Starting phenix.real_space_refine on Tue Feb 11 16:40:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cn1_30413/02_2025/7cn1_30413.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cn1_30413/02_2025/7cn1_30413.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7cn1_30413/02_2025/7cn1_30413.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cn1_30413/02_2025/7cn1_30413.map" model { file = "/net/cci-nas-00/data/ceres_data/7cn1_30413/02_2025/7cn1_30413.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cn1_30413/02_2025/7cn1_30413.cif" } resolution = 3.7 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians K 3 8.98 5 S 29 5.16 5 C 4227 2.51 5 N 1000 2.21 5 O 1031 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6290 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1594 Classifications: {'peptide': 208} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 6, 'TRANS': 201} Chain breaks: 6 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 56 Chain: "B" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1555 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 6, 'TRANS': 194} Chain breaks: 6 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "C" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1575 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 6, 'TRANS': 200} Chain breaks: 7 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'TYR:plan': 1, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 52 Chain: "D" Number of atoms: 1563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1563 Classifications: {'peptide': 206} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 6, 'TRANS': 199} Chain breaks: 5 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 55 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.81, per 1000 atoms: 0.76 Number of scatterers: 6290 At special positions: 0 Unit cell: (116.688, 112.268, 80.444, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 3 19.00 S 29 16.00 O 1031 8.00 N 1000 7.00 C 4227 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: 1.51 Conformation dependent library (CDL) restraints added in 1.0 seconds 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1558 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 0 sheets defined 78.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 404 through 431 removed outlier: 3.994A pdb=" N VAL A 409 " --> pdb=" O PRO A 405 " (cutoff:3.500A) Proline residue: A 426 - end of helix removed outlier: 3.525A pdb=" N PHE A 431 " --> pdb=" O TYR A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 472 removed outlier: 3.695A pdb=" N MET A 462 " --> pdb=" O ILE A 458 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N PHE A 463 " --> pdb=" O VAL A 459 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ILE A 467 " --> pdb=" O PHE A 463 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LEU A 468 " --> pdb=" O ILE A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 497 Processing helix chain 'A' and resid 498 through 505 removed outlier: 4.000A pdb=" N VAL A 503 " --> pdb=" O LEU A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 530 Processing helix chain 'A' and resid 531 through 537 removed outlier: 4.136A pdb=" N VAL A 535 " --> pdb=" O ARG A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.694A pdb=" N TYR A 542 " --> pdb=" O LEU A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 575 removed outlier: 3.721A pdb=" N GLU A 575 " --> pdb=" O ILE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 593 removed outlier: 4.122A pdb=" N GLY A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ASP A 591 " --> pdb=" O HIS A 587 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLN A 592 " --> pdb=" O ASN A 588 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 623 removed outlier: 3.898A pdb=" N LYS A 610 " --> pdb=" O SER A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 666 removed outlier: 3.805A pdb=" N ALA A 653 " --> pdb=" O SER A 649 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE A 656 " --> pdb=" O TYR A 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 431 Proline residue: B 426 - end of helix Processing helix chain 'B' and resid 456 through 473 removed outlier: 3.707A pdb=" N MET B 462 " --> pdb=" O ILE B 458 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ILE B 467 " --> pdb=" O PHE B 463 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU B 468 " --> pdb=" O ILE B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 497 removed outlier: 3.681A pdb=" N TRP B 497 " --> pdb=" O TYR B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 531 removed outlier: 3.535A pdb=" N ALA B 527 " --> pdb=" O LEU B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 539 removed outlier: 3.770A pdb=" N ALA B 536 " --> pdb=" O LEU B 532 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS B 538 " --> pdb=" O ARG B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 574 removed outlier: 4.219A pdb=" N PHE B 551 " --> pdb=" O ALA B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 624 removed outlier: 3.711A pdb=" N ALA B 614 " --> pdb=" O LYS B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 653 Processing helix chain 'B' and resid 654 through 658 Processing helix chain 'B' and resid 662 through 666 Processing helix chain 'C' and resid 406 through 431 Proline residue: C 426 - end of helix Processing helix chain 'C' and resid 456 through 