Starting phenix.real_space_refine on Sun May 11 08:05:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t4g_41030/05_2025/8t4g_41030.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t4g_41030/05_2025/8t4g_41030.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t4g_41030/05_2025/8t4g_41030.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t4g_41030/05_2025/8t4g_41030.map" model { file = "/net/cci-nas-00/data/ceres_data/8t4g_41030/05_2025/8t4g_41030.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t4g_41030/05_2025/8t4g_41030.cif" } resolution = 3.5 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= 0.028 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 4890 2.51 5 N 1355 2.21 5 O 1445 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 7721 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 3417 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 190} Link IDs: {'PTRANS': 18, 'TRANS': 510} Chain breaks: 2 Unresolved non-hydrogen bonds: 683 Unresolved non-hydrogen angles: 881 Unresolved non-hydrogen dihedrals: 545 Unresolved non-hydrogen chiralities: 75 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': 6, 'GLU:plan': 16, 'HIS:plan': 7} Unresolved non-hydrogen planarities: 400 Chain: "B" Number of atoms: 4225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4225 Classifications: {'peptide': 551} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 20, 'TRANS': 530} Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 62 Chain: "C" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 79 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ARG A 529 " occ=0.51 ... (3 atoms not shown) pdb=" CB ARG A 529 " occ=0.51 Time building chain proxies: 5.48, per 1000 atoms: 0.71 Number of scatterers: 7721 At special positions: 0 Unit cell: (69.637, 110.748, 132.562, 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 1445 8.00 N 1355 7.00 C 4890 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: 1.86 Conformation dependent library (CDL) restraints added in 1.1 seconds 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2010 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 5 sheets defined 73.6% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 183 through 202 removed outlier: 3.871A pdb=" N MET A 202 " --> pdb=" O SER A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 218 removed outlier: 3.993A pdb=" N PHE A 206 " --> pdb=" O MET A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 270 removed outlier: 3.740A pdb=" N PHE A 224 " --> pdb=" O SER A 220 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N THR A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU A 230 " --> pdb=" O ARG A 226 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N HIS A 255 " --> pdb=" O ASN A 251 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG A 270 " --> pdb=" O GLY A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 324 Processing helix chain 'A' and resid 324 through 340 Proline residue: A 336 - end of helix Processing helix chain 'A' and resid 340 through 373 removed outlier: 4.541A pdb=" N TRP A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR A 349 " --> pdb=" O VAL A 345 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 380 Processing helix chain 'A' and resid 382 through 437 removed outlier: 3.634A pdb=" N GLU A 396 " --> pdb=" O GLU A 392 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR A 399 " --> pdb=" O GLN A 395 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU A 400 " --> pdb=" O GLU A 396 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLN A 402 " --> pdb=" O LYS A 398 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS A 403 " --> pdb=" O THR A 399 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU A 422 " --> pdb=" O SER A 418 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU A 427 " --> pdb=" O LYS A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 476 removed outlier: 3.714A pdb=" N MET A 452 " --> pdb=" O VAL A 448 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLN A 453 " --> pdb=" O LEU A 449 " (cutoff:3.500A) Proline residue: A 466 - end of helix Processing helix chain 'A' and resid 543 through 545 No H-bonds generated for 'chain 'A' and resid 543 through 545' Processing helix chain 'A' and resid 546 through 552 removed outlier: 3.842A pdb=" N LEU A 550 " --> pdb=" O THR A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 572 removed outlier: 3.994A pdb=" N TYR A 572 " --> pdb=" O LEU