Starting phenix.real_space_refine on Mon Nov 13 23:25:49 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cn1_30413/11_2023/7cn1_30413.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cn1_30413/11_2023/7cn1_30413.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cn1_30413/11_2023/7cn1_30413.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cn1_30413/11_2023/7cn1_30413.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cn1_30413/11_2023/7cn1_30413.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cn1_30413/11_2023/7cn1_30413.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians K 3 8.98 5 S 29 5.16 5 C 4227 2.51 5 N 1000 2.21 5 O 1031 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 534": "NH1" <-> "NH2" Residue "A TYR 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 466": "OD1" <-> "OD2" Residue "B ARG 534": "NH1" <-> "NH2" Residue "B TYR 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 534": "NH1" <-> "NH2" Residue "C PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 534": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 6290 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1594 Classifications: {'peptide': 208} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 6, 'TRANS': 201} Chain breaks: 6 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 56 Chain: "B" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1555 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 6, 'TRANS': 194} Chain breaks: 6 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "C" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1575 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 6, 'TRANS': 200} Chain breaks: 7 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'TYR:plan': 1, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 52 Chain: "D" Number of atoms: 1563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1563 Classifications: {'peptide': 206} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 6, 'TRANS': 199} Chain breaks: 5 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 55 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.93, per 1000 atoms: 0.62 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.28 Conformation dependent library (CDL) restraints added in 1.3 seconds 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1558 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 0 sheets defined 78.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 404 through 431 removed outlier: 3.994A pdb=" N VAL A 409 " --> pdb=" O PRO A 405 " (cutoff:3.500A) Proline residue: A 426 - end of helix removed outlier: 3.525A pdb=" N PHE A 431 " --> pdb=" O TYR A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 472 removed outlier: 3.695A pdb=" N MET A 462 " --> pdb=" O ILE A 458 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N PHE A 463 " --> pdb=" O VAL A 459 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ILE A 467 " --> pdb=" O PHE A 463 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LEU A 468 " --> pdb=" O ILE A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 497 Processing helix chain 'A' and resid 498 through 505 removed outlier: 4.000A pdb=" N VAL A 503 " --> pdb=" O LEU A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 530 Processing helix chain 'A' and resid 531 through 537 removed outlier: 4.136A pdb=" N VAL A 535 " --> pdb=" O ARG A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.694A pdb=" N TYR A 542 " --> pdb=" O LEU A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 575 removed outlier: 3.721A pdb=" N GLU A 575 " --> pdb=" O ILE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 593 removed outlier: 4.122A pdb=" N GLY A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ASP A 591 " --> pdb=" O HIS A 587 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLN A 592 " --> pdb=" O ASN A 588 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 623 removed outlier: 3.898A pdb=" N LYS A 610 " --> pdb=" O SER A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 666 removed outlier: 3.805A pdb=" N ALA A 653 " --> pdb=" O SER A 649 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE A 656 " --> pdb=" O TYR A 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 431 Proline residue: B 426 - end of helix Processing helix chain 'B' and resid 456 through 473 removed outlier: 3.707A pdb=" N MET B 462 " --> pdb=" O ILE B 458 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ILE B 467 " --> pdb=" O PHE B 463 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU B 468 " --> pdb=" O ILE B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 497 removed outlier: 3.681A pdb=" N TRP B 497 " --> pdb=" O TYR B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 531 removed outlier: 3.535A pdb=" N ALA B 527 " --> pdb=" O LEU B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 539 removed outlier: 3.770A pdb=" N ALA B 536 " --> pdb=" O LEU B 532 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS B 538 " --> pdb=" O ARG B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 574 removed outlier: 4.219A pdb=" N PHE B 551 " --> pdb=" O ALA B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 624 removed outlier: 3.711A pdb=" N ALA B 614 " --> pdb=" O LYS B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 653 Processing helix chain 'B' and resid 654 through 658 Processing helix chain 'B' and resid 662 through 666 Processing helix chain 'C' and resid 406 through 431 Proline residue: C 426 - end of helix Processing helix chain 'C' and resid 456 through 472 removed outlier: 3.962A pdb=" N ILE C 467 " --> pdb=" O PHE C 463 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LEU C 468 " --> pdb=" O ILE C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 