Starting phenix.real_space_refine on Wed Mar 12 11:20:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t4h_41031/03_2025/8t4h_41031.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t4h_41031/03_2025/8t4h_41031.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t4h_41031/03_2025/8t4h_41031.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t4h_41031/03_2025/8t4h_41031.map" model { file = "/net/cci-nas-00/data/ceres_data/8t4h_41031/03_2025/8t4h_41031.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t4h_41031/03_2025/8t4h_41031.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 31 5.16 5 C 4874 2.51 5 N 1354 2.21 5 O 1443 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7702 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 3442 Classifications: {'peptide': 533} Incomplete info: {'truncation_to_alanine': 192} Link IDs: {'PTRANS': 18, 'TRANS': 514} Chain breaks: 2 Unresolved non-hydrogen bonds: 693 Unresolved non-hydrogen angles: 894 Unresolved non-hydrogen dihedrals: 554 Unresolved non-hydrogen chiralities: 76 Planarities with less than four sites: {'GLN:plan1': 24, 'ARG:plan': 11, 'TYR:plan': 9, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 9, 'PHE:plan': 7, 'GLU:plan': 16, 'HIS:plan': 7} Unresolved non-hydrogen planarities: 406 Chain: "B" Number of atoms: 4186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4186 Classifications: {'peptide': 547} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 19, 'TRANS': 527} Chain breaks: 1 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 68 Chain: "C" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 74 Classifications: {'peptide': 8} Modifications used: {'COO': 1} Link IDs: {'TRANS': 7} Time building chain proxies: 5.88, per 1000 atoms: 0.76 Number of scatterers: 7702 At special positions: 0 Unit cell: (68.798, 112.426, 135.918, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 31 16.00 O 1443 8.00 N 1354 7.00 C 4874 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.07 Conformation dependent library (CDL) restraints added in 1.2 seconds 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2006 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 6 sheets defined 73.0% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 183 through 202 removed outlier: 4.451A pdb=" N LEU A 189 " --> pdb=" O ARG A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 218 removed outlier: 4.154A pdb=" N PHE A 206 " --> pdb=" O MET A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 250 removed outlier: 4.016A pdb=" N PHE A 224 " --> pdb=" O SER A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 270 Processing helix chain 'A' and resid 292 through 323 Processing helix chain 'A' and resid 324 through 373 removed outlier: 3.735A pdb=" N THR A 328 " --> pdb=" O SER A 324 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL A 330 " --> pdb=" O SER A 326 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N THR A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) Proline residue: A 336 - end of helix removed outlier: 4.074A pdb=" N LEU A 341 " --> pdb=" O LEU A 337 " (cutoff:3.500A) Proline residue: A 342 - end of helix removed outlier: 3.703A pdb=" N LYS A 347 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TRP A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 381 Processing helix chain 'A' and resid 382 through 437 removed outlier: 3.619A pdb=" N LYS A 393 " --> pdb=" O LYS A 389 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN A 402 " --> pdb=" O LYS A 398 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LYS A 403 " --> pdb=" O THR A 399 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 427 " --> pdb=" O LYS A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 482 removed outlier: 3.713A pdb=" N LEU A 449 " --> pdb=" O VAL A 445 " (cutoff:3.500A) Proline residue: A 466 - end of helix removed outlier: 4.100A pdb=" N LYS A 477 " --> pdb=" O GLY A 473 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ILE A 478 " --> pdb=" O SER A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 542 Processing helix chain 'A' and resid 543 through 552 Processing helix chain 'A' and resid 573 through 581 Processing helix chain 'A' and resid 594 through 599 Processing helix chain 'A' and resid 608 through 619 removed outlier: 3.514A pdb=" N ILE A 612 " --> pdb=" O THR A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 628 Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 637 through 641 removed outlier: 3.728A pdb=" N GLY A 640 " --> pdb=" O ASP A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 659 removed outlier: 3.583A pdb=" N ARG A 659 " --> pdb=" O ARG A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 687 Processing helix chain 'A' and resid 702 through 709 