.8383 (m-10) REVERT: A 520 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8772 (tt) REVERT: A 557 MET cc_start: 0.8923 (mmm) cc_final: 0.8658 (mmm) REVERT: B 1 MET cc_start: 0.9105 (tpp) cc_final: 0.8762 (tpp) REVERT: B 11 LEU cc_start: 0.9577 (tp) cc_final: 0.9265 (tp) REVERT: B 90 LEU cc_start: 0.9538 (OUTLIER) cc_final: 0.9201 (tt) REVERT: B 320 LEU cc_start: 0.9419 (tp) cc_final: 0.9188 (tt) REVERT: B 478 LYS cc_start: 0.9520 (mttm) cc_final: 0.8954 (mmtm) REVERT: B 480 MET cc_start: 0.8707 (tpp) cc_final: 0.8292 (tpp) REVERT: B 541 CYS cc_start: 0.8418 (m) cc_final: 0.7992 (m) REVERT: B 592 MET cc_start: 0.7368 (mmm) cc_final: 0.7073 (mmm) outliers start: 33 outliers final: 22 residues processed: 114 average time/residue: 0.0722 time to fit residues: 12.2288 Evaluate side-chains 110 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 84 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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 347 VAL 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 472 VAL 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 51 LEU 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 393 LEU Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 553 THR 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 94 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 71 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 102 optimal weight: 0.0970 chunk 96 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3163 r_free = 0.3163 target = 0.055913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.044978 restraints weight = 58163.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.046788 restraints weight = 30028.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.048044 restraints weight = 19222.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.048943 restraints weight = 13883.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.049495 restraints weight = 10823.525| |-----------------------------------------------------------------------------| r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2967 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2967 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3826 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= 0.127 Angle : 0.746 13.145 11935 Z= 0.343 Chirality : 0.045 0.404 1390 Planarity : 0.004 0.043 1515 Dihedral : 6.213 85.779 1223 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.18 % Favored : 95.64 % Rotamer: Outliers : 3.30 % Allowed : 18.13 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.26), residues: 1101 helix: 1.41 (0.24), residues: 514 sheet: -0.51 (0.35), residues: 219 loop : -1.46 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 464 TYR 0.017 0.001 TYR A 399 PHE 0.024 0.002 PHE A 141 TRP 0.003 0.001 TRP B 22 HIS 0.003 0.001 HIS A 578 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 8784) covalent geometry : angle 0.74632 (11935) hydrogen bonds : bond 0.03617 ( 445) hydrogen bonds : angle 4.38249 ( 1298) *********************** 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 119 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 89 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.9466 (pp) cc_final: 0.9090 (tt) REVERT: A 191 LEU cc_start: 0.9418 (tp) cc_final: 0.9190 (tt) REVERT: A 236 MET cc_start: 0.8560 (mmm) cc_final: 0.8286 (mmm) REVERT: A 256 SER cc_start: 0.9112 (t) cc_final: 0.8589 (p) REVERT: A 301 PHE cc_start: 0.8304 (OUTLIER) cc_final: 0.7534 (m-80) REVERT: A 399 TYR cc_start: 0.8652 (OUTLIER) cc_final: 0.8324 (m-10) REVERT: A 482 MET cc_start: 0.8543 (tpp) cc_final: 0.8214 (tpp) REVERT: A 503 ILE cc_start: 0.9701 (mm) cc_final: 0.9402 (tt) REVERT: A 520 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8715 (tt) REVERT: B 1 MET cc_start: 0.9093 (tpp) cc_final: 0.8753 (tpp) REVERT: B 11 LEU cc_start: 0.9580 (tp) cc_final: 0.9268 (tp) REVERT: B 90 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.9206 (tt) REVERT: B 478 LYS cc_start: 0.9507 (mttm) cc_final: 0.8961 (mmtm) REVERT: B 480 MET cc_start: 0.8718 (tpp) cc_final: 0.8343 (tpp) REVERT: B 541 CYS cc_start: 0.8379 (m) cc_final: 0.7969 (m) REVERT: B 592 MET cc_start: 0.7345 (mmm) cc_final: 0.7079 (mmm) outliers start: 30 outliers final: 20 residues processed: 112 average time/residue: 0.0817 time to fit residues: 13.3570 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 : 0.334 ------------------------------------------------------------------------------- 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 380 LEU Chi-restraints excluded: chain A residue 399 TYR 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 472 VAL 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 51 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 166 VAL 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 553 THR 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 29 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 44 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 109 optimal weight: 10.0000 chunk 108 optimal weight: 0.0770 chunk 104 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 overall best weight: 1.