Starting phenix.real_space_refine on Tue Mar 3 14:46:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cn1_30413/03_2026/7cn1_30413.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cn1_30413/03_2026/7cn1_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 { model { file = "/net/cci-nas-00/data/ceres_data/7cn1_30413/03_2026/7cn1_30413.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cn1_30413/03_2026/7cn1_30413.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7cn1_30413/03_2026/7cn1_30413.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cn1_30413/03_2026/7cn1_30413.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'TYR:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 3, 'GLU:plan': 2, 'HIS:plan': 1, 'ARG:plan': 3, 'ASP:plan': 2} 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: {'ASP:plan': 2, 'ASN:plan1': 2, 'GLU:plan': 3, 'HIS:plan': 1, 'GLN:plan1': 1} 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: {'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 3, 'TYR:plan': 1, 'ARG:plan': 3} 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: {'PHE:plan': 1, 'ASP:plan': 5, 'ASN:plan1': 3, 'ARG:plan': 2, 'TYR:plan': 1, 'GLU: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: 1.57, per 1000 atoms: 0.25 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: 0.39 Conformation dependent library (CDL) restraints added in 229.6 milliseconds 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: 0.17 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: 0.78 Time building geometry restraints manager: 0.51 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: 2.750 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.620 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.870 ------------------------------------------------------------------------------- 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= 0.337 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 : 15.99 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.002 0.000 ARG A 537 TYR 0.026 0.003 TYR A 616 PHE 0.030 0.002 PHE C 619 TRP 0.032 0.002 TRP C 497 HIS 0.004 0.001 HIS B 492 Details of bonding type rmsd covalent geometry : bond 0.00795 ( 6440) covalent geometry : angle 0.77826 ( 8762) hydrogen bonds : bond 0.12125 ( 424) hydrogen bonds : angle 6.01177 ( 1179) *********************** 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 : 0.242 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: 0.7023 (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: 0.0737 time to fit residues: 15.0462 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 : 0.218 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.4071 r_free = 0.4071 target = 0.178975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.144948 restraints weight = 9296.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.143067 restraints weight = 7701.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.144593 restraints weight = 7198.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.144726 restraints weight = 5174.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.145068 restraints weight = 5497.226| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.1842 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= 0.128 Angle : 0.579 7.384 8762 Z= 0.306 Chirality : 0.039 0.157 1053 Planarity : 0.004 0.035 1028 Dihedral : 5.328 55.016 858 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.10 % Allowed : 20.16 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.29), residues: 766 helix: -0.78 (0.20), residues: 600 sheet: None (None), residues: 0 loop : -3.08 (0.48), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 537 TYR 0.018 0.001 TYR A 427 PHE 0.014 0.001 PHE A 498 TRP 0.025 0.002 TRP C 497 HIS 0.004 0.001 HIS C 492 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 6440) covalent geometry : angle 0.57886 ( 8762) hydrogen bonds : bond 0.04159 ( 424) hydrogen bonds : angle 4.35964 ( 1179) *********************** 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 186 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 173 time to evaluate : 0.233 Fit side-chains REVERT: A 532 LEU cc_start: 0.8502 (tp) cc_final: 0.8129 (mt) REVERT: B 427 TYR cc_start: 0.8369 (t80) cc_final: 0.8127 (t80) REVERT: C 432 LEU cc_start: 0.7243 (pt) cc_final: 0.6775 (pp) REVERT: C 462 MET cc_start: 0.6990 (tpp) cc_final: 0.6716 (tpp) REVERT: C 633 ASN cc_start: 0.8252 (t0) cc_final: 0.7856 (t0) REVERT: D 531 ARG cc_start: 0.7209 (mtt180) cc_final: 0.6966 (mtt180) REVERT: D 617 PHE cc_start: 0.7826 (t80) cc_final: 0.7555 (t80) outliers start: 13 outliers final: 8 residues processed: 181 average time/residue: 0.0658 time to fit residues: 16.1034 Evaluate side-chains 152 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 144 time to evaluate : 0.214 ------------------------------------------------------------------------------- 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 613 THR Chi-restraints excluded: chain D residue 634 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 7 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 67 optimal weight: 9.9990 chunk 12 optimal weight: 0.9980 chunk 73 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- 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 = 0.4035 r_free = 0.4035 target = 0.175258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.141432 restraints weight = 9281.