removed outlier: 3.709A pdb=" N LEU A 705 " --> pdb=" O HIS A 702 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN A 708 " --> pdb=" O LEU A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 732 Processing helix chain 'A' and resid 734 through 742 Processing helix chain 'B' and resid 132 through 146 Processing helix chain 'B' and resid 148 through 182 removed outlier: 3.680A pdb=" N GLY B 165 " --> pdb=" O LEU B 161 " (cutoff:3.500A) Proline residue: B 170 - end of helix Processing helix chain 'B' and resid 185 through 235 removed outlier: 3.626A pdb=" N GLY B 208 " --> pdb=" O SER B 204 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS B 209 " --> pdb=" O LEU B 205 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG B 210 " --> pdb=" O SER B 206 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG B 235 " --> pdb=" O SER B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 244 removed outlier: 3.854A pdb=" N PHE B 241 " --> pdb=" O ASP B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 261 removed outlier: 3.579A pdb=" N LEU B 249 " --> pdb=" O LYS B 245 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASP B 256 " --> pdb=" O ARG B 252 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N THR B 257 " --> pdb=" O LEU B 253 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR B 258 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU B 259 " --> pdb=" O SER B 255 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER B 261 " --> pdb=" O THR B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 289 removed outlier: 4.099A pdb=" N VAL B 279 " --> pdb=" O LEU B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 338 removed outlier: 3.598A pdb=" N THR B 293 " --> pdb=" O SER B 289 " (cutoff:3.500A) Proline residue: B 301 - end of helix removed outlier: 3.702A pdb=" N GLY B 338 " --> pdb=" O GLU B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 346 Processing helix chain 'B' and resid 347 through 402 removed outlier: 4.583A pdb=" N LEU B 390 " --> pdb=" O GLY B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 448 removed outlier: 3.824A pdb=" N GLY B 420 " --> pdb=" O GLN B 416 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N SER B 421 " --> pdb=" O GLU B 417 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU B 434 " --> pdb=" O TYR B 430 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N SER B 435 " --> pdb=" O GLY B 431 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N TYR B 446 " --> pdb=" O LYS B 442 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N MET B 447 " --> pdb=" O VAL B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 517 removed outlier: 4.243A pdb=" N ALA B 513 " --> pdb=" O LYS B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 537 Processing helix chain 'B' and resid 538 through 545 removed outlier: 3.576A pdb=" N HIS B 543 " --> pdb=" O HIS B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 565 Processing helix chain 'B' and resid 572 through 583 removed outlier: 3.800A pdb=" N VAL B 576 " --> pdb=" O GLU B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 591 removed outlier: 3.751A pdb=" N GLU B 591 " --> pdb=" O ASP B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 598 removed outlier: 3.986A pdb=" N THR B 598 " --> pdb=" O GLY B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 605 Processing helix chain 'B' and resid 608 through 623 removed outlier: 3.723A pdb=" N ARG B 623 " --> pdb=" O ARG B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 637 Processing helix chain 'B' and resid 638 through 646 Processing helix chain 'B' and resid 648 through 653 removed outlier: 4.437A pdb=" N ASP B 653 " --> pdb=" O ASN B 649 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 519 through 524 removed outlier: 6.664A pdb=" N PHE A 510 " --> pdb=" O VAL A 520 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLN A 522 " --> pdb=" O VAL A 508 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL A 508 " --> pdb=" O GLN A 522 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N LEU A 524 " --> pdb=" O GLN A 506 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 503 " --> pdb=" O LEU A 528 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 519 through 524 removed outlier: 6.664A pdb=" N PHE A 510 " --> pdb=" O VAL A 520 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLN A 522 " --> pdb=" O VAL A 508 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL A 508 " --> pdb=" O GLN A 522 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N LEU A 524 " --> pdb=" O GLN A 506 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N VAL A 508 " --> pdb=" O GLY A 559 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N GLY A 559 " --> pdb=" O VAL A 508 