A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 581 removed outlier: 3.844A pdb=" N ARG A 579 " --> pdb=" O ARG A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 599 Processing helix chain 'A' and resid 608 through 619 Processing helix chain 'A' and resid 621 through 626 Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 637 through 641 Processing helix chain 'A' and resid 644 through 660 Processing helix chain 'A' and resid 674 through 688 Processing helix chain 'A' and resid 689 through 694 removed outlier: 3.676A pdb=" N ARG A 694 " --> pdb=" O GLU A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 709 removed outlier: 3.784A pdb=" N GLU A 707 " --> pdb=" O LEU A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 732 Processing helix chain 'A' and resid 734 through 741 Processing helix chain 'B' and resid 133 through 145 removed outlier: 3.557A pdb=" N LEU B 137 " --> pdb=" O ASN B 133 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER B 145 " --> pdb=" O LEU B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 181 removed outlier: 3.680A pdb=" N LEU B 168 " --> pdb=" O LEU B 164 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE B 169 " --> pdb=" O GLY B 165 " (cutoff:3.500A) Proline residue: B 170 - end of helix Processing helix chain 'B' and resid 188 through 234 Processing helix chain 'B' and resid 237 through 244 removed outlier: 3.592A pdb=" N PHE B 241 " --> pdb=" O ASP B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 255 Processing helix chain 'B' and resid 255 through 260 Processing helix chain 'B' and resid 261 through 263 No H-bonds generated for 'chain 'B' and resid 261 through 263' Processing helix chain 'B' and resid 266 through 289 Processing helix chain 'B' and resid 289 through 338 removed outlier: 4.046A pdb=" N LEU B 295 " --> pdb=" O ARG B 291 " (cutoff:3.500A) Proline residue: B 301 - end of helix removed outlier: 3.586A 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: 3.604A pdb=" N GLU B 351 " --> pdb=" O ALA B 347 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B 365 " --> pdb=" O GLN B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 449 removed outlier: 3.749A pdb=" N SER B 421 " --> pdb=" O GLU B 417 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY B 431 " --> pdb=" O VAL B 427 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N TYR B 446 " --> pdb=" O LYS B 442 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N MET B 447 " --> pdb=" O VAL B 443 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG B 449 " --> pdb=" O SER B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 508 Processing helix chain 'B' and resid 509 through 517 removed outlier: 4.013A pdb=" N ALA B 513 " --> pdb=" O LYS B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 537 No H-bonds generated for 'chain 'B' and resid 535 through 537' Processing helix chain 'B' and resid 538 through 545 removed outlier: 3.663A pdb=" N HIS B 543 " --> pdb=" O HIS B 539 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER B 544 " --> pdb=" O CYS B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 565 Processing helix chain 'B' and resid 572 through 583 Processing helix chain 'B' and resid 585 through 590 Processing helix chain 'B' and resid 594 through 598 Processing helix chain 'B' and resid 601 through 605 Processing helix chain 'B' and resid 608 through 622 Processing helix chain 'B' and resid 633 through 636 Processing helix chain 'B' and resid 638 through 646 Processing helix chain 'B' and resid 648 through 653 removed outlier: 4.765A pdb=" N ASP B 653 " --> pdb=" O ASN B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 668 removed outlier: 3.820A pdb=" N THR B 665 " --> pdb=" O ARG B 662 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 521 through 524 removed outlier: 5.880A pdb=" N GLN A 522 " --> pdb=" O PHE A 510 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N PHE A 510 " --> pdb=" O GLN A 522 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL A 508 " --> pdb=" O GLY A 559 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N GLY A 559 " --> pdb=" O VAL A 508 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 533 through 535 removed outlier: 6.741A pdb=" N THR A 534 " --> pdb=" O LEU A 698 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 712 through 716 removed outlier: 6.686A pdb=" N ILE A 712 " --> pdb=" O GLY A 723 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLY A 723 " --> pdb=" O ILE A 712 