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.140781 restraints weight = 8984.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.141507 restraints weight = 9715.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.142414 restraints weight = 5924.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.142990 restraints weight = 5152.861| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6440 Z= 0.196 Angle : 0.620 7.453 8762 Z= 0.327 Chirality : 0.041 0.162 1053 Planarity : 0.004 0.031 1028 Dihedral : 5.496 59.725 858 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 3.87 % Allowed : 24.52 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.30), residues: 766 helix: -0.47 (0.20), residues: 606 sheet: None (None), residues: 0 loop : -2.43 (0.52), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 528 TYR 0.017 0.002 TYR A 616 PHE 0.015 0.002 PHE B 617 TRP 0.017 0.002 TRP C 497 HIS 0.003 0.001 HIS A 402 Details of bonding type rmsd covalent geometry : bond 0.00455 ( 6440) covalent geometry : angle 0.62020 ( 8762) hydrogen bonds : bond 0.04501 ( 424) hydrogen bonds : angle 4.46673 ( 1179) *********************** 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 170 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 0.176 Fit side-chains REVERT: A 532 LEU cc_start: 0.8558 (tp) cc_final: 0.8156 (mt) REVERT: A 651 MET cc_start: 0.7880 (mtp) cc_final: 0.7430 (ttp) REVERT: C 432 LEU cc_start: 0.7303 (pt) cc_final: 0.6836 (pp) REVERT: C 462 MET cc_start: 0.6912 (tpp) cc_final: 0.6655 (tpp) REVERT: C 633 ASN cc_start: 0.8306 (t160) cc_final: 0.7925 (t0) REVERT: D 554 MET cc_start: 0.8416 (tpp) cc_final: 0.8127 (mmt) outliers start: 24 outliers final: 19 residues processed: 160 average time/residue: 0.0747 time to fit residues: 15.7995 Evaluate side-chains 158 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 0.209 ------------------------------------------------------------------------------- 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 63 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 79 optimal weight: 0.9980 chunk 25 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 69 optimal weight: 0.2980 chunk 30 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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 = 0.4046 r_free = 0.4046 target = 0.176387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.135385 restraints weight = 9310.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.136903 restraints weight = 6025.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.137713 restraints weight = 4331.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.137874 restraints weight = 4186.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.138015 restraints weight = 4016.808| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6440 Z= 0.151 Angle : 0.573 7.357 8762 Z= 0.302 Chirality : 0.039 0.156 1053 Planarity : 0.004 0.038 1028 Dihedral : 5.313 59.550 858 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 4.84 % Allowed : 24.84 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.30), residues: 766 helix: -0.25 (0.21), residues: 618 sheet: None (None), residues: 0 loop : -2.41 (0.53), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 531 TYR 0.014 0.001 TYR A 616 PHE 0.012 0.001 PHE D 640 TRP 0.016 0.001 TRP C 497 HIS 0.003 0.001 HIS A 492 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 6440) covalent geometry : angle 0.57255 ( 8762) hydrogen bonds : bond 0.04153 ( 424) hydrogen bonds : angle 4.22834 ( 1179) *********************** 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 185 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 155 time to evaluate : 0.222 Fit side-chains revert: symmetry clash REVERT: A 532 LEU cc_start: 0.8674 (tp) cc_final: 0.8246 (mt) REVERT: B 427 TYR cc_start: 0.8432 (t80) cc_final: 0.8206 (t80) REVERT: C 432 LEU cc_start: 0.7356 (pt) cc_final: 0.6899 (pp) REVERT: C 462 MET cc_start: 0.6439 (tpp) cc_final: 0.6187 (tpp) REVERT: C 633 ASN cc_start: 0.8177 (OUTLIER) cc_final: 0.7722 (t0) REVERT: D 538 LYS cc_start: 0.8126 (mtmt) cc_final: 0.7925 (mtmt) REVERT: D 617 PHE cc_start: 0.7935 (t80) cc_final: 0.7648 (t80) outliers start: 30 outliers final: 23 residues processed: 172 average time/residue: 0.0669 time to fit residues: 15.7109 Evaluate side-chains 169 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 145 time to evaluate : 0.205 ------------------------------------------------------------------------------- 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 525 LYS 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 586 LEU Chi-restraints excluded: chain C residue 619 PHE 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 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 72 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 29 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 588 ASN B 629 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.178876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.140301 restraints weight = 9481.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.140310 restraints weight = 6150.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.140705 restraints weight = 5015.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.140930 restraints weight = 4361.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.141288 restraints weight = 4324.493| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6440 Z= 0.116 Angle : 0.537 7.235 8762 Z= 0.283 Chirality : 0.038 0.160 1053 Planarity : 0.003 0.034 1028 Dihedral : 4.938 57.682 858 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 4.19 % Allowed : 27.10 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.31), residues: 766 helix: 0.10 (0.21), residues: 613 sheet: None (None), residues: 0 loop : -2.17 (0.55), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 531 TYR 0.014 0.001 TYR B 616 PHE 0.010 0.001 PHE D 640 TRP 0.013 0.001 TRP C 585 HIS 0.003 0.001 HIS A 492 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 6440) covalent geometry : angle 0.53734 ( 8762) hydrogen bonds : bond 0.03817 ( 424) hydrogen bonds : angle 4.01332 ( 1179) *********************** 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 187 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 161 time to evaluate : 0.217 Fit side-chains REVERT: A 532 LEU cc_start: 0.8604 (tp) cc_final: 0.8218 (mt) REVERT: B 406 PHE cc_start: 0.6524 (t80) cc_final: 0.6092 (t80) REVERT: C 432 LEU cc_start: 0.7256 (pt) cc_final: 0.6796 (pp) REVERT: C 462 MET cc_start: 0.6607 (tpp) cc_final: 0.6321 (tpp) REVERT: C 551 PHE cc_start: 0.7356 (t80) cc_final: 0.7151 (t80) REVERT: C 633 ASN cc_start: 0.8015 (OUTLIER) cc_final: 0.7674 (t0) REVERT: D 529 LEU cc_start: 0.8857 (tp) cc_final: 0.8606 (tp) REVERT: D 554 MET cc_start: 0.8258 (tpp) cc_final: 0.8021 (mmt) REVERT: D 617 PHE cc_start: 0.7883 (t80) cc_final: 0.7597 (t80) outliers start: 26 outliers final: 19 residues processed: 176 average time/residue: 0.0657 time to fit residues: 15.8741 Evaluate side-chains 169 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 525 LYS 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 620 SER 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 652 TYR Chi-restraints excluded: chain C residue 482 VAL 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 467 ILE Chi-restraints excluded: chain D residue 539 LEU 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 64 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 chunk 78 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.4069 r_free = 0.4069 target = 0.178558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.136226 restraints weight = 9235.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.139345 restraints weight = 5714.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.140317 restraints weight = 4206.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.141587 restraints weight = 3565.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.141456 restraints weight = 3257.471| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6440 Z= 0.137 Angle : 0.564 7.308 8762 Z= 0.296 Chirality : 0.039 0.158 1053 Planarity : 0.003 0.039 1028 Dihedral : 4.506 42.613 856 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 5.16 % Allowed : 27.58 % Favored : 67.