Starting phenix.real_space_refine on Mon Sep 23 18:49:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vab_21135/09_2024/6vab_21135.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vab_21135/09_2024/6vab_21135.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vab_21135/09_2024/6vab_21135.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vab_21135/09_2024/6vab_21135.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vab_21135/09_2024/6vab_21135.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vab_21135/09_2024/6vab_21135.cif" } resolution = 4.9 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= 0.001 sd= 0.004 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: 3 Type Number sf(0) Gaussians C 2766 2.51 5 N 938 2.21 5 O 938 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 4642 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 897 Classifications: {'peptide': 182} Incomplete info: {'truncation_to_alanine': 160} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 174} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 582 Unresolved non-hydrogen angles: 752 Unresolved non-hydrogen dihedrals: 484 Unresolved non-hydrogen chiralities: 60 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 11, 'TYR:plan': 8, 'ASN:plan1': 8, 'TRP:plan': 1, 'HIS:plan': 9, 'PHE:plan': 8, 'GLU:plan': 9, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 303 Chain: "B" Number of atoms: 1371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 1371 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 242} Link IDs: {'PTRANS': 8, 'TRANS': 267} Chain breaks: 2 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 926 Unresolved non-hydrogen angles: 1174 Unresolved non-hydrogen dihedrals: 778 Unresolved non-hydrogen chiralities: 71 Planarities with less than four sites: {'GLN:plan1': 20, 'ASP:plan': 11, 'TYR:plan': 8, 'ASN:plan1': 11, 'TRP:plan': 2, 'HIS:plan': 9, 'PHE:plan': 18, 'GLU:plan': 24, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 544 Chain: "C" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 897 Classifications: {'peptide': 182} Incomplete info: {'truncation_to_alanine': 160} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 174} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 582 Unresolved non-hydrogen angles: 752 Unresolved non-hydrogen dihedrals: 484 Unresolved non-hydrogen chiralities: 60 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 11, 'TYR:plan': 8, 'ASN:plan1': 8, 'TRP:plan': 1, 'HIS:plan': 9, 'PHE:plan': 8, 'GLU:plan': 9, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 303 Chain: "D" Number of atoms: 1477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 1477 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 259} Link IDs: {'PTRANS': 8, 'TRANS': 289} Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 984 Unresolved non-hydrogen angles: 1247 Unresolved non-hydrogen dihedrals: 823 Unresolved non-hydrogen chiralities: 74 Planarities with less than four sites: {'GLN:plan1': 20, 'ASP:plan': 14, 'TYR:plan': 8, 'ASN:plan1': 14, 'TRP:plan': 2, 'HIS:plan': 10, 'PHE:plan': 18, 'GLU:plan': 27, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 584 Time building chain proxies: 3.87, per 1000 atoms: 0.83 Number of scatterers: 4642 At special positions: 0 Unit cell: (109.6, 110.696, 56.992, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 938 8.00 N 938 7.00 C 2766 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.32 Conformation dependent library (CDL) restraints added in 1.0 seconds 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1780 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 8 sheets defined 53.6% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 19 through 26 Processing helix chain 'A' and resid 43 through 51 removed outlier: 3.889A pdb=" N LEU A 49 " --> pdb=" O SER A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 104 removed outlier: 4.230A pdb=" N LEU A 99 " --> pdb=" O ASP A 95 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA A 100 " --> pdb=" O MET A 96 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ARG A 104 " --> pdb=" O ALA A 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 497 Processing helix chain 'B' and resid 502 through 516 Processing helix chain 'B' and resid 523 through 