Starting phenix.real_space_refine on Sat Dec 28 04:47:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t4g_41030/12_2024/8t4g_41030.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t4g_41030/12_2024/8t4g_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_41030/12_2024/8t4g_41030.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t4g_41030/12_2024/8t4g_41030.map" model { file = "/net/cci-nas-00/data/ceres_data/8t4g_41030/12_2024/8t4g_41030.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t4g_41030/12_2024/8t4g_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 6.19, per 1000 atoms: 0.80 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: 1.95 Conformation dependent library (CDL) restraints added in 1.3 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: 0.92 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: 2.33 Time building geometry restraints manager: 2.24 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: 2.970 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: 22.360 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.760 ------------------------------------------------------------------------------- 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= 0.222 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 *********************** 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 : 0.908 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 99 average time/residue: 0.2241 time to fit residues: 29.6874 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 : 0.862 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 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= 0.163 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 *********************** 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 : 1.016 Fit side-chains outliers start: 16 outliers final: 12 residues processed: 113 average time/residue: 0.2114 time to fit residues: 32.6112 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 : 0.894 ------------------------------------------------------------------------------- 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 54 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 33 optimal weight: 0.2980 chunk 78 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.0753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7846 Z= 0.185 Angle : 0.464 6.260 10689 Z= 0.238 Chirality : 0.037 0.126 1278 Planarity : 0.003 0.049 1397 Dihedral : 3.908 59.205 1157 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % 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: 3.03 (0.27), residues: 1079 helix: 2.94 (0.19), residues: 718 sheet: -0.53 (0.72), residues: 58 loop : 0.21 (0.39), residues: 303 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 0.009 0.001 TYR B 422 ARG 0.002 0.000 ARG A 357 *********************** 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 124 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 0.889 Fit side-chains revert: symmetry clash REVERT: B 269 ASN cc_start: 0.8898 (OUTLIER) cc_final: 0.8606 (t0) outliers start: 23 outliers final: 15 residues processed: 120 average time/residue: 0.2015 time to fit residues: 33.1243 Evaluate side-chains 111 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.847 ------------------------------------------------------------------------------- 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 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 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 96 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 50 optimal weight: 30.0000 chunk 10 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 65 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 51 optimal weight: 20.0000 chunk 92 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 7846 Z= 0.379 Angle : 0.579 9.497 10689 Z= 0.296 Chirality : 0.040 0.145 1278 Planarity : 0.004 0.048 1397 Dihedral : 4.077 53.425 1157 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.95 % Allowed : 21.33 % Favored : 74.72 % 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: 2.58 (0.27), residues: 1079 helix: 2.60 (0.19), residues: 719 sheet: -0.73 (0.72), residues: 58 loop : 0.05 (0.39), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 214 HIS 0.007 0.001 HIS B 670 PHE 0.011 0.002 PHE B 241 TYR 0.014 0.002 TYR B 541 ARG 0.003 0.000 ARG B 273 *********************** 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 122 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 94 time to evaluate : 0.855 Fit side-chains revert: symmetry clash REVERT: A 404 GLU cc_start: 0.8446 (tm-30) cc_final: 0.8000 (tm-30) REVERT: B 168 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8359 (mp) REVERT: B 404 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8272 (mp) outliers start: 28 outliers final: 22 residues processed: 117 average time/residue: 0.2082 time to fit residues: 33.0219 Evaluate side-chains 116 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 0.989 ------------------------------------------------------------------------------- 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 264 VAL Chi-restraints excluded: chain A residue 401 ASN 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 321 ILE Chi-restraints excluded: chain B residue 331 VAL 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 42 optimal weight: 50.0000 chunk 88 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.0995 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= 