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.31), residues: 766 helix: 0.19 (0.21), residues: 612 sheet: None (None), residues: 0 loop : -2.15 (0.54), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 528 TYR 0.013 0.001 TYR A 616 PHE 0.016 0.001 PHE C 617 TRP 0.012 0.001 TRP C 585 HIS 0.002 0.001 HIS A 492 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 6440) covalent geometry : angle 0.56369 ( 8762) hydrogen bonds : bond 0.03904 ( 424) hydrogen bonds : angle 4.02121 ( 1179) *********************** 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 182 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 150 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: A 532 LEU cc_start: 0.8608 (tp) cc_final: 0.8191 (mt) REVERT: C 432 LEU cc_start: 0.7371 (pt) cc_final: 0.6934 (pp) REVERT: C 462 MET cc_start: 0.6306 (tpp) cc_final: 0.6043 (tpp) REVERT: C 551 PHE cc_start: 0.7426 (t80) cc_final: 0.7209 (t80) REVERT: C 633 ASN cc_start: 0.8092 (OUTLIER) cc_final: 0.7671 (t0) REVERT: D 554 MET cc_start: 0.8362 (tpp) cc_final: 0.8121 (mmt) outliers start: 32 outliers final: 27 residues processed: 171 average time/residue: 0.0729 time to fit residues: 16.8155 Evaluate side-chains 173 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 145 time to evaluate : 0.175 ------------------------------------------------------------------------------- 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 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 620 SER 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 652 TYR Chi-restraints excluded: chain B residue 663 ILE 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 586 LEU 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 620 SER 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 66 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 26 optimal weight: 8.9990 chunk 45 optimal weight: 6.9990 chunk 23 optimal weight: 0.0270 chunk 53 optimal weight: 0.0040 chunk 16 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 overall best weight: 0.4650 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.182189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.146232 restraints weight = 9350.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.146460 restraints weight = 7336.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.147766 restraints weight = 6345.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.147931 restraints weight = 4697.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.148119 restraints weight = 4227.909| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.3241 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= 0.105 Angle : 0.525 7.263 8762 Z= 0.275 Chirality : 0.037 0.159 1053 Planarity : 0.003 0.028 1028 Dihedral : 4.153 41.446 856 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 4.19 % Allowed : 28.06 % Favored : 67.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.32), residues: 766 helix: 0.46 (0.22), residues: 610 sheet: None (None), residues: 0 loop : -1.83 (0.55), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 528 TYR 0.008 0.001 TYR B 616 PHE 0.012 0.001 PHE C 617 TRP 0.020 0.001 TRP A 563 HIS 0.002 0.000 HIS A 492 Details of bonding type rmsd covalent geometry : bond 0.00214 ( 6440) covalent geometry : angle 0.52523 ( 8762) hydrogen bonds : bond 0.03528 ( 424) hydrogen bonds : angle 3.82115 ( 1179) *********************** 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 188 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 162 time to evaluate : 0.229 Fit side-chains REVERT: A 532 LEU cc_start: 0.8503 (tp) cc_final: 0.8200 (mt) REVERT: B 406 PHE cc_start: 0.6611 (t80) cc_final: 0.6224 (t80) REVERT: C 432 LEU cc_start: 0.7365 (pt) cc_final: 0.6947 (pp) REVERT: C 462 MET cc_start: 0.6698 (tpp) cc_final: 0.6376 (tpp) REVERT: C 551 PHE cc_start: 0.7241 (t80) cc_final: 0.6997 (t80) REVERT: C 633 ASN cc_start: 0.7918 (OUTLIER) cc_final: 0.7533 (t0) REVERT: D 534 ARG cc_start: 0.7162 (mmt90) cc_final: 0.6801 (tpp80) outliers start: 26 outliers final: 16 residues processed: 178 average time/residue: 0.0621 time to fit residues: 15.3470 Evaluate side-chains 167 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 150 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 VAL 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 586 LEU Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain B residue 497 TRP 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 535 VAL Chi-restraints excluded: chain D residue 539 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 29 optimal weight: 5.9990 chunk 35 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.4105 r_free = 0.4105 target = 0.181666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.141276 restraints weight = 9335.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.141678 restraints weight = 5829.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.142649 restraints weight = 4843.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.143156 restraints weight = 4086.