546 Proline residue: B 530 - end of helix Processing helix chain 'B' and resid 552 through 573 removed outlier: 3.806A pdb=" N PHE B 563 " --> pdb=" O LYS B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 595 removed outlier: 4.081A pdb=" N ARG B 582 " --> pdb=" O GLU B 578 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE B 594 " --> pdb=" O ALA B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 614 removed outlier: 4.048A pdb=" N VAL B 602 " --> pdb=" O ASN B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 638 removed outlier: 3.635A pdb=" N ALA B 627 " --> pdb=" O ALA B 623 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU B 630 " --> pdb=" O ALA B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 659 removed outlier: 3.584A pdb=" N ALA B 654 " --> pdb=" O ARG B 650 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS B 659 " --> pdb=" O LEU B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 676 Processing helix chain 'B' and resid 696 through 708 removed outlier: 3.708A pdb=" N LEU B 700 " --> pdb=" O VAL B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 733 removed outlier: 4.119A pdb=" N ILE B 728 " --> pdb=" O LEU B 724 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N TYR B 729 " --> pdb=" O ASN B 725 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N PHE B 730 " --> pdb=" O ARG B 726 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N TYR B 731 " --> pdb=" O TYR B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 751 removed outlier: 4.223A pdb=" N GLN B 745 " --> pdb=" O GLN B 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 778 Processing helix chain 'C' and resid 19 through 26 Processing helix chain 'C' and resid 43 through 51 removed outlier: 3.889A pdb=" N LEU C 49 " --> pdb=" O SER C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 104 removed outlier: 4.229A pdb=" N LEU C 99 " --> pdb=" O ASP C 95 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA C 100 " --> pdb=" O MET C 96 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN C 103 " --> pdb=" O LEU C 99 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ARG C 104 " --> pdb=" O ALA C 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 487 removed outlier: 3.786A pdb=" N ASP D 486 " --> pdb=" O ASP D 483 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU D 487 " --> pdb=" O PHE D 484 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 483 through 487' Processing helix chain 'D' and resid 488 through 500 removed outlier: 3.620A pdb=" N HIS D 496 " --> pdb=" O GLY D 492 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG D 499 " --> pdb=" O ILE D 495 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER D 500 " --> pdb=" O HIS D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 517 Processing helix chain 'D' and resid 523 through 546 Proline residue: D 530 - end of helix Processing helix chain 'D' and resid 552 through 573 Processing helix chain 'D' and resid 578 through 595 removed outlier: 4.147A pdb=" N ARG D 582 " --> pdb=" O GLU D 578 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE D 594 " --> pdb=" O ALA D 590 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY D 595 " --> pdb=" O ALA D 591 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 614 Processing helix chain 'D' and resid 620 through 637 removed outlier: 3.715A pdb=" N ARG D 637 " --> pdb=" O GLY D 633 " (cutoff:3.500A) Processing helix chain 'D' and resid 642 through 659 Proline residue: D 648 - end of helix removed outlier: 3.563A pdb=" N THR D 651 " --> pdb=" O GLU D 647 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N CYS D 653 " --> pdb=" O LEU D 649 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA D 654 " --> pdb=" O ARG D 650 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA D 656 " --> pdb=" O GLN D 652 " (cutoff:3.500A) Processing helix chain 'D' and resid 662 through 679 removed outlier: 3.728A pdb=" N GLN D 666 " --> pdb=" O LYS D 662 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N HIS D 675 " --> pdb=" O SER D 671 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU D 676 " --> pdb=" O THR D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 695 through 707 Processing helix chain 'D' and resid 712 through 730 Processing helix chain 