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 533 through 535 removed outlier: 6.614A pdb=" N THR A 534 " --> pdb=" O LEU A 698 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 712 through 716 removed outlier: 6.425A pdb=" N ILE A 712 " --> pdb=" O GLY A 723 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N GLY A 723 " --> pdb=" O ILE A 712 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N PHE A 714 " --> pdb=" O ARG A 721 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 484 through 493 removed outlier: 7.374A pdb=" N VAL B 485 " --> pdb=" O ALA B 476 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ALA B 476 " --> pdb=" O VAL B 485 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LYS B 487 " --> pdb=" O SER B 474 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N SER B 474 " --> pdb=" O LYS B 487 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LEU B 489 " --> pdb=" O ASP B 472 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL B 468 " --> pdb=" O LEU B 493 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLN B 471 " --> pdb=" O GLN B 526 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN B 526 " --> pdb=" O GLN B 471 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL B 473 " --> pdb=" O GLY B 524 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N GLY B 524 " --> pdb=" O VAL B 473 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 546 through 549 removed outlier: 6.891A pdb=" N VAL B 547 " --> pdb=" O ILE B 629 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N ASP B 631 " --> pdb=" O VAL B 547 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N VAL B 549 " --> pdb=" O ASP B 631 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL B 498 " --> pdb=" O GLN B 671 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N LEU B 673 " --> pdb=" O VAL B 498 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ALA B 500 " --> pdb=" O LEU B 673 " (cutoff:3.500A) 584 hydrogen bonds defined for protein. 1713 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.20 Time building geometry restraints manager: 2.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2608 1.34 - 1.46: 1670 1.46 - 1.58: 3493 1.58 - 1.70: 0 1.70 - 1.82: 53 Bond restraints: 7824 Sorted by residual: bond pdb=" CA LEU B 286 " pdb=" C LEU B 286 " ideal model delta sigma weight residual 1.524 1.502 0.022 1.27e-02 6.20e+03 3.02e+00 bond pdb=" CB THR A 235 " pdb=" CG2 THR A 235 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.50e+00 bond pdb=" CA MET B 285 " pdb=" C MET B 285 " ideal model delta sigma weight residual 1.523 1.503 0.020 1.30e-02 5.92e+03 2.47e+00 bond pdb=" CA ASN A 251 " pdb=" CB ASN A 251 " ideal model delta sigma weight residual 1.530 1.553 -0.023 1.69e-02 3.50e+03 1.85e+00 bond pdb=" SD MET B 196 " pdb=" CE MET B 196 " ideal model delta sigma weight residual 1.791 1.758 0.033 2.50e-02 1.60e+03 1.77e+00 ... (remaining 7819 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 10539 2.83 - 5.67: 81 5.67 - 8.50: 27 8.50 - 11.33: 6 11.33 - 14.17: 3 Bond angle restraints: 10656 Sorted by residual: angle pdb=" C VAL B 576 " pdb=" N MET B 577 " pdb=" CA MET B 577 " ideal model delta sigma weight residual 121.58 112.36 9.22 1.95e+00 2.63e-01 2.24e+01 angle pdb=" CB MET A 420 " pdb=" CG MET A 420 " pdb=" SD MET A 420 " ideal model delta sigma weight residual 112.70 98.53 14.17 3.00e+00 1.11e-01 2.23e+01 angle pdb=" N LEU B 286 " pdb=" CA LEU B 286 " pdb=" C LEU B 286 " ideal model delta sigma weight residual 111.07 106.13 4.94 1.07e+00 8.73e-01 2.13e+01 angle pdb=" CB MET B 260 " pdb=" CG MET B 260 " pdb=" SD MET B 260 " ideal model delta sigma weight residual 112.70 125.54 -12.84 3.00e+00 1.11e-01 1.83e+01 angle pdb=" CB MET B 592 " pdb=" CG MET B 592 " pdb=" SD MET B 592 " ideal model delta sigma weight residual 112.70 124.34 -11.64 3.00e+00 1.11e-01 1.51e+01 ... (remaining 10651 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.79: 4101 16.79 - 33.57: 423 33.57 - 50.36: 113 50.36 - 67.15: 21 67.15 - 83.93: 11 Dihedral angle restraints: 4669 sinusoidal: 1554 harmonic: 3115 Sorted by residual: dihedral pdb=" CA MET A 420 " pdb=" C MET A 420 " pdb=" N LEU A 421 " pdb=" CA LEU A 421 " ideal model delta harmonic sigma weight residual 180.00 162.75 17.25 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA ASP B 237 " pdb=" CB ASP B 237 " pdb=" CG ASP B 237 " pdb=" OD1 ASP B 237 " ideal model delta sinusoidal sigma weight residual -30.00 -87.81 57.81 1 2.00e+01 2.50e-03 1.12e+01 dihedral pdb=" CA ILE A 319 " pdb=" C ILE A 319 " pdb=" N MET A 320 " pdb=" CA MET A 320 " ideal model delta harmonic sigma weight residual 180.00 163.97 16.03 0 5.00e+00 4.00e-02 1.03e+01 ... (remaining 4666 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 917 0.039 - 