472 removed outlier: 3.962A pdb=" N ILE C 467 " --> pdb=" O PHE C 463 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LEU C 468 " --> pdb=" O ILE C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 490 through 496 removed outlier: 3.621A pdb=" N PHE C 494 " --> pdb=" O ALA C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 505 Processing helix chain 'C' and resid 521 through 536 removed outlier: 3.740A pdb=" N LYS C 525 " --> pdb=" O GLY C 522 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA C 527 " --> pdb=" O LEU C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 574 Processing helix chain 'C' and resid 585 through 593 removed outlier: 3.944A pdb=" N ASP C 591 " --> pdb=" O HIS C 587 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE C 593 " --> pdb=" O LEU C 589 " (cutoff:3.500A) Processing helix chain 'C' and resid 606 through 624 Processing helix chain 'C' and resid 634 through 666 removed outlier: 3.821A pdb=" N GLY C 657 " --> pdb=" O ALA C 653 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N SER C 660 " --> pdb=" O PHE C 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 432 removed outlier: 5.447A pdb=" N TRP D 412 " --> pdb=" O ALA D 408 " (cutoff:3.500A) Proline residue: D 426 - end of helix removed outlier: 3.795A pdb=" N PHE D 431 " --> pdb=" O TYR D 427 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU D 432 " --> pdb=" O SER D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 472 removed outlier: 3.561A pdb=" N MET D 462 " --> pdb=" O ILE D 458 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE D 467 " --> pdb=" O PHE D 463 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU D 468 " --> pdb=" O ILE D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 491 through 496 removed outlier: 3.828A pdb=" N GLY D 496 " --> pdb=" O HIS D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 505 removed outlier: 3.571A pdb=" N MET D 502 " --> pdb=" O PHE D 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 531 Processing helix chain 'D' and resid 532 through 537 removed outlier: 4.211A pdb=" N ALA D 536 " --> pdb=" O LEU D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 543 removed outlier: 3.844A pdb=" N TYR D 542 " --> pdb=" O LYS D 538 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER D 543 " --> pdb=" O LEU D 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 538 through 543' Processing helix chain 'D' and resid 545 through 575 removed outlier: 4.200A pdb=" N PHE D 551 " --> pdb=" O ALA D 547 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLU D 575 " --> pdb=" O ILE D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 585 through 593 removed outlier: 3.984A pdb=" N ASP D 591 " --> pdb=" O HIS D 587 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLN D 592 " --> pdb=" O ASN D 588 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE D 593 " --> pdb=" O LEU D 589 " (cutoff:3.500A) Processing helix chain 'D' and resid 606 through 624 removed outlier: 3.829A pdb=" N ALA D 614 " --> pdb=" O LYS D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 665 removed outlier: 4.139A pdb=" N ALA D 653 " --> pdb=" O SER D 649 " (cutoff:3.500A) 424 hydrogen bonds defined for protein. 1179 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.64 Time building geometry restraints manager: 1.80 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: 1717 1.34 - 1.45: 1278 1.45 - 1.57: 3398 1.57 - 1.69: 0 1.69 - 1.81: 47 Bond restraints: 6440 Sorted by residual: bond pdb=" CG1 ILE B 642 " pdb=" CD1 ILE B 642 " ideal model delta sigma weight residual 1.513 1.446 0.067 3.90e-02 6.57e+02 2.98e+00 bond pdb=" CG1 ILE A 642 " pdb=" CD1 ILE A 642 " ideal model delta sigma weight residual 1.513 1.451 0.062 3.90e-02 6.57e+02 2.54e+00 bond pdb=" CG LEU A 589 " pdb=" CD1 LEU A 589 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.29e+00 bond pdb=" CB THR D 613 " pdb=" CG2 THR D 613 " ideal model delta sigma weight residual 1.521 1.472 0.049 3.30e-02 9.18e+02 2.22e+00 bond pdb=" CG1 ILE D 642 " pdb=" CD1 ILE D 642 " ideal model delta sigma weight residual 1.513 1.456 0.057 3.90e-02 6.57e+02 2.15e+00 ... (remaining 6435 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 8340 1.57 - 3.14: 349 3.14 - 4.71: 50 4.71 - 6.28: 16 6.28 - 7.86: 7 Bond angle restraints: 8762 Sorted by residual: angle pdb=" C LYS D 610 " pdb=" N TYR D 611 " pdb=" CA TYR D 611 " ideal model delta sigma weight residual 121.64 115.37 6.27 2.13e+00 2.20e-01 8.68e+00 angle pdb=" C TRP C 497 " pdb=" N PHE C 498 " pdb=" CA PHE C 498 " ideal model delta sigma weight residual 121.54 115.94 5.60 1.91e+00 2.74e-01 8.61e+00 angle pdb=" CA TYR C 611 " pdb=" CB TYR C 611 " pdb=" CG TYR C 611 " ideal model delta sigma weight residual 113.90 108.90 5.00 1.80e+00 3.09e-01 7.71e+00 angle pdb=" C PHE C 424 " pdb=" N THR C 425 " pdb=" CA THR C 425 " ideal model delta sigma weight residual 121.80 115.51 6.29 2.44e+00 1.68e-01 6.65e+00 angle pdb=" C LYS A 610 " pdb=" N TYR A 611 " pdb=" CA TYR A 611 " ideal model delta sigma weight residual 120.28 116.84 3.44 1.34e+00 5.57e-01 6.58e+00 ... (remaining 8757 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.95: 3234 16.95 - 33.89: 365 33.89 - 50.84: 52 50.84 - 67.79: 3 67.79 - 84.73: 1 Dihedral angle restraints: 3655 sinusoidal: 1263 harmonic: 2392 Sorted by residual: dihedral pdb=" CA THR B 634 " pdb=" C THR B 634 " pdb=" N ASN B 635 " pdb=" CA