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3158 r_free = 0.3158 target = 0.055847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.044097 restraints weight = 77264.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.046137 restraints weight = 35647.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.047560 restraints weight = 21571.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.048548 restraints weight = 14991.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.049184 restraints weight = 11427.822| |-----------------------------------------------------------------------------| r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2954 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2954 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3964 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= 0.134 Angle : 0.752 13.917 11935 Z= 0.346 Chirality : 0.045 0.407 1390 Planarity : 0.004 0.043 1515 Dihedral : 5.992 83.695 1219 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.27 % Favored : 95.55 % Rotamer: Outliers : 2.86 % Allowed : 18.46 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.27), residues: 1101 helix: 1.47 (0.24), residues: 514 sheet: -0.51 (0.34), residues: 221 loop : -1.32 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 464 TYR 0.022 0.001 TYR A 399 PHE 0.024 0.001 PHE A 141 TRP 0.003 0.001 TRP B 22 HIS 0.003 0.001 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 8784) covalent geometry : angle 0.75186 (11935) hydrogen bonds : bond 0.03628 ( 445) hydrogen bonds : angle 4.38537 ( 1298) *********************** 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 110 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 84 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.9464 (pp) cc_final: 0.9115 (tt) REVERT: A 191 LEU cc_start: 0.9410 (tp) cc_final: 0.9192 (tt) REVERT: A 236 MET cc_start: 0.8580 (mmm) cc_final: 0.8276 (mmm) REVERT: A 256 SER cc_start: 0.9125 (t) cc_final: 0.8599 (p) REVERT: A 301 PHE cc_start: 0.8319 (OUTLIER) cc_final: 0.7558 (m-80) REVERT: A 384 SER cc_start: 0.8855 (m) cc_final: 0.8583 (p) REVERT: A 557 MET cc_start: 0.8954 (mmm) cc_final: 0.8709 (mmm) REVERT: B 1 MET cc_start: 0.9103 (tpp) cc_final: 0.8740 (tpp) REVERT: B 478 LYS cc_start: 0.9517 (mttm) cc_final: 0.8997 (mmtm) REVERT: B 503 MET cc_start: 0.9349 (ttm) cc_final: 0.9033 (mmm) REVERT: B 541 CYS cc_start: 0.8329 (m) cc_final: 0.7961 (m) REVERT: B 592 MET cc_start: 0.7334 (mmm) cc_final: 0.7061 (mmm) outliers start: 26 outliers final: 21 residues processed: 103 average time/residue: 0.0764 time to fit residues: 11.8095 Evaluate side-chains 103 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.330 ------------------------------------------------------------------------------- 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 466 LEU 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 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 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 553 THR Chi-restraints excluded: chain B residue 601 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 60 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 89 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.055899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.043674 restraints weight = 100950.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.045873 restraints weight = 42216.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.047398 restraints weight = 24329.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.048456 restraints weight = 16591.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.049225 restraints weight = 12469.030| |-----------------------------------------------------------------------------| r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2958 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2958 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.4127 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= 0.122 Angle : 0.731 13.077 11935 Z= 0.335 Chirality : 0.043 0.186 1390 Planarity : 0.004 0.041 1515 Dihedral : 5.702 82.574 1217 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.82 % Favored : 96.00 % Rotamer: Outliers : 2.31 % Allowed : 19.45 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.27), residues: 1101 helix: 1.51 (0.24), residues: 514 sheet: -0.38 (0.35), residues: 221 loop : -1.26 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 464 TYR 0.019 0.001 TYR A 399 PHE 0.024 0.001 PHE A 141 TRP 0.004 0.001 TRP A 467 HIS 0.003 0.001 HIS B 105 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 8784) covalent geometry : angle 0.73108 (11935) hydrogen bonds : bond 0.03474 ( 445) hydrogen bonds : angle 4.30479 ( 1298) *********************** 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 105 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.9457 (pp) cc_final: 0.9145 (tt) REVERT: A 191 LEU cc_start: 0.9405 (tp) cc_final: 0.9195 (tt) REVERT: A 236 MET cc_start: 0.8660 (mmm) cc_final: 0.8319 (mmm) REVERT: A 256 SER cc_start: 0.9119 (t) cc_final: 0.8786 (p) REVERT: A 301 PHE cc_start: 0.8229 (OUTLIER) cc_final: 