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N PHE A 714 " --> pdb=" O ARG A 721 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 486 through 489 removed outlier: 5.895A pdb=" N LYS B 487 " --> pdb=" O PHE B 475 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N PHE B 475 " --> pdb=" O LYS B 487 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL B 473 " --> pdb=" O GLY B 524 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLY B 524 " --> pdb=" O VAL B 473 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 546 through 548 removed outlier: 6.478A pdb=" N VAL B 498 " --> pdb=" O GLN B 671 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N LEU B 673 " --> pdb=" O VAL B 498 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ALA B 500 " --> pdb=" O LEU B 673 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LEU B 675 " --> pdb=" O ALA B 500 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N VAL B 502 " --> pdb=" O LEU B 675 " (cutoff:3.500A) 586 hydrogen bonds defined for protein. 1701 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: 2.24 Time building geometry restraints manager: 2.16 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: 2615 1.34 - 1.46: 879 1.46 - 1.57: 4299 1.57 - 1.69: 0 1.69 - 1.81: 53 Bond restraints: 7846 Sorted by residual: bond pdb=" C VAL B 547 " pdb=" O VAL B 547 " ideal model delta sigma weight residual 1.236 1.222 0.014 1.02e-02 9.61e+03 1.83e+00 bond pdb=" CA VAL B 547 " pdb=" CB VAL B 547 " ideal model delta sigma weight residual 1.544 1.526 0.017 1.32e-02 5.74e+03 1.66e+00 bond pdb=" C PHE B 195 " pdb=" O PHE B 195 " ideal model delta sigma weight residual 1.236 1.222 0.015 1.15e-02 7.56e+03 1.63e+00 bond pdb=" CA VAL B 467 " pdb=" CB VAL B 467 " ideal model delta sigma weight residual 1.533 1.547 -0.015 1.14e-02 7.69e+03 1.63e+00 bond pdb=" C LEU A 241 " pdb=" N GLU A 242 " ideal model delta sigma weight residual 1.334 1.318 0.016 1.27e-02 6.20e+03 1.62e+00 ... (remaining 7841 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 10436 1.46 - 2.93: 203 2.93 - 4.39: 34 4.39 - 5.85: 12 5.85 - 7.31: 4 Bond angle restraints: 10689 Sorted by residual: angle pdb=" N VAL B 485 " pdb=" CA VAL B 485 " pdb=" C VAL B 485 " ideal model delta sigma weight residual 113.47 109.64 3.83 1.01e+00 9.80e-01 1.44e+01 angle pdb=" C PHE B 194 " pdb=" N PHE B 195 " pdb=" CA PHE B 195 " ideal model delta sigma weight residual 120.65 116.07 4.58 1.32e+00 5.74e-01 1.21e+01 angle pdb=" CA GLN A 451 " pdb=" CB GLN A 451 " pdb=" CG GLN A 451 " ideal model delta sigma weight residual 114.10 120.21 -6.11 2.00e+00 2.50e-01 9.34e+00 angle pdb=" N VAL B 419 " pdb=" CA VAL B 419 " pdb=" C VAL B 419 " ideal model delta sigma weight residual 110.62 113.22 -2.60 1.02e+00 9.61e-01 6.52e+00 angle pdb=" N GLU A 242 " pdb=" CA GLU A 242 " pdb=" C GLU A 242 " ideal model delta sigma weight residual 111.07 108.48 2.59 1.07e+00 8.73e-01 5.84e+00 ... (remaining 10684 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 4153 17.89 - 35.77: 410 35.77 - 53.66: 99 53.66 - 71.54: 12 71.54 - 89.43: 9 Dihedral angle restraints: 4683 sinusoidal: 1562 harmonic: 3121 Sorted by residual: dihedral pdb=" CA PHE A 339 " pdb=" C PHE A 339 " pdb=" N LEU A 340 " pdb=" CA LEU A 340 " ideal model delta harmonic sigma weight residual 180.00 162.69 17.31 0 5.00e+00 4.00e-02 1.20e+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 -87.40 57.40 1 2.00e+01 2.50e-03 1.11e+01 dihedral pdb=" CB GLU B 351 " pdb=" CG GLU B 351 " pdb=" CD GLU B 351 " pdb=" OE1 GLU B 351 " ideal model delta sinusoidal sigma weight residual 0.00 -87.56 87.56 1 3.00e+01 1.11e-03 1.02e+01 ... (remaining 4680 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 755 0.027 - 0.054: 346 0.054 - 0.080: 108 0.080 - 0.107: 54 0.107 - 0.134: 15 Chirality restraints: 1278 Sorted by residual: chirality pdb=" CB THR A 294 " pdb=" CA THR A 294 " pdb=" OG1 THR A 294 " pdb=" CG2 THR A 294 " both_signs ideal model delta sigma weight residual False 2.55 2.42 0.13 2.00e-01 2.50e+01 4.48e-01 chirality pdb=" CA MET A 374 " pdb=" N MET A 374 " pdb=" C MET A 374 " pdb=" CB MET A 374 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.14e-01 chirality pdb=" CA ILE A 699 " pdb=" N ILE A 699 " pdb=" C ILE A 699 " pdb=" CB ILE A 699 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.69e-01 ... (remaining 1275 not shown) Planarity restraints: 1397 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 567 " 0.041 5.00e-02 4.00e+02 6.31e-02 6.37e+00 pdb=" N PRO A 568 