ASN B 635 " ideal model delta harmonic sigma weight residual 180.00 -156.10 -23.90 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CA PHE D 656 " pdb=" C PHE D 656 " pdb=" N GLY D 657 " pdb=" CA GLY D 657 " ideal model delta harmonic sigma weight residual 180.00 156.74 23.26 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA PHE A 656 " pdb=" C PHE A 656 " pdb=" N GLY A 657 " pdb=" CA GLY A 657 " ideal model delta harmonic sigma weight residual 180.00 157.94 22.06 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 3652 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 640 0.039 - 0.078: 320 0.078 - 0.116: 76 0.116 - 0.155: 12 0.155 - 0.194: 5 Chirality restraints: 1053 Sorted by residual: chirality pdb=" CA THR C 425 " pdb=" N THR C 425 " pdb=" C THR C 425 " pdb=" CB THR C 425 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.19 2.00e-01 2.50e+01 9.39e-01 chirality pdb=" CA THR A 425 " pdb=" N THR A 425 " pdb=" C THR A 425 " pdb=" CB THR A 425 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.19 2.00e-01 2.50e+01 9.35e-01 chirality pdb=" CA PHE A 656 " pdb=" N PHE A 656 " pdb=" C PHE A 656 " pdb=" CB PHE A 656 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.58e-01 ... (remaining 1050 not shown) Planarity restraints: 1028 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 497 " -0.015 2.00e-02 2.50e+03 1.15e-02 3.33e+00 pdb=" CG TRP C 497 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP C 497 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP C 497 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 497 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 497 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 497 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 497 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 497 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 497 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 619 " 0.010 2.00e-02 2.50e+03 1.32e-02 3.04e+00 pdb=" CG PHE C 619 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE C 619 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE C 619 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE C 619 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE C 619 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE C 619 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 609 " 0.008 2.00e-02 2.50e+03 1.67e-02 2.80e+00 pdb=" C ASP B 609 " -0.029 2.00e-02 2.50e+03 pdb=" O ASP B 609 " 0.011 2.00e-02 2.50e+03 pdb=" N LYS B 610 " 0.010 2.00e-02 2.50e+03 ... (remaining 1025 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.75: 1011 2.75 - 3.34: 7655 3.34 - 3.94: 11079 3.94 - 4.54: 15300 4.54 - 5.14: 22459 Nonbonded interactions: 57504 Sorted by model distance: nonbonded pdb=" O ILE C 469 " pdb=" OG1 THR C 473 " model vdw 2.147 3.040 nonbonded pdb=" OH TYR B 616 " pdb=" OD1 ASN B 629 " model vdw 2.157 3.040 nonbonded pdb=" ND2 ASN C 477 " pdb=" O GLU C 481 " model vdw 2.165 3.120 nonbonded pdb=" O PHE D 619 " pdb=" OG1 THR D 623 " model vdw 2.181 3.040 nonbonded pdb=" O THR D 421 " pdb=" OG1 THR D 425 " model vdw 2.185 3.040 ... (remaining 57499 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 405 through 410 or (resid 411 and (name N or name CA or na \ me C or name O or name CB )) or resid 412 through 460 or (resid 461 and (name N \ or name CA or name C or name O or name CB )) or resid 462 or (resid 463 and (nam \ e N or name CA or name C or name O or name CB )) or resid 464 through 465 or (re \ sid 466 and (name N or name CA or name C or name O or name CB )) or resid 467 th \ rough 468 or (resid 469 through 470 and (name N or name CA or name C or name O o \ r name CB )) or resid 471 or (resid 472 and (name N or name CA or name C or name \ O or name CB )) or resid 477 through 481 or (resid 490 through 491 and (name N \ or name CA or name C or name O or name CB )) or resid 492 or (resid 493 and (nam \ e N or name CA or name C or name O or name CB )) or resid 494 through 500 or (re \ sid 501 through 502 and (name N or name CA or name C or name O or name CB )) or \ resid 503 through 506 or resid 523 through 524 or (resid 525 and (name N or name \ CA or name C or name O or name CB )) or resid 526 through 536 or (resid 537 and \ (name N or name CA or name C or name O or name CB )) or resid 538 through 539 o \ r resid 549 through 554 or (resid 555 and (name N or name CA or name C or name O \ or name CB )) or resid 556 through 573 or (resid 574 through 575 and (name N or \ name CA or name C or name O or name CB )) or resid 584 through 586 or (resid 58 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 588 through \ 605 or (resid 606 and (name N or name CA or name C or name O or name CB )) or re \ sid 607 through 653 or (resid 654 and (name N or name CA or name C or name O or \ name CB )) or resid 655 through 663 or (resid 664 through 666 and (name N or nam \ e CA or name C or name O or name CB )))) selection = (chain 'B' and (resid 405 or (resid 406 and (name N or name CA or name C or name \ O or name CB )) or resid 407 through 416 or (resid 417 and (name N or name CA o \ r name C or name O or name CB )) or resid 418 through 432 or (resid 458 and (nam \ e N or name CA or name C or name O or name CB )) or resid 459 through 462 or (re \ sid 463 and (name N or name CA or name C or name O or name CB )) or resid 464 or \ (resid 465 through 466 and (name N or name CA or name C or