'D' and resid 742 through 750 removed outlier: 4.486A pdb=" N GLN D 748 " --> pdb=" O ASN D 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 760 through 777 removed outlier: 3.658A pdb=" N GLU D 764 " --> pdb=" O SER D 760 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN D 765 " --> pdb=" O GLU D 761 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 58 removed outlier: 4.691A pdb=" N HIS A 33 " --> pdb=" O LEU A 2 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 4 " --> pdb=" O HIS A 33 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU A 35 " --> pdb=" O LEU A 4 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL A 5 " --> pdb=" O VAL A 151 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N VAL A 151 " --> pdb=" O VAL A 5 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N PHE A 150 " --> pdb=" O TYR A 165 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE A 168 " --> pdb=" O ASP A 171 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASP A 171 " --> pdb=" O ILE A 168 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 55 through 58 removed outlier: 4.691A pdb=" N HIS A 33 " --> pdb=" O LEU A 2 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 4 " --> pdb=" O HIS A 33 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU A 35 " --> pdb=" O LEU A 4 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL A 5 " --> pdb=" O VAL A 151 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N VAL A 151 " --> pdb=" O VAL A 5 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N PHE A 150 " --> pdb=" O TYR A 165 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TYR A 179 " --> pdb=" O VAL A 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 74 through 77 removed outlier: 3.844A pdb=" N PHE A 80 " --> pdb=" O VAL A 77 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 110 through 112 removed outlier: 6.625A pdb=" N LEU A 111 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 55 through 58 removed outlier: 4.691A pdb=" N HIS C 33 " --> pdb=" O LEU C 2 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU C 4 " --> pdb=" O HIS C 33 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU C 35 " --> pdb=" O LEU C 4 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL C 5 " --> pdb=" O VAL C 151 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N VAL C 151 " --> pdb=" O VAL C 5 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE C 150 " --> pdb=" O TYR C 165 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE C 168 " --> pdb=" O ASP C 171 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASP C 171 " --> pdb=" O ILE C 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 55 through 58 removed outlier: 4.691A pdb=" N HIS C 33 " --> pdb=" O LEU C 2 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU C 4 " --> pdb=" O HIS C 33 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU C 35 " --> pdb=" O LEU C 4 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL C 5 " --> pdb=" O VAL C 151 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N VAL C 151 " --> pdb=" O VAL C 5 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE C 150 " --> pdb=" O TYR C 165 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TYR C 179 " --> pdb=" O VAL C 160 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 74 through 77 removed outlier: 3.844A pdb=" N PHE C 80 " --> pdb=" O VAL C 77 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 110 through 112 removed outlier: 6.625A pdb=" N LEU C 111 " --> pdb=" O ILE C 130 " (cutoff:3.500A) 392 hydrogen bonds defined for protein. 1164 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: 1.45 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 938 1.29 - 1.35: 931 1.35 - 1.42: 1 1.42 - 1.49: 938 1.49 - 1.56: 1828 Bond restraints: 4636 Sorted by residual: bond pdb=" C LYS D 663 " pdb=" N PRO D 664 " ideal model delta sigma weight residual 1.334 1.394 -0.060 2.34e-02 1.83e+03 6.54e+00 bond pdb=" CA ALA D 564 " pdb=" C ALA D 564 " ideal model delta sigma weight residual 1.524 1.500 0.024 1.24e-02 6.50e+03 3.80e+00 bond pdb=" N ILE A 11 " pdb=" CA ILE A 11 " ideal model delta sigma weight residual 1.460 1.446 0.014 7.30e-03 1.88e+04 3.62e+00 bond pdb=" N ILE C 11 " pdb=" CA ILE C 11 " ideal model delta sigma