490 through 496 removed outlier: 3.621A pdb=" N PHE C 494 " --> pdb=" O ALA C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 505 Processing helix chain 'C' and resid 521 through 536 removed outlier: 3.740A pdb=" N LYS C 525 " --> pdb=" O GLY C 522 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA C 527 " --> pdb=" O LEU C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 574 Processing helix chain 'C' and resid 585 through 593 removed outlier: 3.944A pdb=" N ASP C 591 " --> pdb=" O HIS C 587 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE C 593 " --> pdb=" O LEU C 589 " (cutoff:3.500A) Processing helix chain 'C' and resid 606 through 624 Processing helix chain 'C' and resid 634 through 666 removed outlier: 3.821A pdb=" N GLY C 657 " --> pdb=" O ALA C 653 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N SER C 660 " --> pdb=" O PHE C 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 432 removed outlier: 5.447A pdb=" N TRP D 412 " --> pdb=" O ALA D 408 " (cutoff:3.500A) Proline residue: D 426 - end of helix removed outlier: 3.795A pdb=" N PHE D 431 " --> pdb=" O TYR D 427 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU D 432 " --> pdb=" O SER D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 472 removed outlier: 3.561A pdb=" N MET D 462 " --> pdb=" O ILE D 458 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE D 467 " --> pdb=" O PHE D 463 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU D 468 " --> pdb=" O ILE D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 491 through 496 removed outlier: 3.828A pdb=" N GLY D 496 " --> pdb=" O HIS D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 505 removed outlier: 3.571A pdb=" N MET D 502 " --> pdb=" O PHE D 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 531 Processing helix chain 'D' and resid 532 through 537 removed outlier: 4.211A pdb=" N ALA D 536 " --> pdb=" O LEU D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 543 removed outlier: 3.844A pdb=" N TYR D 542 " --> pdb=" O LYS D 538 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER D 543 " --> pdb=" O LEU D 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 538 through 543' Processing helix chain 'D' and resid 545 through 575 removed outlier: 4.200A pdb=" N PHE D 551 " --> pdb=" O ALA D 547 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLU D 575 " --> pdb=" O ILE D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 585 through 593 removed outlier: 3.984A pdb=" N ASP D 591 " --> pdb=" O HIS D 587 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLN D 592 " --> pdb=" O ASN D 588 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE D 593 " --> pdb=" O LEU D 589 " (cutoff:3.500A) Processing helix chain 'D' and resid 606 through 624 removed outlier: 3.829A pdb=" N ALA D 614 " --> pdb=" O LYS D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 665 removed outlier: 4.139A pdb=" N ALA D 653 " --> pdb=" O SER D 649 " (cutoff:3.500A) 424 hydrogen bonds defined for protein. 1179 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.61 Time building geometry restraints manager: 2.46 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: 98.35 - 105.51: 83 105.51 - 112.66: 3552 112.66 - 119.82: 2109 119.82 - 126.97: 2919 126.97 - 134.13: 99 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 2.440 nonbonded pdb=" OH TYR B 616 " pdb=" OD1 ASN B 629 " model vdw 2.157 2.440 nonbonded pdb=" ND2 ASN C 477 " pdb=" O GLU C 481 " model vdw 2.165 2.520 nonbonded pdb=" O PHE D 619 " pdb=" OG1 THR D 623 " model vdw 2.181 2.440 nonbonded pdb=" O THR D 421 " pdb=" OG1 THR D 425 " model vdw 2.185 2.440 ... (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 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: 2.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.110 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 20.560 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 6440 Z= 0.505 Angle : 0.778 7.856 8762 Z= 0.420 Chirality : 0.046 0.194 1053 Planarity : 0.004 0.040 1028 Dihedral : 13.724 84.732 2097 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.18 % Favored : 89.82 % Rotamer: Outliers : 0.32 % Allowed : 14.52 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.65 (0.26), residues: 766 helix: -2.06 (0.18), residues: 559 sheet: None (None), residues: 0 loop : -2.93 (0.42), residues: 207 *********************** 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 fitting. rotamer outliers: 2 poor density : 153 time to evaluate : 0.729 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 155 average time/residue: 0.1915 time to fit residues: 38.5607 Evaluate side-chains 123 residues out of total 705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 121 time to evaluate : 0.639 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0661 time to fit residues: 1.2092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 chunk 40 optimal weight: 0.8980 chunk 32 optimal weight: 0.4980 chunk 62 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 46 optimal weight: 9.9990 chunk 72 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 562 HIS A 576 GLN ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 HIS C 470 ASN D 562 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.1781 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= 0.166 Angle : 0.562 7.390 8762 Z= 0.296 Chirality : 0.038 0.158 1053 Planarity : 0.004 0.036 1028 Dihedral : 4.660 18.910 854 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 2.42 % Allowed : 19.