name O or name CB )) \ or resid 467 through 468 or (resid 469 through 470 and (name N or name CA or na \ me C or name O or name CB )) or resid 471 or (resid 472 and (name N or name CA o \ r name C or name O or name CB )) or resid 477 through 481 or resid 490 through 4 \ 92 or (resid 493 and (name N or name CA or name C or name O or name CB )) or res \ id 494 through 500 or (resid 501 through 502 and (name N or name CA or name C or \ name O or name CB )) or resid 503 through 506 or resid 523 through 524 or (resi \ d 525 and (name N or name CA or name C or name O or name CB )) or resid 526 thro \ ugh 536 or (resid 537 and (name N or name CA or name C or name O or name CB )) o \ r resid 538 or (resid 539 and (name N or name CA or name C or name O or name CB \ )) or resid 549 through 554 or (resid 555 and (name N or name CA or name C or na \ me O or name CB )) or resid 556 through 573 or (resid 574 through 575 and (name \ N or name CA or name C or name O or name CB )) or resid 584 through 605 or (resi \ d 606 and (name N or name CA or name C or name O or name CB )) or resid 607 thro \ ugh 653 or (resid 654 and (name N or name CA or name C or name O or name CB )) o \ r resid 655 through 657 or (resid 658 and (name N or name CA or name C or name O \ or name CB )) or resid 659 through 664 or (resid 665 through 666 and (name N or \ name CA or name C or name O or name CB )))) selection = (chain 'C' and (resid 405 or (resid 406 and (name N or name CA or name C or name \ O or name CB )) or resid 407 through 410 or (resid 411 and (name N or name CA o \ r name C or name O or name CB )) or resid 412 through 416 or (resid 417 and (nam \ e N or name CA or name C or name O or name CB )) or resid 418 through 432 or (re \ sid 458 and (name N or name CA or name C or name O or name CB )) or resid 459 th \ rough 464 or (resid 465 through 466 and (name N or name CA or name C or name O o \ r name CB )) or resid 467 through 469 or (resid 470 and (name N or name CA or na \ me C or name O or name CB )) or resid 471 or (resid 472 and (name N or name CA o \ r name C or name O or name CB )) or (resid 477 through 481 and (name N or name C \ A or name C or name O or name CB )) or resid 490 through 506 or resid 523 throug \ h 524 or (resid 525 and (name N or name CA or name C or name O or name CB )) or \ resid 526 through 538 or (resid 539 and (name N or name CA or name C or name O o \ r name CB )) or resid 549 through 575 or resid 584 through 586 or (resid 587 and \ (name N or name CA or name C or name O or name CB )) or resid 588 through 597 o \ r resid 605 or (resid 606 and (name N or name CA or name C or name O or name CB \ )) or resid 607 through 657 or (resid 658 and (name N or name CA or name C or na \ me O or name CB )) or resid 659 through 663 or (resid 664 through 666 and (name \ N or name CA or name C or name O or name CB )))) selection = (chain 'D' and (resid 405 through 416 or (resid 417 and (name N or name CA or na \ me C or name O or name CB )) or resid 418 through 432 or (resid 458 and (name N \ or name CA or name C or name O or name CB )) or resid 459 through 462 or (resid \ 463 and (name N or name CA or name C or name O or name CB )) or resid 464 throug \ h 472 or (resid 477 through 481 and (name N or name CA or name C or name O or na \ me CB )) or resid 490 through 492 or (resid 493 and (name N or name CA or name C \ or name O or name CB )) or resid 494 through 500 or (resid 501 through 502 and \ (name N or name CA or name C or name O or name CB )) or resid 503 through 506 or \ resid 523 through 536 or (resid 537 and (name N or name CA or name C or name O \ or name CB )) or resid 538 or (resid 539 and (name N or name CA or name C or nam \ e O or name CB )) or resid 549 through 554 or (resid 555 and (name N or name CA \ or name C or name O or name CB )) or resid 556 through 574 or (resid 575 and (na \ me N or name CA or name C or name O or name CB )) or resid 584 through 586 or (r \ esid 587 and (name N or name CA or name C or name O or name CB )) or resid 588 t \ hrough 653 or (resid 654 and (name N or name CA or name C or name O or name CB ) \ ) or resid 655 through 663 or (resid 664 through 666 and (name N or name CA or n \ ame C or name O or name CB )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.520 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: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.500 Find NCS groups from input model: 0.340 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: 24.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 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 : 0.008 0.067 6440 Z= 0.505 Angle : 0.778 7.856 8762 Z= 0.420 Chirality : 0.046 0.194 1053 Planarity : 0.004 0.040 1028 Dihedral : 13.724 84.732 2097 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.18 % Favored : 89.82 % Rotamer: Outliers : 0.32 % Allowed : 14.52 % Favored : 85.16 % 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: -3.65 (0.26), residues: 766 helix: -2.06 (0.18), residues: 559 sheet: None (None), residues: 0 loop : -2.93 (0.42), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 497 HIS 0.004 0.001 HIS B 492 PHE 0.030 0.002 PHE C 619 TYR 0.026 0.003 TYR A 616 ARG 0.002 0.000 ARG A 537 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 153 time to evaluate : 0.662 Fit side-chains REVERT: A 651 MET cc_start: 0.8447 (mtp) cc_final: 0.7959 (ttp) REVERT: B 574 MET cc_start: 