0.078: 264 0.078 - 0.116: 77 0.116 - 0.155: 12 0.155 - 0.194: 6 Chirality restraints: 1276 Sorted by residual: chirality pdb=" CB ILE B 169 " pdb=" CA ILE B 169 " pdb=" CG1 ILE B 169 " pdb=" CG2 ILE B 169 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.41e-01 chirality pdb=" CG LEU A 316 " pdb=" CB LEU A 316 " pdb=" CD1 LEU A 316 " pdb=" CD2 LEU A 316 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.74e-01 chirality pdb=" CA MET B 577 " pdb=" N MET B 577 " pdb=" C MET B 577 " pdb=" CB MET B 577 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.19e-01 ... (remaining 1273 not shown) Planarity restraints: 1391 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 251 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.20e+00 pdb=" C ASN A 251 " -0.035 2.00e-02 2.50e+03 pdb=" O ASN A 251 " 0.013 2.00e-02 2.50e+03 pdb=" N THR A 252 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 257 " -0.011 2.00e-02 2.50e+03 1.58e-02 3.74e+00 pdb=" CG HIS A 257 " 0.033 2.00e-02 2.50e+03 pdb=" ND1 HIS A 257 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 HIS A 257 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 HIS A 257 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS A 257 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 404 " 0.009 2.00e-02 2.50e+03 1.81e-02 3.29e+00 pdb=" CD GLU A 404 " -0.031 2.00e-02 2.50e+03 pdb=" OE1 GLU A 404 " 0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU A 404 " 0.011 2.00e-02 2.50e+03 ... (remaining 1388 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1938 2.79 - 3.32: 7749 3.32 - 3.85: 12888 3.85 - 4.37: 12954 4.37 - 4.90: 23270 Nonbonded interactions: 58799 Sorted by model distance: nonbonded pdb=" OE1 GLU B 307 " pdb=" OH TYR B 376 " model vdw 2.267 3.040 nonbonded pdb=" O LEU B 253 " pdb=" OG1 THR B 257 " model vdw 2.295 3.040 nonbonded pdb=" O ASN A 443 " pdb=" OG1 THR A 446 " model vdw 2.331 3.040 nonbonded pdb=" NH1 ARG A 186 " pdb=" OG1 THR A 252 " model vdw 2.337 3.120 nonbonded pdb=" NH2 ARG A 378 " pdb=" O GLN B 236 " model vdw 2.340 3.120 ... (remaining 58794 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.770 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: 0.280 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 22.310 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 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 0.052 7824 Z= 0.229 Angle : 0.760 14.168 10656 Z= 0.371 Chirality : 0.042 0.194 1276 Planarity : 0.004 0.044 1391 Dihedral : 15.551 83.931 2663 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.57 % Allowed : 20.43 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.25), residues: 1076 helix: 1.78 (0.19), residues: 720 sheet: -1.23 (0.75), residues: 54 loop : -0.31 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 322 HIS 0.021 0.002 HIS A 257 PHE 0.011 0.001 PHE A 224 TYR 0.010 0.001 TYR B 422 ARG 0.009 0.000 ARG C 2 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 126 time to evaluate : 0.801 Fit side-chains revert: symmetry clash REVERT: A 329 MET cc_start: 0.8048 (mmm) cc_final: 0.7595 (mmt) REVERT: A 339 PHE cc_start: 0.7991 (m-80) cc_final: 0.7595 (m-10) REVERT: A 408 TYR cc_start: 0.8111 (t80) cc_final: 0.7789 (t80) REVERT: B 166 GLU cc_start: 0.8409 (mm-30) cc_final: 0.7723 (mt-10) REVERT: B 269 ASN cc_start: 0.8235 (t0) cc_final: 0.7876 (t0) REVERT: B 294 LEU cc_start: 0.7505 (mt) cc_final: 0.7088 (tp) REVERT: B 298 LEU cc_start: 0.8840 (mm) cc_final: 0.8466 (mp) outliers start: 4 outliers final: 2 residues processed: 128 average time/residue: 0.2039 time to fit residues: 35.0945 Evaluate side-chains 91 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 89 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain B residue 419 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.1980 chunk 81 optimal weight: 0.6980 chunk 45 optimal weight: 10.0000 chunk 27 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 43 optimal weight: 20.0000 chunk 83 optimal weight: 0.9980 chunk 32 optimal weight: 20.0000 chunk 50 optimal weight: 9.9990 chunk 62 optimal weight: 0.9980 chunk 97 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 ASN ** B 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.143212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.113515 restraints weight = 13443.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.116970 restraints weight = 6752.