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.29), residues: 766 helix: -0.77 (0.20), residues: 594 sheet: None (None), residues: 0 loop : -2.78 (0.50), residues: 172 *********************** 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 fitting. rotamer outliers: 15 poor density : 171 time to evaluate : 0.879 Fit side-chains outliers start: 15 outliers final: 9 residues processed: 177 average time/residue: 0.1629 time to fit residues: 38.4821 Evaluate side-chains 149 residues out of total 705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 140 time to evaluate : 0.683 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0562 time to fit residues: 1.8601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 60 optimal weight: 0.2980 chunk 49 optimal weight: 0.7980 chunk 20 optimal weight: 6.9990 chunk 72 optimal weight: 0.4980 chunk 78 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 470 ASN C 633 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6440 Z= 0.144 Angle : 0.529 7.577 8762 Z= 0.279 Chirality : 0.037 0.156 1053 Planarity : 0.003 0.036 1028 Dihedral : 4.231 17.354 854 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.10 % Allowed : 24.19 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.31), residues: 766 helix: -0.07 (0.21), residues: 597 sheet: None (None), residues: 0 loop : -2.23 (0.53), residues: 169 *********************** 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 178 residues out of total 705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 165 time to evaluate : 0.706 Fit side-chains outliers start: 13 outliers final: 7 residues processed: 171 average time/residue: 0.1707 time to fit residues: 38.8736 Evaluate side-chains 163 residues out of total 705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 156 time to evaluate : 0.692 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0600 time to fit residues: 1.7375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 73 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 69 optimal weight: 0.3980 chunk 20 optimal weight: 10.0000 chunk 64 optimal weight: 9.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 573 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2427 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= 0.212 Angle : 0.562 7.627 8762 Z= 0.294 Chirality : 0.039 0.177 1053 Planarity : 0.003 0.026 1028 Dihedral : 4.284 18.011 854 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 2.10 % Allowed : 27.26 % Favored : 70.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.31), residues: 766 helix: -0.00 (0.21), residues: 607 sheet: None (None), residues: 0 loop : -2.28 (0.53), residues: 159 *********************** 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 168 residues out of total 705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 155 time to evaluate : 0.708 Fit side-chains outliers start: 13 outliers final: 6 residues processed: 164 average time/residue: 0.1689 time to fit residues: 36.9181 Evaluate side-chains 154 residues out of total 705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 148 time to evaluate : 0.602 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0607 time to fit residues: 1.5230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 65 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 0 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 69 optimal weight: 0.2980 chunk 19 optimal weight: 1.9990 chunk 26 optimal weight: 8.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6440 Z= 0.152 Angle : 0.524 7.724 8762 Z= 0.272 Chirality : 0.037 0.153 1053 Planarity : 0.003 0.033 1028 Dihedral : 4.051 16.763 854 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.58 % Allowed : 26.94 % Favored : 70.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.32), residues: 766 helix: 0.25 (0.22), residues: 602 sheet: None (None), residues: 0 loop : -1.89 (0.53), residues: 164 *********************** 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 174 residues out of total 705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 158 time to evaluate : 0.744 Fit side-chains outliers start: 16 outliers final: 9 residues processed: 165 average time/residue: 0.1591 time to fit residues: 35.5082 Evaluate side-chains 156 residues out of total 705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 147 time to evaluate : 0.705 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1007 time to fit residues: 2.3277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 77 optimal weight: 0.3980 chunk 64 optimal weight: 9.9990 chunk 35 optimal weight: 0.9990 chunk 6 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2993 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= 0.151 Angle : 0.543 7.767 8762 Z= 0.280 Chirality : 0.037 0.153 1053 Planarity : 0.003 0.029 1028 Dihedral : 4.014 16.206 854 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 1.61 % Allowed : 28.87 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.32), residues: 766 helix: 0.37 (0.22), residues: 602 sheet: None (None), residues: 0 loop : -1.79 (0.53), residues: 164 *********************** 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 174 residues out of total 705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 164 time to evaluate : 0.712 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 172 average time/residue: 0.1688 time to fit residues: 38.9802 Evaluate side-chains 158 residues out of total 705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 151 time to evaluate : 0.720 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0626 time to fit residues: 1.7253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 0.0980 chunk 44 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 65 optimal weight: 9.9990 chunk 77 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6440 Z= 0.149 Angle : 0.532 7.780 8762 Z= 0.277 Chirality : 0.037 0.154 1053 Planarity : 0.003 0.028 1028 Dihedral : 3.921 15.536 854 