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.143381 restraints weight = 3981.400| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.3293 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= 0.126 Angle : 0.586 8.415 8762 Z= 0.300 Chirality : 0.039 0.158 1053 Planarity : 0.003 0.028 1028 Dihedral : 3.960 16.275 854 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.71 % Allowed : 28.87 % Favored : 67.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.32), residues: 766 helix: 0.51 (0.22), residues: 610 sheet: None (None), residues: 0 loop : -1.92 (0.55), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 528 TYR 0.012 0.001 TYR B 616 PHE 0.024 0.001 PHE B 617 TRP 0.027 0.002 TRP C 585 HIS 0.001 0.000 HIS C 492 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 6440) covalent geometry : angle 0.58611 ( 8762) hydrogen bonds : bond 0.03744 ( 424) hydrogen bonds : angle 3.88867 ( 1179) *********************** 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 176 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 153 time to evaluate : 0.219 Fit side-chains REVERT: A 532 LEU cc_start: 0.8605 (tp) cc_final: 0.8184 (mt) REVERT: A 534 ARG cc_start: 0.7808 (tpp-160) cc_final: 0.7549 (mmt-90) REVERT: B 406 PHE cc_start: 0.6483 (t80) cc_final: 0.6036 (t80) REVERT: B 554 MET cc_start: 0.7920 (mmm) cc_final: 0.7687 (tpt) REVERT: C 432 LEU cc_start: 0.7370 (pt) cc_final: 0.6956 (pp) REVERT: C 462 MET cc_start: 0.6383 (tpp) cc_final: 0.6055 (tpp) REVERT: C 551 PHE cc_start: 0.7330 (t80) cc_final: 0.7116 (t80) REVERT: C 633 ASN cc_start: 0.7971 (OUTLIER) cc_final: 0.7504 (t0) REVERT: D 534 ARG cc_start: 0.7211 (mmt90) cc_final: 0.6818 (tpp80) REVERT: D 597 TYR cc_start: 0.6954 (p90) cc_final: 0.6690 (p90) outliers start: 23 outliers final: 20 residues processed: 168 average time/residue: 0.0602 time to fit residues: 14.1590 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 : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 503 VAL 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 620 SER 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 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 535 VAL Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 620 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 6.9990 chunk 59 optimal weight: 0.0000 chunk 75 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 62 optimal weight: 0.4980 chunk 21 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.181508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.147854 restraints weight = 9589.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.144833 restraints weight = 7347.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.146351 restraints weight = 7382.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.146563 restraints weight = 5107.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.147043 restraints weight = 5128.537| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6440 Z= 0.116 Angle : 0.572 8.625 8762 Z= 0.291 Chirality : 0.038 0.157 1053 Planarity : 0.003 0.030 1028 Dihedral : 3.881 16.300 854 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.71 % Allowed : 28.87 % Favored : 67.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.32), residues: 766 helix: 0.58 (0.22), residues: 610 sheet: None (None), residues: 0 loop : -1.87 (0.55), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 528 TYR 0.011 0.001 TYR B 597 PHE 0.022 0.001 PHE B 617 TRP 0.031 0.002 TRP A 563 HIS 0.001 0.000 HIS C 562 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 6440) covalent geometry : angle 0.57215 ( 8762) hydrogen bonds : bond 0.03626 ( 424) hydrogen bonds : angle 3.83090 ( 1179) *********************** 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 177 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 154 time to evaluate : 0.205 Fit side-chains REVERT: A 532 LEU cc_start: 0.8546 (tp) cc_final: 0.8188 (mt) REVERT: A 534 ARG cc_start: 0.7768 (tpp-160) cc_final: 0.7505 (mmt-90) REVERT: B 406 PHE cc_start: 0.6661 (t80) cc_final: 0.6152 (t80) REVERT: B 554 MET cc_start: 0.7856 (mmm) cc_final: 0.7617 (tpt) REVERT: C 432 LEU cc_start: 0.7287 (pt) cc_final: 0.6865 (pp) REVERT: C 462 MET cc_start: 0.6495 (tpp) cc_final: 0.6179 (tpp) REVERT: C 551 PHE cc_start: 0.7295 (t80) cc_final: 0.7033 (t80) REVERT: C 633 ASN cc_start: 0.7880 (OUTLIER) cc_final: 0.7467 (t0) REVERT: D 597 TYR cc_start: 0.6961 (p90) cc_final: 0.6676 (p90) outliers start: 23 outliers final: 19 residues processed: 168 average time/residue: 0.0653 time to fit residues: 15.1467 Evaluate side-chains 170 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 0.161 ------------------------------------------------------------------------------- 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 535 VAL Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 620 SER 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 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 535 VAL Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 620 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 22 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 33 optimal weight: 0.0370 chunk 6 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.8060 ------------------------------------------------------------------------------- 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 = 0.4110 r_free = 0.4110 target = 0.181795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.141939 restraints weight = 9327.