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 568 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 568 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 467 " -0.007 2.00e-02 2.50e+03 1.40e-02 1.97e+00 pdb=" C VAL B 467 " 0.024 2.00e-02 2.50e+03 pdb=" O VAL B 467 " -0.009 2.00e-02 2.50e+03 pdb=" N VAL B 468 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 672 " -0.006 2.00e-02 2.50e+03 1.23e-02 1.51e+00 pdb=" C ILE B 672 " 0.021 2.00e-02 2.50e+03 pdb=" O ILE B 672 " -0.008 2.00e-02 2.50e+03 pdb=" N LEU B 673 " -0.007 2.00e-02 2.50e+03 ... (remaining 1394 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1739 2.78 - 3.31: 7829 3.31 - 3.84: 12702 3.84 - 4.37: 12818 4.37 - 4.90: 23874 Nonbonded interactions: 58962 Sorted by model distance: nonbonded pdb=" O LEU A 338 " pdb=" OG SER A 418 " model vdw 2.254 3.040 nonbonded pdb=" OE1 GLU B 307 " pdb=" OH TYR B 376 " model vdw 2.259 3.040 nonbonded pdb=" O GLU B 593 " pdb=" OG1 THR B 598 " model vdw 2.288 3.040 nonbonded pdb=" OD1 ASN B 250 " pdb=" OG SER B 254 " model vdw 2.318 3.040 nonbonded pdb=" NH1 ARG B 327 " pdb=" OE1 GLN B 361 " model vdw 2.363 3.120 ... (remaining 58957 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=0.51 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: 3.280 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.560 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 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 : 0.003 0.026 7846 Z= 0.162 Angle : 0.534 7.314 10689 Z= 0.294 Chirality : 0.038 0.134 1278 Planarity : 0.003 0.063 1397 Dihedral : 15.823 89.430 2673 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.14 % Allowed : 19.35 % Favored : 80.51 % 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: 2.80 (0.26), residues: 1079 helix: 2.78 (0.19), residues: 708 sheet: -0.55 (0.73), residues: 59 loop : 0.18 (0.37), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 214 HIS 0.012 0.001 HIS B 670 PHE 0.009 0.001 PHE B 201 TYR 0.010 0.001 TYR B 422 ARG 0.002 0.000 ARG A 210 Details of bonding type rmsd hydrogen bonds : bond 0.11986 ( 586) hydrogen bonds : angle 4.21136 ( 1701) covalent geometry : bond 0.00338 ( 7846) covalent geometry : angle 0.53411 (10689) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 98 time to evaluate : 0.867 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 99 average time/residue: 0.2192 time to fit residues: 29.0834 Evaluate side-chains 97 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 96 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 0.0020 chunk 27 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 43 optimal weight: 10.0000 chunk 83 optimal weight: 0.1980 chunk 32 optimal weight: 20.0000 chunk 50 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- 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 = 0.4186 r_free = 0.4186 target = 0.169293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.126265 restraints weight = 10304.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.129708 restraints weight = 6012.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.131759 restraints weight = 4328.196| |-----------------------------------------------------------------------------| r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3774 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3774 r_free = 0.3774 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3773 r_free = 0.3773 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3773 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.0625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7846 Z= 0.117 Angle : 0.465 5.838 10689 Z= 0.243 Chirality : 0.037 0.120 1278 Planarity : 0.003 0.056 1397 Dihedral : 3.943 58.281 1157 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.26 % Allowed : 19.21 % Favored : 78.53 % 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: 2.99 (0.27), residues: 1079 helix: 2.89 (0.19), residues: 718 sheet: -0.49 (0.72), residues: 58 loop : 0.27 (0.39), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 214 HIS 0.010 0.001 HIS B 670 PHE 0.019 0.001 PHE B 588 TYR 0.009 0.001 TYR B 422 ARG 0.002 0.000 ARG B 381 Details of bonding type rmsd hydrogen bonds : bond 0.04482 ( 586) hydrogen bonds : angle 3.44623 ( 1701) covalent geometry : bond 0.00248 ( 7846) covalent geometry : angle 0.46516 (10689) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.870 Fit side-chains outliers start: 16 outliers final: 12 residues processed: 113 average time/residue: 0.2058 time to fit residues: 31.6251 Evaluate side-chains 109 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 447 PHE Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain C residue 1 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 102 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 48 optimal weight: 20.0000 chunk 43 optimal weight: 8.9990 chunk 54 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.167867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.122080 restraints weight = 10854.