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 1.77 % Allowed : 29.03 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.32), residues: 766 helix: 0.45 (0.22), residues: 603 sheet: None (None), residues: 0 loop : -1.82 (0.53), residues: 163 *********************** 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 166 residues out of total 705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 155 time to evaluate : 0.702 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 159 average time/residue: 0.1624 time to fit residues: 34.8941 Evaluate side-chains 154 residues out of total 705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 147 time to evaluate : 0.654 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0649 time to fit residues: 1.6810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 14 optimal weight: 0.0770 chunk 49 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 60 optimal weight: 0.3980 chunk 70 optimal weight: 0.0770 chunk 73 optimal weight: 6.9990 chunk 67 optimal weight: 8.9990 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.3533 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= 0.136 Angle : 0.535 9.672 8762 Z= 0.274 Chirality : 0.036 0.157 1053 Planarity : 0.003 0.027 1028 Dihedral : 3.764 14.287 854 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.32 % Allowed : 29.03 % Favored : 70.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.32), residues: 766 helix: 0.62 (0.22), residues: 604 sheet: None (None), residues: 0 loop : -1.76 (0.54), residues: 162 *********************** 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 160 residues out of total 705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 158 time to evaluate : 0.726 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 160 average time/residue: 0.1533 time to fit residues: 33.8813 Evaluate side-chains 148 residues out of total 705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 0.746 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 43 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 64 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 75 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6440 Z= 0.199 Angle : 0.576 8.287 8762 Z= 0.298 Chirality : 0.039 0.186 1053 Planarity : 0.003 0.027 1028 Dihedral : 3.900 14.986 854 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.48 % Allowed : 30.97 % Favored : 68.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.32), residues: 766 helix: 0.43 (0.21), residues: 615 sheet: None (None), residues: 0 loop : -1.92 (0.56), residues: 151 *********************** 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 152 residues out of total 705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 149 time to evaluate : 0.702 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 150 average time/residue: 0.1515 time to fit residues: 31.1343 Evaluate side-chains 148 residues out of total 705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 147 time to evaluate : 0.719 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0611 time to fit residues: 1.0538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 4.9990 chunk 52 optimal weight: 0.0870 chunk 79 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 49 optimal weight: 8.9990 chunk 38 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 67 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6440 Z= 0.168 Angle : 0.559 8.754 8762 Z= 0.289 Chirality : 0.038 0.156 1053 Planarity : 0.003 0.027 1028 Dihedral : 3.845 14.525 854 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.48 % Allowed : 31.29 % Favored : 68.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.32), residues: 766 helix: 0.47 (0.21), residues: 616 sheet: None (None), residues: 0 loop : -1.96 (0.56), residues: 150 ********************** 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 149 residues out of total 705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 146 time to evaluate : 0.725 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 147 average time/residue: 0.1480 time to fit residues: 29.9101 Evaluate side-chains 147 residues out of total 705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 144 time to evaluate : 0.657 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0686 time to fit residues: 1.2384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 0.6980 chunk 9 optimal weight: 4.9990 chunk 17 optimal weight: 0.0970 chunk 63 optimal weight: 0.8980 chunk 26 optimal weight: 8.9990 chunk 65 optimal weight: 9.9990 chunk 8 optimal weight: 0.0770 chunk 11 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 3 optimal weight: 0.4980 chunk 45 optimal weight: 20.0000 overall best weight: 0.4136 ------------------------------------------------------------------------------- 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 = 0.4156 r_free = 0.4156 target = 0.186437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.152107 restraints weight = 9189.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.150196 restraints weight = 7275.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.151926 restraints weight = 6574.334| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6440 Z= 0.134 Angle : 0.539 8.697 8762 Z= 0.278 Chirality : 0.037 0.162 1053 Planarity : 0.003 0.026 1028 Dihedral : 3.658 13.810 854 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.32 % Allowed : 31.77 % Favored : 67.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.32), residues: 766 helix: 0.69 (0.22), residues: 609 sheet: None (None), residues: 0 loop : -1.43 (0.57), residues: 157 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1517.31 seconds wall clock time: 28 minutes 26.00 seconds (1706.00 seconds total)