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.142450 restraints weight = 6066.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.143306 restraints weight = 4843.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.143492 restraints weight = 4126.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.143894 restraints weight = 4021.063| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.3504 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= 0.115 Angle : 0.581 8.746 8762 Z= 0.294 Chirality : 0.038 0.165 1053 Planarity : 0.003 0.041 1028 Dihedral : 3.824 15.815 854 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.39 % Allowed : 29.84 % Favored : 66.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.32), residues: 766 helix: 0.67 (0.22), residues: 606 sheet: None (None), residues: 0 loop : -1.72 (0.56), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 528 TYR 0.015 0.001 TYR A 475 PHE 0.021 0.001 PHE B 617 TRP 0.032 0.002 TRP A 563 HIS 0.001 0.000 HIS A 562 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 6440) covalent geometry : angle 0.58142 ( 8762) hydrogen bonds : bond 0.03609 ( 424) hydrogen bonds : angle 3.82193 ( 1179) ********************** 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 175 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 0.197 Fit side-chains REVERT: A 532 LEU cc_start: 0.8543 (tp) cc_final: 0.8148 (mt) REVERT: A 534 ARG cc_start: 0.7794 (tpp-160) cc_final: 0.7528 (mmt-90) REVERT: B 406 PHE cc_start: 0.6577 (t80) cc_final: 0.6029 (t80) REVERT: B 554 MET cc_start: 0.7891 (mmm) cc_final: 0.7669 (tpt) REVERT: C 432 LEU cc_start: 0.7353 (pt) cc_final: 0.6939 (pp) REVERT: C 462 MET cc_start: 0.6403 (tpp) cc_final: 0.6063 (tpp) REVERT: C 633 ASN cc_start: 0.7871 (OUTLIER) cc_final: 0.7414 (t0) REVERT: D 534 ARG cc_start: 0.7315 (mmt90) cc_final: 0.6912 (tpp80) REVERT: D 597 TYR cc_start: 0.6917 (p90) cc_final: 0.6675 (p90) outliers start: 21 outliers final: 20 residues processed: 167 average time/residue: 0.0633 time to fit residues: 14.5132 Evaluate side-chains 172 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 151 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 535 VAL 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 620 SER 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 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 535 VAL Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 620 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 22 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 67 optimal weight: 9.9990 chunk 79 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.4055 r_free = 0.4055 target = 0.177113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.144192 restraints weight = 9503.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.143003 restraints weight = 10720.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.144505 restraints weight = 8299.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.145259 restraints weight = 5578.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.146006 restraints weight = 5243.909| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 6440 Z= 0.200 Angle : 0.660 8.478 8762 Z= 0.339 Chirality : 0.042 0.166 1053 Planarity : 0.004 0.061 1028 Dihedral : 4.282 16.977 854 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 4.19 % Allowed : 29.52 % Favored : 66.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.31), residues: 766 helix: 0.28 (0.21), residues: 621 sheet: None (None), residues: 0 loop : -2.40 (0.55), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 528 TYR 0.017 0.002 TYR A 616 PHE 0.017 0.002 PHE B 617 TRP 0.033 0.002 TRP A 563 HIS 0.002 0.001 HIS C 492 Details of bonding type rmsd covalent geometry : bond 0.00465 ( 6440) covalent geometry : angle 0.66017 ( 8762) hydrogen bonds : bond 0.04283 ( 424) hydrogen bonds : angle 4.18316 ( 1179) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1079.70 seconds wall clock time: 19 minutes 22.74 seconds (1162.74 seconds total)