0.257 Angle : 0.511 8.294 10689 Z= 0.263 Chirality : 0.038 0.134 1278 Planarity : 0.003 0.047 1397 Dihedral : 3.990 52.104 1157 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.81 % Allowed : 22.46 % Favored : 73.73 % 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: 2.69 (0.27), residues: 1079 helix: 2.71 (0.19), residues: 719 sheet: -0.77 (0.71), residues: 58 loop : 0.04 (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 0.011 0.001 TYR B 172 ARG 0.001 0.000 ARG B 273 *********************** 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 120 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 93 time to evaluate : 0.856 Fit side-chains revert: symmetry clash REVERT: A 404 GLU cc_start: 0.8457 (tm-30) cc_final: 0.8011 (tm-30) REVERT: B 168 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8346 (mp) REVERT: B 269 ASN cc_start: 0.8915 (OUTLIER) cc_final: 0.8694 (t0) REVERT: B 404 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8231 (mp) outliers start: 27 outliers final: 21 residues processed: 117 average time/residue: 0.2080 time to fit residues: 33.2079 Evaluate side-chains 116 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 0.846 ------------------------------------------------------------------------------- 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 401 ASN 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 425 THR 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 C residue 1 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 20.0000 chunk 93 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 103 optimal weight: 0.0020 chunk 85 optimal weight: 2.9990 chunk 47 optimal weight: 20.0000 chunk 8 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 99 optimal weight: 0.2980 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1047 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= 0.156 Angle : 0.467 7.224 10689 Z= 0.239 Chirality : 0.036 0.122 1278 Planarity : 0.003 0.046 1397 Dihedral : 3.785 52.066 1157 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.11 % Allowed : 23.87 % 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: 2.97 (0.19), residues: 719 sheet: -0.75 (0.71), residues: 58 loop : 0.11 (0.39), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 214 HIS 0.002 0.001 HIS B 543 PHE 0.012 0.001 PHE B 588 TYR 0.022 0.001 TYR B 541 ARG 0.001 0.000 ARG A 357 *********************** 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 118 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.860 Fit side-chains revert: symmetry clash REVERT: A 404 GLU cc_start: 0.8470 (tm-30) cc_final: 0.8002 (tm-30) REVERT: B 269 ASN cc_start: 0.8847 (OUTLIER) cc_final: 0.8624 (t0) REVERT: B 404 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8166 (mp) outliers start: 22 outliers final: 14 residues processed: 115 average time/residue: 0.2090 time to fit residues: 32.6745 Evaluate side-chains 111 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 404 LEU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 547 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 11 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 57 optimal weight: 0.0010 chunk 103 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 47 optimal weight: 20.0000 chunk 63 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1111 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= 0.177 Angle : 0.474 6.938 10689 Z= 0.242 Chirality : 0.037 0.122 1278 Planarity : 0.003 0.045 1397 Dihedral : 3.612 51.736 1157 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.82 % Allowed : 24.58 % Favored : 72.60 % 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: 2.98 (0.19), residues: 721 sheet: -0.71 (0.72), residues: 58 loop : 0.17 (0.40), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 214 HIS 0.002 0.001 HIS B 543 PHE 0.011 0.001 PHE B 588 TYR 0.012 0.001 TYR B 428 ARG 0.001 0.000 ARG A 357 *********************** 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 116 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.773 Fit side-chains revert: symmetry clash REVERT: A 404 GLU cc_start: 0.8455 (tm-30) cc_final: 0.8019 (tm-30) REVERT: B 269 ASN cc_start: 0.8866 (OUTLIER) cc_final: 0.8645 (t0) REVERT: B 404 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8158 (mp) outliers start: 20 outliers final: 15 residues processed: 113 average time/residue: 0.2112 time to fit residues: 32.4634 Evaluate side-chains 114 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL 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 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 404 LEU Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 443 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 65 optimal weight: 0.3980 chunk 70 optimal weight: 0.9990 chunk 50 optimal weight: 40.0000 chunk 9 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7846 Z= 0.248 Angle : 0.515 7.331 10689 Z= 0.261 Chirality : 0.038 0.130 1278 Planarity : 0.003 0.044 1397 Dihedral : 3.599 52.186 1157 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.95 % Allowed : 23.31 % Favored : 72.74 % 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: 2.88 (0.27), residues: 1079 helix: 2.87 (0.19), residues: 719 sheet: -0.72 (0.72), residues: 58 loop : 0.05 (0.39), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 214 HIS 0.003 0.001 HIS B 171 PHE 0.009 0.001 PHE B 241 TYR 0.011 0.001 TYR B 428 ARG 0.002 0.000 ARG B 273 *********************** 