weight residual 1.460 1.446 0.014 7.30e-03 1.88e+04 3.61e+00 bond pdb=" N MET D 711 " pdb=" CA MET D 711 " ideal model delta sigma weight residual 1.457 1.480 -0.023 1.29e-02 6.01e+03 3.19e+00 ... (remaining 4631 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 5998 1.62 - 3.24: 389 3.24 - 4.86: 49 4.86 - 6.47: 12 6.47 - 8.09: 4 Bond angle restraints: 6452 Sorted by residual: angle pdb=" N GLU B 647 " pdb=" CA GLU B 647 " pdb=" C GLU B 647 " ideal model delta sigma weight residual 113.57 120.12 -6.55 1.38e+00 5.25e-01 2.25e+01 angle pdb=" C ALA B 574 " pdb=" N GLU B 575 " pdb=" CA GLU B 575 " ideal model delta sigma weight residual 122.61 128.76 -6.15 1.56e+00 4.11e-01 1.55e+01 angle pdb=" N GLU D 647 " pdb=" CA GLU D 647 " pdb=" C GLU D 647 " ideal model delta sigma weight residual 109.81 117.90 -8.09 2.21e+00 2.05e-01 1.34e+01 angle pdb=" C ALA D 574 " pdb=" N GLU D 575 " pdb=" CA GLU D 575 " ideal model delta sigma weight residual 122.08 127.43 -5.35 1.47e+00 4.63e-01 1.33e+01 angle pdb=" C GLY A 114 " pdb=" N HIS A 115 " pdb=" CA HIS A 115 " ideal model delta sigma weight residual 121.54 128.44 -6.90 1.91e+00 2.74e-01 1.31e+01 ... (remaining 6447 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 6.54: 2283 6.54 - 13.08: 314 13.08 - 19.61: 92 19.61 - 26.15: 18 26.15 - 32.69: 5 Dihedral angle restraints: 2712 sinusoidal: 0 harmonic: 2712 Sorted by residual: dihedral pdb=" CA ILE D 750 " pdb=" C ILE D 750 " pdb=" N ARG D 751 " pdb=" CA ARG D 751 " ideal model delta harmonic sigma weight residual 180.00 147.31 32.69 0 5.00e+00 4.00e-02 4.27e+01 dihedral pdb=" CA LEU B 777 " pdb=" C LEU B 777 " pdb=" N ARG B 778 " pdb=" CA ARG B 778 " ideal model delta harmonic sigma weight residual 180.00 150.64 29.36 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA ILE D 509 " pdb=" C ILE D 509 " pdb=" N LEU D 510 " pdb=" CA LEU D 510 " ideal model delta harmonic sigma weight residual 180.00 152.96 27.04 0 5.00e+00 4.00e-02 2.93e+01 ... (remaining 2709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 585 0.050 - 0.101: 230 0.101 - 0.151: 63 0.151 - 0.201: 10 0.201 - 0.251: 2 Chirality restraints: 890 Sorted by residual: chirality pdb=" CA GLU B 647 " pdb=" N GLU B 647 " pdb=" C GLU B 647 " pdb=" CB GLU B 647 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CA GLU D 647 " pdb=" N GLU D 647 " pdb=" C GLU D 647 " pdb=" CB GLU D 647 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA THR B 763 " pdb=" N THR B 763 " pdb=" C THR B 763 " pdb=" CB THR B 763 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 9.11e-01 ... (remaining 887 not shown) Planarity restraints: 932 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 743 " 0.011 2.00e-02 2.50e+03 2.13e-02 4.54e+00 pdb=" C LEU D 743 " -0.037 2.00e-02 2.50e+03 pdb=" O LEU D 743 " 0.014 2.00e-02 2.50e+03 pdb=" N ASN D 744 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS C 115 " -0.009 2.00e-02 2.50e+03 1.89e-02 3.56e+00 pdb=" C HIS C 115 " 0.033 2.00e-02 2.50e+03 pdb=" O HIS C 115 " -0.012 2.00e-02 2.50e+03 pdb=" N THR C 116 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 115 " 0.009 2.00e-02 2.50e+03 1.88e-02 3.52e+00 pdb=" C HIS A 115 " -0.032 2.00e-02 2.50e+03 pdb=" O HIS A 115 " 0.012 2.00e-02 2.50e+03 pdb=" N THR A 116 " 0.011 2.00e-02 2.50e+03 ... (remaining 929 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 1700 2.84 - 3.36: 4676 3.36 - 3.87: 6864 3.87 - 4.39: 7772 4.39 - 4.90: 10814 Nonbonded interactions: 31826 Sorted by model distance: nonbonded pdb=" O LYS B 749 " pdb=" N ASP B 753 " model vdw 2.330 3.120 nonbonded pdb=" O ALA D 513 " pdb=" N GLY D 518 " model vdw 2.382 3.120 nonbonded pdb=" O LYS D 749 " pdb=" N ASP D 753 " model vdw 2.399 3.120 nonbonded pdb=" O ALA B 513 " pdb=" N GLY B 518 " model vdw 2.405 3.120 nonbonded pdb=" O GLU D 752 " pdb=" N ASN D 756 " model vdw 2.476 3.120 ... (remaining 31821 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' selection = chain 'C' } ncs_group { reference = chain 'B' selection = (chain 'D' and (resid 484 through 678 or resid 695 through 733 or resid 739 thro \ ugh 780)) } 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: 0.