0.7042 (mtt) cc_final: 0.6830 (mtm) REVERT: C 432 LEU cc_start: 0.7474 (pt) cc_final: 0.7022 (pp) REVERT: C 462 MET cc_start: 0.6373 (tpp) cc_final: 0.5895 (tpp) outliers start: 2 outliers final: 2 residues processed: 155 average time/residue: 0.1907 time to fit residues: 38.1948 Evaluate side-chains 123 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 121 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 619 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 0.8980 chunk 60 optimal weight: 0.0970 chunk 33 optimal weight: 0.8980 chunk 20 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 chunk 72 optimal weight: 0.8980 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 562 HIS B 470 ASN B 562 HIS C 470 ASN D 562 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.179621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.144074 restraints weight = 9180.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.143712 restraints weight = 7320.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.145027 restraints weight = 6766.218| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6440 Z= 0.164 Angle : 0.573 7.357 8762 Z= 0.303 Chirality : 0.039 0.152 1053 Planarity : 0.004 0.035 1028 Dihedral : 5.281 54.966 858 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.94 % Allowed : 19.52 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.29), residues: 766 helix: -0.71 (0.20), residues: 600 sheet: None (None), residues: 0 loop : -3.06 (0.48), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 497 HIS 0.004 0.001 HIS A 402 PHE 0.015 0.001 PHE A 498 TYR 0.019 0.001 TYR A 427 ARG 0.007 0.000 ARG D 531 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 176 time to evaluate : 0.660 Fit side-chains REVERT: A 532 LEU cc_start: 0.8487 (tp) cc_final: 0.8135 (mt) REVERT: B 427 TYR cc_start: 0.8396 (t80) cc_final: 0.8183 (t80) REVERT: C 432 LEU cc_start: 0.7236 (pt) cc_final: 0.6766 (pp) REVERT: C 462 MET cc_start: 0.6962 (tpp) cc_final: 0.6689 (tpp) REVERT: C 633 ASN cc_start: 0.8250 (t0) cc_final: 0.7844 (t0) REVERT: D 617 PHE cc_start: 0.7876 (t80) cc_final: 0.7608 (t80) outliers start: 12 outliers final: 8 residues processed: 183 average time/residue: 0.1640 time to fit residues: 39.9137 Evaluate side-chains 151 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 143 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 619 PHE Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain D residue 634 THR Chi-restraints excluded: chain D residue 643 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 56 optimal weight: 0.1980 chunk 78 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 47 optimal weight: 7.9990 chunk 59 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 629 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.179960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.138810 restraints weight = 9269.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.140423 restraints weight = 5878.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.141566 restraints weight = 4134.081| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6440 Z= 0.153 Angle : 0.535 7.227 8762 Z= 0.284 Chirality : 0.038 0.159 1053 Planarity : 0.003 0.032 1028 Dihedral : 4.981 59.690 858 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.90 % Allowed : 23.71 % Favored : 73.39 % 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: -0.98 (0.31), residues: 766 helix: -0.10 (0.21), residues: 602 sheet: None (None), residues: 0 loop : -2.37 (0.52), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 497 HIS 0.003 0.001 HIS A 492 PHE 0.012 0.001 PHE C 617 TYR 0.012 0.001 TYR B 616 ARG 0.001 0.000 ARG A 534 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 162 time to evaluate : 0.614 Fit side-chains REVERT: A 532 LEU cc_start: 0.8633 (tp) cc_final: 0.8221 (mt) REVERT: B 427 TYR cc_start: 0.8590 (t80) cc_final: 0.8342 (t80) REVERT: B 525 LYS cc_start: 0.8569 (ptmm) cc_final: 0.8311 (ptmm) REVERT: C 432 LEU cc_start: 0.7317 (pt) cc_final: 0.6857 (pp) REVERT: C 462 MET cc_start: 0.6461 (tpp) cc_final: 0.6143 (tpp) REVERT: C 633 ASN cc_start: 0.8133 (t0) cc_final: 0.7655 (t0) REVERT: D 529 LEU cc_start: 0.9068 (tp) cc_final: 0.8856 (tp) REVERT: D 538 LYS cc_start: 0.7946 (mttt) cc_final: 0.7640 (mtmt) outliers start: 18 outliers final: 13 residues processed: 171 average time/residue: 0.1863 time to fit residues: 42.3447 Evaluate side-chains 167 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 154 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 619 PHE Chi-restraints excluded: chain C residue 651 MET Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 643 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 15 optimal weight: 2.9990 chunk 63 optimal weight: 0.1980 chunk 10 optimal weight: 7.9990 chunk 6 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 43 optimal weight: 7.9990 chunk 33 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 GLN C 633 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.177309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.137779 restraints weight = 9334.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.137107 restraints weight = 6583.