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 123 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 95 time to evaluate : 0.877 Fit side-chains revert: symmetry clash REVERT: A 404 GLU cc_start: 0.8407 (tm-30) cc_final: 0.7980 (tm-30) REVERT: B 269 ASN cc_start: 0.8889 (OUTLIER) cc_final: 0.8565 (t0) REVERT: B 404 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8159 (mp) outliers start: 28 outliers final: 22 residues processed: 119 average time/residue: 0.2088 time to fit residues: 33.8266 Evaluate side-chains 118 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 94 time to evaluate : 0.884 ------------------------------------------------------------------------------- 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 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 528 LEU 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 90 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 57 optimal weight: 0.0050 chunk 41 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 29 optimal weight: 40.0000 chunk 86 optimal weight: 0.8980 chunk 95 optimal weight: 0.2980 chunk 63 optimal weight: 0.8980 chunk 101 optimal weight: 0.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7846 Z= 0.175 Angle : 0.487 7.135 10689 Z= 0.245 Chirality : 0.037 0.133 1278 Planarity : 0.003 0.044 1397 Dihedral : 3.493 52.347 1157 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.11 % Allowed : 24.29 % Favored : 72.60 % 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: 3.06 (0.27), residues: 1079 helix: 3.00 (0.19), residues: 721 sheet: -0.74 (0.71), residues: 58 loop : 0.13 (0.40), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 214 HIS 0.002 0.001 HIS A 255 PHE 0.010 0.001 PHE B 201 TYR 0.024 0.001 TYR B 541 ARG 0.002 0.000 ARG A 357 *********************** 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 119 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.967 Fit side-chains revert: symmetry clash REVERT: A 404 GLU cc_start: 0.8432 (tm-30) cc_final: 0.8009 (tm-30) REVERT: B 269 ASN cc_start: 0.8841 (OUTLIER) cc_final: 0.8532 (t0) REVERT: B 404 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8128 (mp) outliers start: 22 outliers final: 19 residues processed: 115 average time/residue: 0.2106 time to fit residues: 33.3066 Evaluate side-chains 118 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.864 ------------------------------------------------------------------------------- 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 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 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 425 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 0.4980 chunk 48 optimal weight: 20.0000 chunk 70 optimal weight: 0.6980 chunk 106 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 84 optimal weight: 0.1980 chunk 8 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 52 optimal weight: 0.3980 chunk 67 optimal weight: 0.8980 chunk 90 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7846 Z= 0.156 Angle : 0.485 7.839 10689 Z= 0.243 Chirality : 0.036 0.137 1278 Planarity : 0.003 0.045 1397 Dihedral : 3.389 52.062 1157 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.54 % Allowed : 25.00 % Favored : 72.46 % 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: 3.16 (0.27), residues: 1079 helix: 3.06 (0.19), residues: 725 sheet: -0.65 (0.72), residues: 58 loop : 0.16 (0.40), residues: 296 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 0.010 0.001 PHE B 201 TYR 0.011 0.001 TYR A 408 ARG 0.001 0.000 ARG A 357 ********************** 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 119 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 1.094 Fit side-chains revert: symmetry clash REVERT: B 269 ASN cc_start: 0.8754 (OUTLIER) cc_final: 0.8503 (t0) REVERT: B 404 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.8030 (mp) outliers start: 18 outliers final: 15 residues processed: 115 average time/residue: 0.2690 time to fit residues: 41.6879 Evaluate side-chains 115 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 87 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4166 r_free = 0.4166 target = 0.167705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.124118 restraints weight = 10393.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.127614 restraints weight = 5968.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.129791 restraints weight = 4255.609| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3745 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3745 r_free = 0.3745 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3744 r_free = 0.3744 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3744 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1297 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= 0.197 Angle : 0.498 7.620 10689 Z= 0.249 Chirality : 0.037 0.134 1278 Planarity : 0.003 0.044 1397 Dihedral : 3.424 52.112 1157 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.11 % Allowed : 24.29 % Favored : 72.60 % 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: 3.08 (0.27), residues: 1079 helix: 2.99 (0.19), residues: 727 sheet: -0.66 (0.72), residues: 58 loop : 0.14 (0.40), residues: 294 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 0.010 0.001 PHE B 201 TYR 0.013 0.001 TYR B 428 ARG 0.001 0.000 ARG A 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1828.89 seconds wall clock time: 34 minutes 20.03 seconds (2060.03 seconds total)