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.119119 restraints weight = 4252.726| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7824 Z= 0.181 Angle : 0.537 7.116 10656 Z= 0.276 Chirality : 0.037 0.142 1276 Planarity : 0.003 0.029 1391 Dihedral : 3.730 34.941 1157 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.26 % Allowed : 20.28 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.26), residues: 1076 helix: 2.22 (0.19), residues: 736 sheet: -1.04 (0.77), residues: 54 loop : -0.30 (0.36), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 322 HIS 0.009 0.001 HIS A 257 PHE 0.022 0.001 PHE A 224 TYR 0.010 0.001 TYR A 309 ARG 0.003 0.000 ARG B 561 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 0.861 Fit side-chains REVERT: A 202 MET cc_start: 0.7417 (tpp) cc_final: 0.7093 (ttm) REVERT: A 338 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8807 (tt) REVERT: A 339 PHE cc_start: 0.7768 (m-80) cc_final: 0.7424 (m-10) REVERT: A 420 MET cc_start: 0.7865 (ttt) cc_final: 0.7527 (mtp) REVERT: B 298 LEU cc_start: 0.8508 (mm) cc_final: 0.8260 (mp) REVERT: B 390 LEU cc_start: 0.8559 (tt) cc_final: 0.8343 (tp) outliers start: 23 outliers final: 15 residues processed: 109 average time/residue: 0.1670 time to fit residues: 26.0664 Evaluate side-chains 102 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain C residue 4 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 32 optimal weight: 10.0000 chunk 95 optimal weight: 4.9990 chunk 12 optimal weight: 0.2980 chunk 58 optimal weight: 1.9990 chunk 36 optimal weight: 30.0000 chunk 66 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 30 optimal weight: 8.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 416 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 = 0.3979 r_free = 0.3979 target = 0.142877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.113296 restraints weight = 13606.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.116749 restraints weight = 6769.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.119028 restraints weight = 4231.236| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7824 Z= 0.173 Angle : 0.506 6.230 10656 Z= 0.261 Chirality : 0.037 0.126 1276 Planarity : 0.003 0.032 1391 Dihedral : 3.540 33.000 1157 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.55 % Allowed : 21.28 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.26), residues: 1076 helix: 2.40 (0.19), residues: 736 sheet: -0.97 (0.77), residues: 54 loop : -0.18 (0.36), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 322 HIS 0.006 0.001 HIS A 257 PHE 0.024 0.001 PHE A 224 TYR 0.014 0.001 TYR A 408 ARG 0.003 0.000 ARG B 252 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 0.901 Fit side-chains REVERT: A 202 MET cc_start: 0.7464 (tpp) cc_final: 0.6973 (ttm) REVERT: A 231 MET cc_start: 0.8519 (ttp) cc_final: 0.8288 (ttp) REVERT: A 338 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8873 (tt) REVERT: A 339 PHE cc_start: 0.7774 (m-80) cc_final: 0.7485 (m-80) REVERT: B 260 MET cc_start: 0.7271 (mmp) cc_final: 0.6986 (mmp) REVERT: B 298 LEU cc_start: 0.8487 (mm) cc_final: 0.8228 (mp) REVERT: B 399 MET cc_start: 0.8124 (OUTLIER) cc_final: 0.7314 (ttt) outliers start: 25 outliers final: 14 residues processed: 110 average time/residue: 0.2000 time to fit residues: 31.7944 Evaluate side-chains 98 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain C residue 4 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 33 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 35 optimal weight: 30.0000 chunk 77 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 34 optimal weight: 8.9990 chunk 52 optimal weight: 20.0000 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 HIS ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 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 = 0.3915 r_free = 0.3915 target = 0.137886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.107785 restraints weight = 13554.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.111119 restraints weight = 6937.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.113199 restraints weight = 4430.957| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 7824 Z= 0.289 Angle : 0.590 9.553 10656 Z= 0.302 Chirality : 0.040 0.132 1276 Planarity : 0.003 0.034 1391 Dihedral : 3.621 32.513 1156 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 4.96 % Allowed : 20.57 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.26), residues: 1076 helix: 2.30 (0.19), residues: 730 sheet: -1.20 (0.76), residues: 54 loop : -0.30 (0.36), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 322 HIS 0.007 0.001 HIS A 257 PHE 0.021 0.002 PHE A 224 TYR 0.015 0.002 TYR A 408 ARG 0.004 0.000 ARG B 252 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 90 time to evaluate : 0.950 Fit side-chains REVERT: A 199 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8585 (mm) REVERT: A 214 TRP cc_start: 0.8115 (t60) cc_final: 0.7892 (t60) REVERT: A 231 MET cc_start: 0.8536 (ttp) cc_final: 0.8248 (ttp) REVERT: A 338 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8846 (tt) REVERT: A 339 PHE cc_start: 