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.138097 restraints weight = 5299.180| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6440 Z= 0.216 Angle : 0.564 7.372 8762 Z= 0.299 Chirality : 0.039 0.160 1053 Planarity : 0.003 0.032 1028 Dihedral : 5.048 57.808 858 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.71 % Allowed : 25.32 % Favored : 70.97 % 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: -0.88 (0.31), residues: 766 helix: -0.05 (0.21), residues: 613 sheet: None (None), residues: 0 loop : -2.37 (0.54), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 497 HIS 0.003 0.001 HIS A 402 PHE 0.012 0.001 PHE D 640 TYR 0.014 0.002 TYR A 616 ARG 0.003 0.000 ARG D 531 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 0.806 Fit side-chains REVERT: A 532 LEU cc_start: 0.8671 (tp) cc_final: 0.8243 (mt) REVERT: B 427 TYR cc_start: 0.8616 (t80) cc_final: 0.8280 (t80) REVERT: C 432 LEU cc_start: 0.7341 (pt) cc_final: 0.6910 (pp) REVERT: C 462 MET cc_start: 0.6538 (tpp) cc_final: 0.6198 (tpp) REVERT: C 633 ASN cc_start: 0.8142 (t160) cc_final: 0.7653 (t0) REVERT: D 554 MET cc_start: 0.8403 (tpp) cc_final: 0.8143 (mmt) outliers start: 23 outliers final: 19 residues processed: 167 average time/residue: 0.1699 time to fit residues: 37.8576 Evaluate side-chains 168 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain B residue 497 TRP Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 619 PHE Chi-restraints excluded: chain C residue 651 MET Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 634 THR Chi-restraints excluded: chain D residue 643 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 3 optimal weight: 9.9990 chunk 79 optimal weight: 0.9980 chunk 61 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 47 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 4 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.4081 r_free = 0.4081 target = 0.179653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.143441 restraints weight = 9289.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.143782 restraints weight = 7507.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.145256 restraints weight = 6514.795| |-----------------------------------------------------------------------------| r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6440 Z= 0.157 Angle : 0.531 7.314 8762 Z= 0.280 Chirality : 0.038 0.155 1053 Planarity : 0.003 0.031 1028 Dihedral : 4.810 57.029 858 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 4.52 % Allowed : 25.97 % Favored : 69.52 % 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: -0.45 (0.32), residues: 766 helix: 0.22 (0.22), residues: 608 sheet: None (None), residues: 0 loop : -2.03 (0.54), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 497 HIS 0.002 0.001 HIS A 402 PHE 0.014 0.001 PHE C 617 TYR 0.011 0.001 TYR B 597 ARG 0.001 0.000 ARG D 531 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 156 time to evaluate : 0.781 Fit side-chains REVERT: A 532 LEU cc_start: 0.8572 (tp) cc_final: 0.8237 (mt) REVERT: C 432 LEU cc_start: 0.7335 (pt) cc_final: 0.6917 (pp) REVERT: C 462 MET cc_start: 0.6722 (tpp) cc_final: 0.6436 (tpp) REVERT: C 633 ASN cc_start: 0.8007 (OUTLIER) cc_final: 0.7583 (t0) REVERT: D 531 ARG cc_start: 0.7721 (mtm-85) cc_final: 0.7484 (ttp-170) REVERT: D 538 LYS cc_start: 0.8068 (mtmt) cc_final: 0.7868 (mtmt) REVERT: D 554 MET cc_start: 0.8267 (tpp) cc_final: 0.8042 (mmt) outliers start: 28 outliers final: 19 residues processed: 171 average time/residue: 0.1772 time to fit residues: 40.8297 Evaluate side-chains 171 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 151 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 525 LYS Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain B residue 497 TRP Chi-restraints excluded: chain B residue 597 TYR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 633 ASN Chi-restraints excluded: chain C residue 651 MET Chi-restraints excluded: chain D residue 643 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 0 optimal weight: 10.0000 chunk 60 optimal weight: 0.0770 chunk 59 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 54 optimal weight: 0.2980 chunk 33 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 57 optimal weight: 0.6980 chunk 9 optimal weight: 8.9990 overall best weight: 0.7940 ------------------------------------------------------------------------------- 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 = 0.4098 r_free = 0.4098 target = 0.181070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.145312 restraints weight = 9180.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.145630 restraints weight = 7260.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.146891 restraints weight = 6638.876| |-----------------------------------------------------------------------------| r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6440 Z= 0.150 Angle : 0.538 7.314 8762 Z= 0.282 Chirality : 0.038 0.159 1053 Planarity : 0.003 0.028 1028 Dihedral : 4.248 42.022 856 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 4.19 % Allowed : 26.13 % Favored : 69.68 % 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: -0.20 (0.32), residues: 766 helix: 0.39 (0.22), residues: 610 sheet: None (None), residues: 0 loop : -1.93 (0.55), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 563 HIS 0.002 0.000 HIS A 402 PHE 0.014 0.001 PHE D 640 TYR 0.021 0.001 TYR B 427 ARG 0.001 0.000 ARG A 534 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 159 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 532 LEU cc_start: 0.8502 (tp) cc_final: 0.8219 (mt) REVERT: B 406 PHE cc_start: 0.6569 (t80) cc_final: 0.6136 (t80) REVERT: C 432 LEU cc_start: 0.7304 (pt) cc_final: 0.6889 (pp) REVERT: C 462 MET cc_start: 0.6731 (tpp) cc_final: 0.6424 (tpp) REVERT: C 551 PHE cc_start: 0.7268 (t80) cc_final: 0.7052 (t80) REVERT: C 633 ASN cc_start: 0.7946 (OUTLIER) cc_final: 0.7512 (t0) REVERT: D 554 MET cc_start: 0.8047 (tpp) cc_final: 0.7832 (mmt) outliers start: 26 outliers final: 21 residues processed: 174 average time/residue: 0.1615 time to fit residues: 37.4898 Evaluate side-chains 170 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain B residue 497 TRP Chi-restraints excluded: chain B residue 597 TYR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 633 ASN Chi-restraints excluded: chain C residue 651 MET Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 643 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 11 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 7 optimal weight: 10.0000 chunk 59 optimal weight: 0.0000 chunk 68 optimal weight: 0.8980 chunk 26 optimal weight: 8.9990 chunk 60 optimal weight: 0.3980 chunk 8 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 588 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.183268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.147980 restraints weight = 9163.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.148000 restraints weight = 7300.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.149404 restraints weight = 6551.630| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6440 Z= 0.141 Angle : 0.538 7.368 8762 Z= 0.279 Chirality : 0.038 0.166 1053 Planarity : 0.003 0.028 1028 Dihedral : 3.829 16.305 854 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 4.35 % Allowed : 26.61 % Favored : 69.03 % 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: 0.02 (0.32), residues: 766 helix: 0.53 (0.22), residues: 611 sheet: None (None), residues: 0 loop : -1.78 (0.56), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 585 HIS 0.001 0.000 HIS A 402 PHE 0.011 0.001 PHE D 640 TYR 0.011 0.001 TYR B 597 ARG 0.002 0.000 ARG D 528 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 0.709 Fit side-chains revert: symmetry clash REVERT: A 532 LEU cc_start: 0.8518 (tp) cc_final: 0.8223 (mt) REVERT: B 406 PHE cc_start: 0.6540 (t80) cc_final: 0.6160 (t80) REVERT: C 432 LEU cc_start: 0.7282 (pt) cc_final: 0.6882 (pp) REVERT: C 462 MET cc_start: 0.6735 (tpp) cc_final: 0.6415 (tpp) REVERT: C 551 PHE cc_start: 0.7165 (t80) cc_final: 0.6900 (t80) REVERT: C 633 ASN cc_start: 0.7849 (OUTLIER) cc_final: 0.7463 (t0) REVERT: D 528 ARG cc_start: 0.7042 (mtp85) cc_final: 0.6778 (mmt180) outliers start: 27 outliers final: 21 residues processed: 171 average time/residue: 0.1618 time to fit residues: 37.6279 Evaluate side-chains 172 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain B residue 497 TRP Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 585 TRP Chi-restraints excluded: chain B residue 597 TYR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 633 ASN Chi-restraints excluded: chain C residue 651 MET Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 643 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 78 optimal weight: 0.7980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 629 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.179101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.138655 restraints weight = 9225.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.139245 restraints weight = 5996.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.139662 restraints weight = 4699.606| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6440 Z= 0.224 Angle : 0.598 8.877 8762 Z= 0.308 Chirality : 0.040 0.159 1053 Planarity : 0.003 0.029 1028 Dihedral : 4.107 17.927 854 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.71 % Allowed : 27.58 % Favored : 68.71 % 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: -0.17 (0.32), residues: 766 helix: 0.40 (0.22), residues: 616 sheet: None (None), residues: 0 loop : -1.91 (0.56), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 585 HIS 0.002 0.001 HIS C 492 PHE 0.017 0.001 PHE D 640 TYR 0.016 0.002 TYR B 616 ARG 0.002 0.000 ARG A 534 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 0.768 Fit side-chains REVERT: A 532 LEU cc_start: 0.8679 (tp) cc_final: 0.8246 (mt) REVERT: B 406 PHE cc_start: 0.6556 (t80) cc_final: 0.6103 (t80) REVERT: B 554 MET cc_start: 0.7929 (mmm) cc_final: 0.7687 (tpt) REVERT: C 415 LEU cc_start: 0.7546 (tt) cc_final: 0.7336 (tt) REVERT: C 432 LEU cc_start: 0.7379 (pt) cc_final: 0.6994 (pp) REVERT: C 462 MET cc_start: 0.6454 (tpp) cc_final: 0.6086 (tpp) REVERT: C 633 ASN cc_start: 0.7970 (OUTLIER) cc_final: 0.7517 (t0) REVERT: D 528 ARG cc_start: 0.7362 (mtp85) cc_final: 0.6891 (mmt180) outliers start: 23 outliers final: 20 residues processed: 162 average time/residue: 0.1749 time to fit residues: 38.1353 Evaluate side-chains 168 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain B residue 497 TRP Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 597 TYR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 633 ASN Chi-restraints excluded: chain C residue 651 MET Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 643 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 8.9990 chunk 9 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 39 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 = 0.4059 r_free = 0.4059 target = 0.177583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.134253 restraints weight = 9400.