Starting phenix.real_space_refine on Thu Dec 7 20:59:49 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vab_21135/12_2023/6vab_21135.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vab_21135/12_2023/6vab_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_21135/12_2023/6vab_21135.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vab_21135/12_2023/6vab_21135.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vab_21135/12_2023/6vab_21135.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vab_21135/12_2023/6vab_21135.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 3.31, per 1000 atoms: 0.71 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 - 3.50 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: 2.20 Conformation dependent library (CDL) restraints added in 1.3 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: 0.66 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: 1.49 Time building geometry restraints manager: 2.35 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: 102.46 - 107.72: 63 107.72 - 112.98: 2509 112.98 - 118.24: 964 118.24 - 123.50: 2829 123.50 - 128.76: 87 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 2.520 nonbonded pdb=" O ALA D 513 " pdb=" N GLY D 518 " model vdw 2.382 2.520 nonbonded pdb=" O LYS D 749 " pdb=" N ASP D 753 " model vdw 2.399 2.520 nonbonded pdb=" O ALA B 513 " pdb=" N GLY B 518 " model vdw 2.405 2.520 nonbonded pdb=" O GLU D 752 " pdb=" N ASN D 756 " model vdw 2.476 2.520 ... (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 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: 0.010 Normalize map: mean=0, sd=1: 0.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.160 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 18.600 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.510 ------------------------------------------------------------------------------- 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 : 0.531 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0490 time to fit residues: 2.2096 Evaluate side-chains 16 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.523 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6890 ------------------------------------------------------------------------------- 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: 9.9990 chunk 69 optimal weight: 8.9990 chunk 38 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 47 optimal weight: 50.0000 chunk 37 optimal weight: 5.9990 chunk 72 optimal weight: 20.0000 chunk 27 optimal weight: 20.0000 chunk 43 optimal weight: 9.9990 chunk 53 optimal weight: 20.0000 chunk 83 optimal weight: 20.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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: 0.6813 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4636 Z= 0.254 Angle : 0.575 6.553 6452 Z= 0.385 Chirality : 0.044 0.129 890 Planarity : 0.004 0.017 932 Dihedral : 5.750 23.172 932 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % 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: -2.69 (0.25), residues: 926 helix: -1.61 (0.21), residues: 473 sheet: -0.22 (0.61), residues: 82 loop : -2.26 (0.29), residues: 371 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 : 0.478 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0426 time to fit residues: 1.9824 Evaluate side-chains 16 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.467 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6138 ------------------------------------------------------------------------------- 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: 40.0000 chunk 56 optimal weight: 40.0000 chunk 23 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 90 optimal weight: 0.0570 chunk 74 optimal weight: 5.9990 chunk 82 optimal weight: 0.3980 chunk 28 optimal weight: 10.0000 chunk 67 optimal weight: 0.8980 overall best weight: 2.6702 ------------------------------------------------------------------------------- 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: 0.6754 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 4636 Z= 0.128 Angle : 0.396 3.894 6452 Z= 0.262 Chirality : 0.042 0.132 890 Planarity : 0.002 0.010 932 Dihedral : 4.640 19.282 932 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % 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: -1.45 (0.26), residues: 926 helix: -0.35 (0.22), residues: 500 sheet: -0.26 (0.61), residues: 84 loop : -1.97 (0.31), residues: 342 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 : 0.535 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0455 time to fit residues: 2.1743 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 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7065 ------------------------------------------------------------------------------- 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: 0.9990 chunk 62 optimal weight: 50.0000 chunk 43 optimal weight: 1.9990 chunk 9 optimal weight: 20.0000 chunk 39 optimal weight: 20.0000 chunk 56 optimal weight: 50.0000 chunk 83 optimal weight: 9.9990 chunk 88 optimal weight: 20.0000 chunk 79 optimal weight: 0.4980 chunk 23 optimal weight: 10.0000 chunk 74 optimal weight: 