0.7923 (m-80) cc_final: 0.7560 (m-80) REVERT: A 420 MET cc_start: 0.8283 (mtt) cc_final: 0.8075 (mtt) REVERT: B 294 LEU cc_start: 0.7976 (mt) cc_final: 0.7739 (tp) REVERT: B 298 LEU cc_start: 0.8634 (mm) cc_final: 0.8305 (mp) REVERT: B 399 MET cc_start: 0.8520 (OUTLIER) cc_final: 0.7970 (ttm) outliers start: 35 outliers final: 27 residues processed: 117 average time/residue: 0.1709 time to fit residues: 28.4921 Evaluate side-chains 112 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 82 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 573 ASP Chi-restraints excluded: chain C residue 4 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 77 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 56 optimal weight: 0.0970 chunk 66 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 75 optimal weight: 0.6980 chunk 46 optimal weight: 10.0000 chunk 23 optimal weight: 0.5980 chunk 96 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 83 optimal weight: 0.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 ASN ** A 451 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 = 0.3964 r_free = 0.3964 target = 0.141846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.112153 restraints weight = 13539.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.115664 restraints weight = 6740.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.117902 restraints weight = 4207.874| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7824 Z= 0.158 Angle : 0.523 8.091 10656 Z= 0.261 Chirality : 0.037 0.154 1276 Planarity : 0.003 0.034 1391 Dihedral : 3.442 32.240 1156 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.83 % Allowed : 22.13 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.26), residues: 1076 helix: 2.50 (0.19), residues: 735 sheet: -1.12 (0.75), residues: 54 loop : -0.27 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 322 HIS 0.008 0.001 HIS A 257 PHE 0.019 0.001 PHE A 224 TYR 0.014 0.001 TYR A 465 ARG 0.003 0.000 ARG B 252 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 87 time to evaluate : 0.873 Fit side-chains REVERT: A 202 MET cc_start: 0.7471 (tpp) cc_final: 0.7158 (ttm) REVERT: A 214 TRP cc_start: 0.8020 (t60) cc_final: 0.7805 (t60) REVERT: A 338 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8894 (tt) REVERT: A 339 PHE cc_start: 0.7890 (m-80) cc_final: 0.7595 (m-80) REVERT: B 298 LEU cc_start: 0.8632 (mm) cc_final: 0.8315 (mp) REVERT: B 388 GLN cc_start: 0.8377 (tp40) cc_final: 0.8120 (tp40) REVERT: B 399 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.7993 (ttm) outliers start: 27 outliers final: 19 residues processed: 109 average time/residue: 0.1648 time to fit residues: 25.9054 Evaluate side-chains 101 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 80 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 571 CYS Chi-restraints excluded: chain C residue 4 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 0.4980 chunk 50 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 56 optimal weight: 0.3980 chunk 86 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 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 = 0.3935 r_free = 0.3935 target = 0.139269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.109372 restraints weight = 13565.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.112739 restraints weight = 6869.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.114915 restraints weight = 4341.779| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7824 Z= 0.226 Angle : 0.543 6.573 10656 Z= 0.277 Chirality : 0.039 0.145 1276 Planarity : 0.003 0.034 1391 Dihedral : 3.485 32.064 1156 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.96 % Allowed : 21.99 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.26), residues: 1076 helix: 2.50 (0.19), residues: 729 sheet: -1.20 (0.74), residues: 54 loop : -0.28 (0.35), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 322 HIS 0.003 0.001 HIS B 543 PHE 0.018 0.001 PHE A 224 TYR 0.014 0.001 TYR B 282 ARG 0.004 0.000 ARG B 252 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 88 time to evaluate : 0.775 Fit side-chains revert: symmetry clash REVERT: A 199 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8574 (mm) REVERT: A 338 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8860 (tt) REVERT: A 339 PHE cc_start: 0.8011 (m-80) cc_final: 0.7738 (m-80) REVERT: B 260 MET cc_start: 0.7055 (mmp) cc_final: 0.6841 (mmp) REVERT: B 298 LEU cc_start: 0.8617 (mm) cc_final: 0.8344 (mp) REVERT: B 390 LEU cc_start: 0.8617 (tt) cc_final: 0.8342 (tp) REVERT: B 399 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.8091 (ttm) REVERT: C 6 THR cc_start: 0.8937 (t) cc_final: 0.8706 (p) outliers start: 35 outliers final: 25 residues processed: 116 average time/residue: 0.1701 time to fit residues: 28.3610 Evaluate side-chains 108 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 80 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain C residue 4 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 8 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 2 optimal weight: 0.3980 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 30.0000 chunk 37 optimal weight: 0.0060 chunk 51 optimal weight: 0.9990 chunk 81 optimal weight: 0.5980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 ASN A 451 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.142095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.112530 restraints weight = 13461.