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.000 Find NCS groups from input model: 0.370 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6892 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 : 0.005 0.060 4636 Z= 0.331 Angle : 0.913 8.092 6452 Z= 0.597 Chirality : 0.057 0.251 890 Planarity : 0.005 0.021 932 Dihedral : 8.702 32.689 932 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -3.84 (0.22), residues: 926 helix: -3.43 (0.17), residues: 364 sheet: -0.19 (0.61), residues: 78 loop : -2.20 (0.23), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 93 PHE 0.000 0.000 PHE A 22 TYR 0.000 0.000 TYR A 46 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.711 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0554 time to fit residues: 2.4014 Evaluate side-chains 16 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 10.0000 chunk 69 optimal weight: 0.0170 chunk 38 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 47 optimal weight: 50.0000 chunk 37 optimal weight: 5.9990 chunk 72 optimal weight: 20.0000 chunk 27 optimal weight: 30.0000 chunk 43 optimal weight: 20.0000 chunk 53 optimal weight: 10.0000 chunk 83 optimal weight: 8.9990 overall best weight: 3.3822 ------------------------------------------------------------------------------- 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: 0.6720 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4636 Z= 0.170 Angle : 0.484 5.788 6452 Z= 0.319 Chirality : 0.043 0.134 890 Planarity : 0.003 0.016 932 Dihedral : 5.498 22.661 932 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 0.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.24), residues: 926 helix: -1.77 (0.20), residues: 492 sheet: 0.01 (0.62), residues: 80 loop : -2.42 (0.28), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 93 PHE 0.000 0.000 PHE A 22 TYR 0.000 0.000 TYR A 46 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.497 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0421 time to fit residues: 1.9833 Evaluate side-chains 16 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 50.0000 chunk 25 optimal weight: 5.9990 chunk 69 optimal weight: 0.0270 chunk 56 optimal weight: 50.0000 chunk 23 optimal weight: 7.9990 chunk 83 optimal weight: 50.0000 chunk 90 optimal weight: 0.9980 chunk 74 optimal weight: 50.0000 chunk 82 optimal weight: 6.9990 chunk 28 optimal weight: 8.9990 chunk 67 optimal weight: 10.0000 overall best weight: 4.4044 ------------------------------------------------------------------------------- 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: 0.6776 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 4636 Z= 0.180 Angle : 0.448 4.563 6452 Z= 0.300 Chirality : 0.042 0.138 890 Planarity : 0.002 0.011 932 Dihedral : 4.691 20.507 932 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -1.42 (0.27), residues: 926 helix: -0.36 (0.23), residues: 510 sheet: -0.13 (0.63), residues: 84 loop : -1.96 (0.31), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 93 PHE 0.000 0.000 PHE A 22 TYR 0.000 0.000 TYR A 46 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.520 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0445 time to fit residues: 2.1448 Evaluate side-chains 16 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 20.0000 chunk 62 optimal weight: 50.0000 chunk 43 optimal weight: 0.2980 chunk 9 optimal weight: 0.6980 chunk 39 optimal weight: 20.0000 chunk 56 optimal weight: 30.0000 chunk 83 optimal weight: 0.9980 chunk 88 optimal weight: 20.0000 chunk 79 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 74 optimal weight: 1.9990 overall best weight: 2.5984 ------------------------------------------------------------------------------- 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: 0.6727 moved from start: 0.4735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.009 4636 Z= 0.111 Angle : 0.370 3.826 6452 Z= 0.242 Chirality : 0.042 0.131 890 Planarity : 0.002 0.009 932 Dihedral : 4.104 16.435 932 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 0.