40.0000 overall best weight: 4.6990 ------------------------------------------------------------------------------- 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: 0.6819 moved from start: 0.5270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 4636 Z= 0.188 Angle : 0.451 4.640 6452 Z= 0.303 Chirality : 0.043 0.130 890 Planarity : 0.002 0.012 932 Dihedral : 4.704 15.597 932 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % 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: -0.92 (0.27), residues: 926 helix: -0.01 (0.23), residues: 509 sheet: 0.02 (0.63), residues: 84 loop : -1.62 (0.33), residues: 333 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 : 0.485 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0443 time to fit residues: 2.0817 Evaluate side-chains 16 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.477 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6567 ------------------------------------------------------------------------------- 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: 9.9990 chunk 1 optimal weight: 50.0000 chunk 66 optimal weight: 30.0000 chunk 36 optimal weight: 9.9990 chunk 75 optimal weight: 10.0000 chunk 61 optimal weight: 20.0000 chunk 0 optimal weight: 40.0000 chunk 45 optimal weight: 70.0000 chunk 79 optimal weight: 40.0000 chunk 22 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 overall best weight: 8.9994 ------------------------------------------------------------------------------- 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: 0.6956 moved from start: 0.7135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4636 Z= 0.317 Angle : 0.592 4.846 6452 Z= 0.408 Chirality : 0.043 0.131 890 Planarity : 0.004 0.021 932 Dihedral : 5.799 20.532 932 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % 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: -1.50 (0.27), residues: 926 helix: -0.67 (0.22), residues: 490 sheet: -0.01 (0.60), residues: 94 loop : -1.59 (0.33), residues: 342 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 : 0.518 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0444 time to fit residues: 2.0964 Evaluate side-chains 16 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.529 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6685 ------------------------------------------------------------------------------- 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: 7.9990 chunk 52 optimal weight: 50.0000 chunk 21 optimal weight: 20.0000 chunk 89 optimal weight: 7.9990 chunk 73 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 7 optimal weight: 50.0000 chunk 29 optimal weight: 8.9990 chunk 46 optimal weight: 50.0000 chunk 85 optimal weight: 3.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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: 0.6877 moved from start: 0.7995 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= 0.236 Angle : 0.488 4.138 6452 Z= 0.334 Chirality : 0.042 0.130 890 Planarity : 0.003 0.022 932 Dihedral : 5.218 19.519 932 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % 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: -1.07 (0.27), residues: 926 helix: -0.29 (0.23), residues: 494 sheet: 0.08 (0.60), residues: 94 loop : -1.42 (0.34), residues: 338 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 : 0.541 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0459 time to fit residues: 2.2023 Evaluate side-chains 16 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.525 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5205 ------------------------------------------------------------------------------- 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: 40.0000 chunk 50 optimal weight: 30.0000 chunk 65 optimal weight: 5.9990 chunk 74 optimal weight: 30.0000 chunk 49 optimal weight: 50.0000 chunk 88 optimal weight: 30.0000 chunk 55 optimal weight: 5.9990 chunk 54 optimal weight: 50.0000 chunk 40 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 52 optimal weight: 50.0000 overall best weight: 10.5992 ------------------------------------------------------------------------------- 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: 0.6972 moved from start: 0.8936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 4636 Z= 0.372 Angle : 0.622 5.189 6452 Z= 0.433 Chirality : 0.044 0.139 890 Planarity : 0.004 0.030 932 Dihedral : 5.941 20.444 932 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % 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: -1.58 (0.27), residues: 926 helix: -0.72 (0.22), residues: 491 sheet: -0.10 (0.59), residues: 94 loop : -1.63 (0.33), residues: 341 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 : 0.535 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0461 time to fit residues: 2.2257 Evaluate side-chains 16 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.535 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6916 ------------------------------------------------------------------------------- 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: 9.9990 chunk 17 optimal weight: 6.9990 chunk 56 optimal weight: 40.0000 chunk 60 optimal weight: 40.0000 chunk 