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.125479 restraints weight = 6413.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.127713 restraints weight = 4660.808| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.0740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7846 Z= 0.180 Angle : 0.513 6.887 10689 Z= 0.264 Chirality : 0.038 0.135 1278 Planarity : 0.003 0.050 1397 Dihedral : 4.017 58.214 1157 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.25 % Allowed : 20.06 % Favored : 76.69 % 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: 2.79 (0.27), residues: 1079 helix: 2.76 (0.19), residues: 719 sheet: -0.62 (0.72), residues: 58 loop : 0.10 (0.39), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 214 HIS 0.009 0.001 HIS B 670 PHE 0.009 0.001 PHE B 201 TYR 0.011 0.001 TYR B 422 ARG 0.002 0.000 ARG B 273 Details of bonding type rmsd hydrogen bonds : bond 0.04952 ( 586) hydrogen bonds : angle 3.51235 ( 1701) covalent geometry : bond 0.00429 ( 7846) covalent geometry : angle 0.51302 (10689) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.897 Fit side-chains revert: symmetry clash REVERT: B 269 ASN cc_start: 0.8943 (OUTLIER) cc_final: 0.8646 (t0) outliers start: 23 outliers final: 18 residues processed: 113 average time/residue: 0.2116 time to fit residues: 32.7165 Evaluate side-chains 112 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 447 PHE Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain C residue 1 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 35 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 99 optimal weight: 0.0470 chunk 17 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 28 optimal weight: 9.9990 chunk 80 optimal weight: 1.9990 chunk 95 optimal weight: 0.0070 chunk 87 optimal weight: 2.9990 overall best weight: 0.8102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.169208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.123853 restraints weight = 10657.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.127269 restraints weight = 6277.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.129487 restraints weight = 4547.221| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.0824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7846 Z= 0.132 Angle : 0.472 6.644 10689 Z= 0.243 Chirality : 0.037 0.127 1278 Planarity : 0.003 0.047 1397 Dihedral : 3.942 57.101 1157 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.53 % Allowed : 20.76 % Favored : 75.71 % 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: 2.93 (0.27), residues: 1079 helix: 2.88 (0.19), residues: 719 sheet: -0.62 (0.71), residues: 58 loop : 0.15 (0.39), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 214 HIS 0.008 0.001 HIS B 670 PHE 0.010 0.001 PHE B 201 TYR 0.010 0.001 TYR B 172 ARG 0.001 0.000 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.04616 ( 586) hydrogen bonds : angle 3.37666 ( 1701) covalent geometry : bond 0.00301 ( 7846) covalent geometry : angle 0.47167 (10689) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 98 time to evaluate : 0.781 Fit side-chains revert: symmetry clash REVERT: A 404 GLU cc_start: 0.8405 (tm-30) cc_final: 0.8184 (tm-30) REVERT: B 168 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8334 (mp) REVERT: B 269 ASN cc_start: 0.8899 (OUTLIER) cc_final: 0.8654 (t0) REVERT: B 404 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8112 (mp) outliers start: 25 outliers final: 16 residues processed: 120 average time/residue: 0.1911 time to fit residues: 31.2200 Evaluate side-chains 114 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 447 PHE Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain C residue 1 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 28 optimal weight: 20.0000 chunk 101 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 45 optimal weight: 20.0000 chunk 81 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 29 optimal weight: 20.0000 chunk 12 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.4155 r_free = 0.4155 target = 0.168253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.122810 restraints weight = 10626.