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -0.64 (0.28), residues: 926 helix: 0.28 (0.23), residues: 525 sheet: 0.24 (0.65), residues: 84 loop : -1.72 (0.32), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 93 PHE 0.000 0.000 PHE A 22 TYR 0.000 0.000 TYR A 46 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.534 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0387 time to fit residues: 1.8012 Evaluate side-chains 16 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 0.0770 chunk 1 optimal weight: 40.0000 chunk 66 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 75 optimal weight: 20.0000 chunk 61 optimal weight: 0.6980 chunk 0 optimal weight: 40.0000 chunk 45 optimal weight: 60.0000 chunk 79 optimal weight: 20.0000 chunk 22 optimal weight: 6.9990 chunk 29 optimal weight: 50.0000 overall best weight: 4.1544 ------------------------------------------------------------------------------- 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: 0.6793 moved from start: 0.5689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 4636 Z= 0.174 Angle : 0.419 4.022 6452 Z= 0.278 Chirality : 0.043 0.133 890 Planarity : 0.002 0.009 932 Dihedral : 4.279 17.359 932 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -0.37 (0.28), residues: 926 helix: 0.40 (0.23), residues: 527 sheet: 0.54 (0.62), residues: 94 loop : -1.56 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 93 PHE 0.000 0.000 PHE A 22 TYR 0.000 0.000 TYR A 46 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.474 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0416 time to fit residues: 2.1138 Evaluate side-chains 16 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 20.0000 chunk 17 optimal weight: 6.9990 chunk 52 optimal weight: 50.0000 chunk 21 optimal weight: 20.0000 chunk 89 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 41 optimal weight: 20.0000 chunk 7 optimal weight: 40.0000 chunk 29 optimal weight: 50.0000 chunk 46 optimal weight: 40.0000 chunk 85 optimal weight: 30.0000 overall best weight: 10.7992 ------------------------------------------------------------------------------- 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: 0.6993 moved from start: 0.8154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 4636 Z= 0.392 Angle : 0.712 6.976 6452 Z= 0.486 Chirality : 0.045 0.150 890 Planarity : 0.005 0.021 932 Dihedral : 6.567 23.431 932 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.26), residues: 926 helix: -1.36 (0.21), residues: 478 sheet: -0.08 (0.65), residues: 82 loop : -1.41 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 93 PHE 0.000 0.000 PHE A 22 TYR 0.000 0.000 TYR A 46 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.565 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0439 time to fit residues: 2.1072 Evaluate side-chains 16 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 20.0000 chunk 50 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 74 optimal weight: 8.9990 chunk 49 optimal weight: 10.0000 chunk 88 optimal weight: 40.0000 chunk 55 optimal weight: 9.9990 chunk 54 optimal weight: 0.6980 chunk 40 optimal weight: 9.9990 chunk 35 optimal weight: 0.9980 chunk 52 optimal weight: 50.0000 overall best weight: 4.7386 ------------------------------------------------------------------------------- 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: 0.6864 moved from start: 0.8274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 4636 Z= 0.186 Angle : 0.455 3.774 6452 Z= 0.306 Chirality : 0.042 0.134 890 Planarity : 0.003 0.017 932 Dihedral : 5.256 19.781 932 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -1.37 (0.27), residues: 926 helix: -0.64 (0.21), residues: 509 sheet: 0.08 (0.59), residues: 94 loop : -1.43 (0.34), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 93 PHE 0.000 0.000 PHE A 22 TYR 0.000 0.000 TYR A 46 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.511 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0429 time to fit residues: 2.0525 Evaluate side-chains 16 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 8.9990 chunk 17 optimal weight: 30.0000 chunk 56 optimal weight: 50.0000 chunk 60 optimal weight: 50.0000 chunk 43 optimal weight: 20.0000 chunk 8 optimal weight: 4.9990 chunk 69 optimal weight: 50.0000 chunk 80 optimal weight: 6.9990 chunk 84 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 82 optimal weight: 7.