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.116001 restraints weight = 6652.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.118238 restraints weight = 4160.489| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7824 Z= 0.161 Angle : 0.528 8.477 10656 Z= 0.264 Chirality : 0.037 0.137 1276 Planarity : 0.003 0.033 1391 Dihedral : 3.377 29.445 1156 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 4.26 % Allowed : 23.69 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.26), residues: 1076 helix: 2.69 (0.19), residues: 723 sheet: -1.13 (0.74), residues: 54 loop : -0.30 (0.35), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 214 HIS 0.005 0.001 HIS A 257 PHE 0.017 0.001 PHE A 224 TYR 0.013 0.001 TYR A 408 ARG 0.003 0.000 ARG B 252 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 91 time to evaluate : 0.747 Fit side-chains REVERT: A 199 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8490 (mm) REVERT: A 319 ILE cc_start: 0.9240 (tt) cc_final: 0.8952 (tt) REVERT: A 338 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8906 (tt) REVERT: A 339 PHE cc_start: 0.7925 (m-80) cc_final: 0.7686 (m-80) REVERT: A 347 LYS cc_start: 0.7903 (mmmm) cc_final: 0.7556 (mtmt) REVERT: B 298 LEU cc_start: 0.8551 (mm) cc_final: 0.8291 (mp) REVERT: B 399 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.7947 (ttt) outliers start: 30 outliers final: 20 residues processed: 115 average time/residue: 0.1650 time to fit residues: 27.2329 Evaluate side-chains 107 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 527 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 16 optimal weight: 0.6980 chunk 104 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 29 optimal weight: 30.0000 chunk 15 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 416 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 = 0.3953 r_free = 0.3953 target = 0.140750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.111038 restraints weight = 13676.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.114444 restraints weight = 6800.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.116707 restraints weight = 4279.200| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7824 Z= 0.206 Angle : 0.574 13.164 10656 Z= 0.283 Chirality : 0.038 0.134 1276 Planarity : 0.003 0.033 1391 Dihedral : 3.279 14.024 1154 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.97 % Allowed : 24.68 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.26), residues: 1076 helix: 2.63 (0.19), residues: 722 sheet: -1.18 (0.73), residues: 54 loop : -0.26 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 322 HIS 0.004 0.001 HIS A 257 PHE 0.016 0.001 PHE A 224 TYR 0.015 0.001 TYR B 430 ARG 0.004 0.000 ARG B 252 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 89 time to evaluate : 0.920 Fit side-chains REVERT: A 199 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8541 (mm) REVERT: A 329 MET cc_start: 0.7380 (mmt) cc_final: 0.7090 (tpp) REVERT: A 338 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8833 (tt) REVERT: A 339 PHE cc_start: 0.7937 (m-80) cc_final: 0.7666 (m-80) REVERT: B 298 LEU cc_start: 0.8569 (mm) cc_final: 0.8310 (mp) REVERT: B 390 LEU cc_start: 0.8609 (tt) cc_final: 0.8335 (tp) REVERT: B 399 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8104 (ttm) outliers start: 28 outliers final: 24 residues processed: 112 average time/residue: 0.2171 time to fit residues: 34.8123 Evaluate side-chains 108 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 81 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 527 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 32 optimal weight: 0.8980 chunk 35 optimal weight: 20.0000 chunk 86 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 41 optimal weight: 8.9990 chunk 79 optimal weight: 0.7980 chunk 60 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.141081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.111388 restraints weight = 13728.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.114935 restraints weight = 6682.