0.7620 (m-80) REVERT: A 384 SER cc_start: 0.8869 (m) cc_final: 0.8585 (p) REVERT: A 556 MET cc_start: 0.9295 (ttp) cc_final: 0.8735 (tmm) REVERT: A 557 MET cc_start: 0.8912 (mmm) cc_final: 0.8405 (mmm) REVERT: A 573 MET cc_start: 0.8224 (mmm) cc_final: 0.7159 (mpp) REVERT: B 1 MET cc_start: 0.9083 (tpp) cc_final: 0.8704 (tpp) REVERT: B 69 MET cc_start: 0.9143 (ptp) cc_final: 0.8934 (ptm) REVERT: B 480 MET cc_start: 0.8739 (tpp) cc_final: 0.8364 (tpp) REVERT: B 503 MET cc_start: 0.9333 (ttm) cc_final: 0.9019 (mmm) REVERT: B 504 MET cc_start: 0.8551 (tpp) cc_final: 0.8320 (tpp) REVERT: B 541 CYS cc_start: 0.8333 (m) cc_final: 0.7945 (m) REVERT: B 592 MET cc_start: 0.7335 (mmm) cc_final: 0.7027 (mmm) outliers start: 21 outliers final: 19 residues processed: 101 average time/residue: 0.0766 time to fit residues: 11.5007 Evaluate side-chains 96 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 0.350 ------------------------------------------------------------------------------- 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 347 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 466 LEU 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 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 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 553 THR Chi-restraints excluded: chain B residue 601 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 69 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 chunk 95 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 88 optimal weight: 0.4980 chunk 59 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3169 r_free = 0.3169 target = 0.056171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.043993 restraints weight = 95928.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.046176 restraints weight = 40306.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.047695 restraints weight = 23469.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.048758 restraints weight = 15935.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.049499 restraints weight = 12030.855| |-----------------------------------------------------------------------------| r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2965 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2965 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.4297 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= 0.118 Angle : 0.739 13.229 11935 Z= 0.337 Chirality : 0.043 0.195 1390 Planarity : 0.004 0.040 1515 Dihedral : 5.670 82.176 1217 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.73 % Favored : 96.18 % Rotamer: Outliers : 2.42 % Allowed : 19.45 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.27), residues: 1101 helix: 1.52 (0.24), residues: 513 sheet: -0.21 (0.35), residues: 219 loop : -1.24 (0.34), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 552 TYR 0.018 0.001 TYR A 399 PHE 0.023 0.001 PHE A 141 TRP 0.003 0.001 TRP B 22 HIS 0.002 0.001 HIS B 105 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 8784) covalent geometry : angle 0.73933 (11935) hydrogen bonds : bond 0.03408 ( 445) hydrogen bonds : angle 4.30032 ( 1298) *********************** 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 102 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.9460 (pp) cc_final: 0.9159 (tt) REVERT: A 191 LEU cc_start: 0.9410 (tp) cc_final: 0.9206 (tt) REVERT: A 236 MET cc_start: 0.8716 (mmm) cc_final: 0.8380 (mmm) REVERT: A 256 SER cc_start: 0.9105 (t) cc_final: 0.8762 (p) REVERT: A 344 MET cc_start: 0.8554 (ttm) cc_final: 0.8287 (tpp) REVERT: A 384 SER cc_start: 0.8860 (m) cc_final: 0.8565 (p) REVERT: A 556 MET cc_start: 0.9370 (ttp) cc_final: 0.9160 (ttm) REVERT: A 557 MET cc_start: 0.8922 (mmm) cc_final: 0.8677 (mmm) REVERT: A 573 MET cc_start: 0.8268 (mmm) cc_final: 0.7577 (mpp) REVERT: B 1 MET cc_start: 0.9078 (tpp) cc_final: 0.8750 (tpp) REVERT: B 69 MET cc_start: 0.9149 (ptp) cc_final: 0.8944 (ptm) REVERT: B 480 MET cc_start: 0.8737 (tpp) cc_final: 0.8338 (tpp) REVERT: B 503 MET cc_start: 0.9326 (ttm) cc_final: 0.9019 (mmm) REVERT: B 504 MET cc_start: 0.8521 (tpp) cc_final: 0.8317 (tpp) REVERT: B 541 CYS cc_start: 0.8327 (m) cc_final: 0.7938 (m) REVERT: B 592 MET cc_start: 0.7433 (mmm) cc_final: 0.7088 (mmm) outliers start: 22 outliers final: 18 residues processed: 98 average time/residue: 0.0689 time to fit residues: 10.2622 Evaluate side-chains 94 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.366 ------------------------------------------------------------------------------- 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 380 LEU 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 637 ARG Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 274 THR 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 553 THR Chi-restraints excluded: chain B residue 601 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 109 optimal weight: 6.9990 chunk 43 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 chunk 10 optimal weight: 0.1980 chunk 62 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 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 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 = 0.3173 r_free = 0.3173 target = 0.056309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.045379 restraints weight = 58031.