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- 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: 0.6875 moved from start: 0.8848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 4636 Z= 0.214 Angle : 0.473 3.748 6452 Z= 0.320 Chirality : 0.043 0.133 890 Planarity : 0.002 0.020 932 Dihedral : 5.015 20.528 932 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -0.90 (0.28), residues: 926 helix: -0.17 (0.23), residues: 508 sheet: -0.06 (0.54), residues: 110 loop : -1.31 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 93 PHE 0.000 0.000 PHE A 22 TYR 0.000 0.000 TYR A 46 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.514 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0432 time to fit residues: 2.0590 Evaluate side-chains 16 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 20.0000 chunk 49 optimal weight: 50.0000 chunk 35 optimal weight: 40.0000 chunk 64 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 74 optimal weight: 30.0000 chunk 78 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 54 optimal weight: 0.9990 chunk 87 optimal weight: 0.0970 chunk 53 optimal weight: 20.0000 overall best weight: 3.8186 ------------------------------------------------------------------------------- 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: 0.6817 moved from start: 0.9063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 4636 Z= 0.150 Angle : 0.403 3.119 6452 Z= 0.269 Chirality : 0.042 0.133 890 Planarity : 0.002 0.020 932 Dihedral : 4.634 18.073 932 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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 (0.28), residues: 926 helix: 0.26 (0.23), residues: 515 sheet: 0.10 (0.54), residues: 110 loop : -1.15 (0.37), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 93 PHE 0.000 0.000 PHE A 22 TYR 0.000 0.000 TYR A 46 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.549 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0441 time to fit residues: 2.1414 Evaluate side-chains 16 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 0.0980 chunk 60 optimal weight: 50.0000 chunk 91 optimal weight: 5.9990 chunk 84 optimal weight: 20.0000 chunk 72 optimal weight: 0.9990 chunk 7 optimal weight: 40.0000 chunk 56 optimal weight: 50.0000 chunk 44 optimal weight: 20.0000 chunk 57 optimal weight: 50.0000 chunk 77 optimal weight: 20.0000 chunk 22 optimal weight: 6.9990 overall best weight: 6.8190 ------------------------------------------------------------------------------- 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: 0.6873 moved from start: 0.9521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 4636 Z= 0.237 Angle : 0.479 3.375 6452 Z= 0.328 Chirality : 0.042 0.134 890 Planarity : 0.003 0.025 932 Dihedral : 4.930 20.142 932 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -0.68 (0.28), residues: 926 helix: 0.01 (0.23), residues: 508 sheet: 0.02 (0.53), residues: 110 loop : -1.21 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 93 PHE 0.000 0.000 PHE A 22 TYR 0.000 0.000 TYR A 46 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.541 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0442 time to fit residues: 2.1068 Evaluate side-chains 16 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 9 optimal weight: 30.0000 chunk 13 optimal weight: 50.0000 chunk 64 optimal weight: 0.0970 chunk 4 optimal weight: 0.9990 chunk 52 optimal weight: 50.0000 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.140853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.079056 restraints weight = 9266.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.079001 restraints weight = 10742.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 16)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.078977 restraints weight = 10779.300| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6742 moved from start: 0.9630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.010 4636 Z= 0.102 Angle : 0.366 3.038 6452 Z= 0.236 Chirality : 0.042 0.135 890 Planarity : 0.002 0.018 932 Dihedral : 4.293 18.908 932 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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 (0.28), residues: 926 helix: 0.81 (0.23), residues: 514 sheet: 0.29 (0.54), residues: 110 loop : -1.27 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 93 PHE 0.000 0.000 PHE A 22 TYR 0.000 0.000 TYR A 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 926.08 seconds wall clock time: 17 minutes 10.82 seconds (1030.82 seconds total)