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.117061 restraints weight = 4139.763| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7824 Z= 0.197 Angle : 0.594 12.876 10656 Z= 0.291 Chirality : 0.038 0.150 1276 Planarity : 0.003 0.034 1391 Dihedral : 3.282 14.529 1154 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 4.54 % Allowed : 24.68 % Favored : 70.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.26), residues: 1076 helix: 2.62 (0.19), residues: 725 sheet: -1.17 (0.73), residues: 54 loop : -0.30 (0.35), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 322 HIS 0.003 0.001 HIS A 257 PHE 0.016 0.001 PHE A 224 TYR 0.016 0.001 TYR C 3 ARG 0.004 0.000 ARG B 252 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 89 time to evaluate : 1.408 Fit side-chains revert: symmetry clash REVERT: A 329 MET cc_start: 0.7502 (mmt) cc_final: 0.7218 (tpp) REVERT: A 338 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8883 (tt) REVERT: A 339 PHE cc_start: 0.7983 (m-80) cc_final: 0.7770 (m-80) REVERT: A 347 LYS cc_start: 0.7823 (mmmm) cc_final: 0.7620 (mtmm) REVERT: B 298 LEU cc_start: 0.8643 (mm) cc_final: 0.8360 (mp) REVERT: B 390 LEU cc_start: 0.8619 (tt) cc_final: 0.8354 (tp) REVERT: B 399 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.8074 (ttm) outliers start: 32 outliers final: 26 residues processed: 113 average time/residue: 0.2846 time to fit residues: 45.1948 Evaluate side-chains 115 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 87 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain C residue 4 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 67 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 29 optimal weight: 30.0000 chunk 85 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 23 optimal weight: 0.0000 chunk 45 optimal weight: 0.5980 chunk 105 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.142190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.112724 restraints weight = 13586.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.116239 restraints weight = 6676.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.118519 restraints weight = 4156.494| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7824 Z= 0.178 Angle : 0.583 12.376 10656 Z= 0.282 Chirality : 0.038 0.157 1276 Planarity : 0.003 0.037 1391 Dihedral : 3.227 14.790 1154 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.69 % Allowed : 25.67 % Favored : 70.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.26), residues: 1076 helix: 2.69 (0.19), residues: 725 sheet: -1.13 (0.73), residues: 54 loop : -0.28 (0.35), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 322 HIS 0.004 0.001 HIS A 257 PHE 0.016 0.001 PHE A 224 TYR 0.016 0.001 TYR B 430 ARG 0.003 0.000 ARG B 252 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 86 time to evaluate : 0.779 Fit side-chains revert: symmetry clash REVERT: A 338 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8865 (tt) REVERT: A 339 PHE cc_start: 0.7918 (m-80) cc_final: 0.7683 (m-80) REVERT: A 347 LYS cc_start: 0.7819 (mmmm) cc_final: 0.7524 (mtmm) REVERT: A 417 ILE cc_start: 0.8440 (OUTLIER) cc_final: 0.8104 (tp) REVERT: B 298 LEU cc_start: 0.8612 (mm) cc_final: 0.8339 (mp) REVERT: B 399 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.8072 (ttm) outliers start: 26 outliers final: 22 residues processed: 106 average time/residue: 0.1655 time to fit residues: 24.8123 Evaluate side-chains 108 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 83 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 527 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 22 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 39 optimal weight: 20.0000 chunk 24 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.141447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.111855 restraints weight = 13561.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.115373 restraints weight = 6679.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.117658 restraints weight = 4165.369| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7824 Z= 0.199 Angle : 0.600 12.585 10656 Z= 0.293 Chirality : 0.038 0.161 1276 Planarity : 0.003 0.037 1391 Dihedral : 3.258 14.624 1154 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.83 % Allowed : 25.53 % Favored : 70.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.26), residues: 1076 helix: 2.67 (0.19), residues: 725 sheet: -1.18 (0.72), residues: 54 loop : -0.28 (0.35), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 322 HIS 0.007 0.001 HIS A 257 PHE 0.016 0.001 PHE B 412 TYR 0.014 0.001 TYR B 282 ARG 0.004 0.000 ARG B 252 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3195.19 seconds wall clock time: 58 minutes 4.33 seconds (3484.33 seconds total)