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.126244 restraints weight = 6271.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.128398 restraints weight = 4550.311| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.0900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7846 Z= 0.147 Angle : 0.494 9.159 10689 Z= 0.251 Chirality : 0.038 0.177 1278 Planarity : 0.003 0.047 1397 Dihedral : 3.896 53.713 1157 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.95 % Allowed : 21.75 % Favored : 74.29 % 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: 2.89 (0.27), residues: 1079 helix: 2.85 (0.19), residues: 719 sheet: -0.65 (0.72), residues: 58 loop : 0.12 (0.39), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 214 HIS 0.007 0.001 HIS B 670 PHE 0.010 0.001 PHE B 241 TYR 0.021 0.001 TYR B 541 ARG 0.001 0.000 ARG B 273 Details of bonding type rmsd hydrogen bonds : bond 0.04692 ( 586) hydrogen bonds : angle 3.37561 ( 1701) covalent geometry : bond 0.00343 ( 7846) covalent geometry : angle 0.49373 (10689) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 95 time to evaluate : 0.862 Fit side-chains revert: symmetry clash REVERT: A 404 GLU cc_start: 0.8425 (tm-30) cc_final: 0.7948 (tm-30) REVERT: B 168 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8347 (mp) REVERT: B 269 ASN cc_start: 0.8901 (OUTLIER) cc_final: 0.8695 (t0) REVERT: B 388 GLN cc_start: 0.8500 (tp40) cc_final: 0.8299 (tp40) REVERT: B 404 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8153 (mp) outliers start: 28 outliers final: 22 residues processed: 118 average time/residue: 0.1948 time to fit residues: 31.3198 Evaluate side-chains 119 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 447 PHE Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain C residue 1 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 68 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4167 r_free = 0.4167 target = 0.167732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.124062 restraints weight = 10392.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.127478 restraints weight = 5947.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.129471 restraints weight = 4265.103| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7846 Z= 0.123 Angle : 0.473 8.080 10689 Z= 0.241 Chirality : 0.037 0.125 1278 Planarity : 0.003 0.045 1397 Dihedral : 3.774 51.534 1157 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.67 % Allowed : 22.88 % Favored : 73.45 % 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: 3.04 (0.27), residues: 1079 helix: 2.98 (0.19), residues: 719 sheet: -0.68 (0.72), residues: 58 loop : 0.15 (0.40), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 214 HIS 0.006 0.001 HIS B 670 PHE 0.012 0.001 PHE B 588 TYR 0.009 0.001 TYR B 172 ARG 0.001 0.000 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.04423 ( 586) hydrogen bonds : angle 3.27350 ( 1701) covalent geometry : bond 0.00277 ( 7846) covalent geometry : angle 0.47261 (10689) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 0.855 Fit side-chains revert: symmetry clash REVERT: B 168 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8355 (mp) REVERT: B 269 ASN cc_start: 0.8870 (OUTLIER) cc_final: 0.8648 (t0) REVERT: B 404 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8163 (mp) outliers start: 26 outliers final: 18 residues processed: 118 average time/residue: 0.1962 time to fit residues: 31.5909 Evaluate side-chains 114 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 447 PHE Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain C residue 1 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 32 optimal weight: 30.0000 chunk 102 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4159 r_free = 0.4159 target = 0.166939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.123161 restraints weight = 10466.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.126644 restraints weight = 6005.