43 optimal weight: 8.9990 chunk 8 optimal weight: 40.0000 chunk 69 optimal weight: 40.0000 chunk 80 optimal weight: 40.0000 chunk 84 optimal weight: 20.0000 chunk 77 optimal weight: 8.9990 chunk 82 optimal weight: 7.9990 overall best weight: 8.5990 ------------------------------------------------------------------------------- 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: 0.6917 moved from start: 0.9851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 4636 Z= 0.289 Angle : 0.543 4.782 6452 Z= 0.377 Chirality : 0.043 0.134 890 Planarity : 0.003 0.026 932 Dihedral : 5.733 20.967 932 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % 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: -1.35 (0.27), residues: 926 helix: -0.53 (0.23), residues: 472 sheet: -0.53 (0.51), residues: 114 loop : -1.36 (0.33), residues: 340 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 : 0.542 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0457 time to fit residues: 2.1645 Evaluate side-chains 16 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.545 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7249 ------------------------------------------------------------------------------- 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: 10.0000 chunk 35 optimal weight: 0.0570 chunk 64 optimal weight: 3.9990 chunk 25 optimal weight: 30.0000 chunk 74 optimal weight: 20.0000 chunk 78 optimal weight: 0.0970 chunk 82 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 chunk 87 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 overall best weight: 2.0302 ------------------------------------------------------------------------------- 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: 0.6787 moved from start: 0.9778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 4636 Z= 0.111 Angle : 0.391 3.106 6452 Z= 0.258 Chirality : 0.042 0.133 890 Planarity : 0.002 0.020 932 Dihedral : 4.854 16.941 932 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % 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: -0.36 (0.28), residues: 926 helix: 0.53 (0.23), residues: 489 sheet: -0.25 (0.52), residues: 110 loop : -1.32 (0.35), residues: 327 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 : 0.499 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0435 time to fit residues: 2.0100 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 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6543 ------------------------------------------------------------------------------- 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: 0.0040 chunk 60 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 7 optimal weight: 50.0000 chunk 56 optimal weight: 50.0000 chunk 44 optimal weight: 5.9990 chunk 57 optimal weight: 50.0000 chunk 77 optimal weight: 20.0000 chunk 22 optimal weight: 9.9990 overall best weight: 3.8000 ------------------------------------------------------------------------------- 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: 0.6815 moved from start: 0.9927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 4636 Z= 0.145 Angle : 0.404 3.086 6452 Z= 0.271 Chirality : 0.042 0.131 890 Planarity : 0.002 0.023 932 Dihedral : 4.690 17.264 932 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % 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: -0.01 (0.28), residues: 926 helix: 0.83 (0.24), residues: 489 sheet: -0.18 (0.52), residues: 110 loop : -1.13 (0.35), residues: 327 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 : 0.538 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0450 time to fit residues: 2.1434 Evaluate side-chains 16 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.515 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6780 ------------------------------------------------------------------------------- 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: 10.0000 chunk 10 optimal weight: 40.0000 chunk 20 optimal weight: 8.9990 chunk 73 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 13 optimal weight: 50.0000 chunk 64 optimal weight: 0.9990 chunk 4 optimal weight: 50.0000 chunk 52 optimal weight: 50.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 = 0.4371 r_free = 0.4371 target = 0.129422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.074439 restraints weight = 10663.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.074439 restraints weight = 11935.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.074439 restraints weight = 11935.683| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 moved from start: 1.0405 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= 0.219 Angle : 0.463 3.612 6452 Z= 0.317 Chirality : 0.043 0.134 890 Planarity : 0.003 0.026 932 Dihedral : 4.965 18.719 932 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % 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: -0.31 (0.28), residues: 926 helix: 0.53 (0.24), residues: 484 sheet: -0.24 (0.52), residues: 110 loop : -1.18 (0.34), 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 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 838.01 seconds wall clock time: 15 minutes 47.32 seconds (947.32 seconds total)