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.137266 restraints weight = 6058.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.138616 restraints weight = 4403.034| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6440 Z= 0.245 Angle : 0.609 8.491 8762 Z= 0.315 Chirality : 0.040 0.167 1053 Planarity : 0.003 0.029 1028 Dihedral : 4.238 18.547 854 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 4.52 % Allowed : 26.13 % Favored : 69.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.31), residues: 766 helix: 0.30 (0.21), residues: 617 sheet: None (None), residues: 0 loop : -2.17 (0.54), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 585 HIS 0.002 0.001 HIS A 402 PHE 0.018 0.002 PHE D 640 TYR 0.015 0.002 TYR A 616 ARG 0.002 0.000 ARG A 534 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 147 time to evaluate : 0.716 Fit side-chains REVERT: A 427 TYR cc_start: 0.7360 (t80) cc_final: 0.7131 (t80) REVERT: A 532 LEU cc_start: 0.8626 (tp) cc_final: 0.8157 (mt) REVERT: B 406 PHE cc_start: 0.6604 (t80) cc_final: 0.6130 (t80) REVERT: B 554 MET cc_start: 0.7995 (mmm) cc_final: 0.7780 (tpt) REVERT: C 432 LEU cc_start: 0.7435 (pt) cc_final: 0.7066 (pp) REVERT: C 462 MET cc_start: 0.6323 (tpp) cc_final: 0.5987 (tpp) REVERT: C 633 ASN cc_start: 0.8059 (OUTLIER) cc_final: 0.7641 (t0) REVERT: D 528 ARG cc_start: 0.7458 (mtp85) cc_final: 0.6945 (mmt180) REVERT: D 555 CYS cc_start: 0.6796 (m) cc_final: 0.6511 (m) outliers start: 28 outliers final: 23 residues processed: 163 average time/residue: 0.1657 time to fit residues: 36.3471 Evaluate side-chains 170 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 525 LYS Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain B residue 497 TRP Chi-restraints excluded: chain B residue 597 TYR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 652 TYR Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 633 ASN Chi-restraints excluded: chain C residue 651 MET Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 643 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 68 optimal weight: 9.9990 chunk 70 optimal weight: 1.9990 chunk 49 optimal weight: 0.3980 chunk 26 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 65 optimal weight: 10.0000 chunk 53 optimal weight: 0.6980 chunk 76 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4118 r_free = 0.4118 target = 0.183410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.147792 restraints weight = 9275.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.147856 restraints weight = 7193.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.149152 restraints weight = 6523.074| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6440 Z= 0.148 Angle : 0.565 8.822 8762 Z= 0.288 Chirality : 0.038 0.178 1053 Planarity : 0.003 0.028 1028 Dihedral : 3.919 16.917 854 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.06 % Allowed : 27.90 % Favored : 69.03 % 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: 0.08 (0.32), residues: 766 helix: 0.60 (0.22), residues: 609 sheet: None (None), residues: 0 loop : -1.84 (0.56), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 585 HIS 0.002 0.000 HIS A 402 PHE 0.010 0.001 PHE D 640 TYR 0.011 0.001 TYR A 616 ARG 0.001 0.000 ARG A 534 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 0.731 Fit side-chains REVERT: A 532 LEU cc_start: 0.8630 (tp) cc_final: 0.8239 (mt) REVERT: B 406 PHE cc_start: 0.6741 (t80) cc_final: 0.6225 (t80) REVERT: C 432 LEU cc_start: 0.7276 (pt) cc_final: 0.6882 (pp) REVERT: C 462 MET cc_start: 0.6692 (tpp) cc_final: 0.6374 (tpp) REVERT: C 551 PHE cc_start: 0.7219 (t80) cc_final: 0.6924 (t80) REVERT: C 633 ASN cc_start: 0.7890 (OUTLIER) cc_final: 0.7535 (t0) outliers start: 19 outliers final: 18 residues processed: 169 average time/residue: 0.1611 time to fit residues: 36.8861 Evaluate side-chains 167 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain B residue 597 TYR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 633 ASN Chi-restraints excluded: chain C residue 651 MET Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 539 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 1 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4112 r_free = 0.4112 target = 0.182200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.142899 restraints weight = 9430.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.143548 restraints weight = 5775.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.144695 restraints weight = 4562.828| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6440 Z= 0.154 Angle : 0.571 8.819 8762 Z= 0.290 Chirality : 0.039 0.162 1053 Planarity : 0.003 0.028 1028 Dihedral : 3.850 16.725 854 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.90 % Allowed : 28.71 % Favored : 68.39 % 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: 0.18 (0.32), residues: 766 helix: 0.68 (0.22), residues: 610 sheet: None (None), residues: 0 loop : -1.91 (0.55), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 585 HIS 0.001 0.000 HIS A 402 PHE 0.013 0.001 PHE D 640 TYR 0.012 0.001 TYR D 597 ARG 0.003 0.000 ARG A 531 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2109.53 seconds wall clock time: 38 minutes 51.61 seconds (2331.61 seconds total)