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.128830 restraints weight = 4293.891| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7846 Z= 0.131 Angle : 0.480 7.791 10689 Z= 0.244 Chirality : 0.037 0.128 1278 Planarity : 0.003 0.045 1397 Dihedral : 3.655 51.588 1157 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.67 % Allowed : 22.88 % Favored : 73.45 % 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: 3.00 (0.27), residues: 1079 helix: 2.94 (0.19), residues: 720 sheet: -0.66 (0.73), residues: 58 loop : 0.15 (0.39), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 214 HIS 0.006 0.001 HIS B 670 PHE 0.011 0.001 PHE B 588 TYR 0.010 0.001 TYR B 172 ARG 0.001 0.000 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.04483 ( 586) hydrogen bonds : angle 3.27164 ( 1701) covalent geometry : bond 0.00301 ( 7846) covalent geometry : angle 0.47954 (10689) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 93 time to evaluate : 0.775 Fit side-chains revert: symmetry clash REVERT: A 404 GLU cc_start: 0.8394 (tm-30) cc_final: 0.8153 (tm-30) REVERT: B 168 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8364 (mp) REVERT: B 269 ASN cc_start: 0.8872 (OUTLIER) cc_final: 0.8647 (t0) REVERT: B 404 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8148 (mp) outliers start: 26 outliers final: 20 residues processed: 115 average time/residue: 0.1965 time to fit residues: 30.5821 Evaluate side-chains 116 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 447 PHE Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain C residue 1 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 81 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 44 optimal weight: 30.0000 chunk 37 optimal weight: 20.0000 chunk 45 optimal weight: 6.9990 chunk 5 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.4158 r_free = 0.4158 target = 0.168598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.122953 restraints weight = 10741.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.126415 restraints weight = 6288.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.128618 restraints weight = 4556.037| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7846 Z= 0.141 Angle : 0.495 7.704 10689 Z= 0.251 Chirality : 0.037 0.129 1278 Planarity : 0.003 0.045 1397 Dihedral : 3.560 51.998 1157 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.67 % Allowed : 23.45 % Favored : 72.88 % 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: 2.96 (0.27), residues: 1079 helix: 2.91 (0.19), residues: 720 sheet: -0.64 (0.73), residues: 58 loop : 0.13 (0.39), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 214 HIS 0.006 0.001 HIS B 670 PHE 0.010 0.001 PHE B 588 TYR 0.024 0.001 TYR B 541 ARG 0.001 0.000 ARG B 273 Details of bonding type rmsd hydrogen bonds : bond 0.04584 ( 586) hydrogen bonds : angle 3.28704 ( 1701) covalent geometry : bond 0.00328 ( 7846) covalent geometry : angle 0.49491 (10689) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 98 time to evaluate : 0.791 Fit side-chains revert: symmetry clash REVERT: A 404 GLU cc_start: 0.8395 (tm-30) cc_final: 0.8139 (tm-30) REVERT: B 168 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8364 (mp) REVERT: B 269 ASN cc_start: 0.8883 (OUTLIER) cc_final: 0.8605 (t0) REVERT: B 404 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8125 (mp) outliers start: 26 outliers final: 22 residues processed: 120 average time/residue: 0.1934 time to fit residues: 31.8548 Evaluate side-chains 119 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 447 PHE Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain C residue 1 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 24 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 43 optimal weight: 20.0000 chunk 48 optimal weight: 40.0000 chunk 90 optimal weight: 0.5980 chunk 105 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 = 0.4158 r_free = 0.4158 target = 0.166856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.122953 restraints weight = 10637.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.126505 restraints weight = 6063.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.128715 restraints weight = 4306.756| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7846 Z= 0.133 Angle : 0.493 7.492 10689 Z= 0.250 Chirality : 0.037 0.128 1278 Planarity : 0.003 0.045 1397 Dihedral : 3.497 52.146 1157 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 4.10 % Allowed : 22.88 % Favored : 73.02 % 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: 3.01 (0.27), residues: 1079 helix: 2.95 (0.19), residues: 720 sheet: -0.66 (0.73), residues: 58 loop : 0.13 (0.39), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 214 HIS 0.002 0.001 HIS B 543 PHE 0.010 0.001 PHE B 201 TYR 0.010 0.001 TYR B 172 ARG 0.001 0.000 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.04494 ( 