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.047162 restraints weight = 29912.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.048428 restraints weight = 19179.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.049326 restraints weight = 13827.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.049908 restraints weight = 10794.173| |-----------------------------------------------------------------------------| r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2978 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2978 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.4412 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= 0.118 Angle : 0.763 13.542 11935 Z= 0.344 Chirality : 0.044 0.414 1390 Planarity : 0.004 0.040 1515 Dihedral : 5.577 77.474 1213 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.73 % Favored : 96.18 % Rotamer: Outliers : 2.20 % Allowed : 19.45 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.26), residues: 1101 helix: 1.49 (0.24), residues: 514 sheet: -0.16 (0.35), residues: 219 loop : -1.21 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 552 TYR 0.017 0.001 TYR A 399 PHE 0.023 0.001 PHE A 141 TRP 0.003 0.001 TRP B 22 HIS 0.002 0.001 HIS B 105 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 8784) covalent geometry : angle 0.76338 (11935) hydrogen bonds : bond 0.03436 ( 445) hydrogen bonds : angle 4.32648 ( 1298) ********************** 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 98 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 78 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.9446 (pp) cc_final: 0.9158 (tt) REVERT: A 236 MET cc_start: 0.8715 (mmm) cc_final: 0.8374 (mmm) REVERT: A 256 SER cc_start: 0.9099 (t) cc_final: 0.8751 (p) REVERT: A 301 PHE cc_start: 0.8128 (OUTLIER) cc_final: 0.7715 (m-80) REVERT: A 344 MET cc_start: 0.8555 (ttm) cc_final: 0.8328 (tpp) REVERT: A 384 SER cc_start: 0.8842 (m) cc_final: 0.8542 (p) REVERT: A 556 MET cc_start: 0.9355 (ttp) cc_final: 0.9150 (ttm) REVERT: A 557 MET cc_start: 0.8926 (mmm) cc_final: 0.8685 (mmm) REVERT: A 573 MET cc_start: 0.8257 (mmm) cc_final: 0.7565 (mpp) REVERT: B 1 MET cc_start: 0.8979 (tpp) cc_final: 0.8777 (tpp) REVERT: B 503 MET cc_start: 0.9310 (ttm) cc_final: 0.9019 (mmm) REVERT: B 504 MET cc_start: 0.8546 (tpp) cc_final: 0.8321 (tpp) REVERT: B 541 CYS cc_start: 0.8323 (m) cc_final: 0.7941 (m) REVERT: B 592 MET cc_start: 0.7416 (mmm) cc_final: 0.7084 (mmm) outliers start: 20 outliers final: 19 residues processed: 95 average time/residue: 0.0619 time to fit residues: 9.1552 Evaluate side-chains 97 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 0.324 ------------------------------------------------------------------------------- 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 347 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 466 LEU 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 525 VAL 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 263 ILE Chi-restraints excluded: chain B residue 274 THR 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 601 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 71 optimal weight: 8.9990 chunk 85 optimal weight: 0.0020 chunk 1 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 3 optimal weight: 0.0570 chunk 92 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 109 optimal weight: 10.0000 chunk 89 optimal weight: 0.9980 chunk 26 optimal weight: 0.3980 overall best weight: 0.4306 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.057048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.045265 restraints weight = 81710.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.047363 restraints weight = 37156.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.048785 restraints weight = 22345.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.049786 restraints weight = 15492.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.050502 restraints weight = 11791.733| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2994 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.4491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 8784 Z= 0.108 Angle : 0.747 20.632 11935 Z= 0.334 Chirality : 0.042 0.195 1390 Planarity : 0.004 0.039 1515 Dihedral : 5.503 79.904 1213 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.09 % Allowed : 19.45 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.27), residues: 1101 helix: 1.64 (0.24), residues: 507 sheet: -0.06 (0.36), residues: 213 loop : -1.15 (0.34), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 552 TYR 0.016 0.001 TYR A 399 PHE 0.022 0.001 PHE A 141 TRP 0.004 0.001 TRP B 22 HIS 0.002 0.001 HIS B 105 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 8784) covalent geometry : angle 0.74733 (11935) hydrogen bonds : bond 0.03260 ( 445) hydrogen bonds : angle 4.24269 ( 1298) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1503.97 seconds wall clock time: 26 minutes 40.33 seconds (1600.33 seconds total)