586) hydrogen bonds : angle 3.25378 ( 1701) covalent geometry : bond 0.00308 ( 7846) covalent geometry : angle 0.49321 (10689) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 92 time to evaluate : 0.784 Fit side-chains revert: symmetry clash REVERT: B 168 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8362 (mp) REVERT: B 269 ASN cc_start: 0.8833 (OUTLIER) cc_final: 0.8512 (t0) REVERT: B 404 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8172 (mp) outliers start: 29 outliers final: 22 residues processed: 117 average time/residue: 0.1973 time to fit residues: 31.3277 Evaluate side-chains 119 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 447 PHE Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain C residue 1 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 10 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 78 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 33 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 chunk 80 optimal weight: 0.5980 chunk 38 optimal weight: 10.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4160 r_free = 0.4160 target = 0.167168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.123377 restraints weight = 10459.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.126841 restraints weight = 6010.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.129061 restraints weight = 4291.068| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7846 Z= 0.128 Angle : 0.500 8.213 10689 Z= 0.251 Chirality : 0.037 0.134 1278 Planarity : 0.003 0.044 1397 Dihedral : 3.472 52.215 1157 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.53 % Allowed : 23.45 % Favored : 73.02 % 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: 3.05 (0.27), residues: 1079 helix: 2.97 (0.19), residues: 721 sheet: -0.65 (0.73), residues: 58 loop : 0.17 (0.40), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 214 HIS 0.002 0.001 HIS B 543 PHE 0.009 0.001 PHE B 201 TYR 0.012 0.001 TYR B 428 ARG 0.001 0.000 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.04419 ( 586) hydrogen bonds : angle 3.22907 ( 1701) covalent geometry : bond 0.00294 ( 7846) covalent geometry : angle 0.49972 (10689) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 0.895 Fit side-chains revert: symmetry clash REVERT: B 168 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8363 (mp) REVERT: B 269 ASN cc_start: 0.8834 (OUTLIER) cc_final: 0.8516 (t0) REVERT: B 404 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8174 (mp) outliers start: 25 outliers final: 22 residues processed: 118 average time/residue: 0.2060 time to fit residues: 33.3555 Evaluate side-chains 121 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 447 PHE Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain C residue 1 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 91 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 36 optimal weight: 8.9990 chunk 29 optimal weight: 30.0000 chunk 105 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 84 optimal weight: 0.2980 chunk 6 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 39 optimal weight: 9.9990 chunk 50 optimal weight: 20.0000 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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 = 0.4113 r_free = 0.4113 target = 0.162392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.118216 restraints weight = 10601.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.121443 restraints weight = 6239.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.123572 restraints weight = 4543.471| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 7846 Z= 0.234 Angle : 0.593 8.599 10689 Z= 0.301 Chirality : 0.040 0.138 1278 Planarity : 0.004 0.045 1397 Dihedral : 3.744 52.539 1157 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.81 % Allowed : 23.16 % Favored : 73.02 % 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 (0.27), residues: 1079 helix: 2.61 (0.19), residues: 721 sheet: -0.89 (0.72), residues: 58 loop : -0.06 (0.39), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 214 HIS 0.005 0.001 HIS B 171 PHE 0.012 0.002 PHE A 339 TYR 0.025 0.002 TYR B 428 ARG 0.003 0.000 ARG B 273 Details of bonding type rmsd hydrogen bonds : bond 0.05429 ( 586) hydrogen bonds : angle 3.55866 ( 1701) covalent geometry : bond 0.00568 ( 7846) covalent geometry : angle 0.59343 (10689) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2752.96 seconds wall clock time: 48 minutes 41.97 seconds (2921.97 seconds total)