Starting phenix.real_space_refine on Sat Nov 16 19:27:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8c_36067/11_2024/8j8c_36067.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8c_36067/11_2024/8j8c_36067.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8c_36067/11_2024/8j8c_36067.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8c_36067/11_2024/8j8c_36067.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8c_36067/11_2024/8j8c_36067.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8c_36067/11_2024/8j8c_36067.cif" } resolution = 2.69 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 7492 2.51 5 N 2004 2.21 5 O 2104 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 11650 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 717, 5825 Classifications: {'peptide': 717} Link IDs: {'PTRANS': 28, 'TRANS': 688} Chain breaks: 3 Chain: "B" Number of atoms: 5825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 717, 5825 Classifications: {'peptide': 717} Link IDs: {'PTRANS': 28, 'TRANS': 688} Chain breaks: 3 Time building chain proxies: 7.40, per 1000 atoms: 0.64 Number of scatterers: 11650 At special positions: 0 Unit cell: (108.73, 107.9, 105.41, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 2104 8.00 N 2004 7.00 C 7492 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: 2.69 Conformation dependent library (CDL) restraints added in 1.6 seconds 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2688 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 16 sheets defined 48.3% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'A' and resid 428 through 431 Processing helix chain 'A' and resid 439 through 451 Processing helix chain 'A' and resid 452 through 456 Processing helix chain 'A' and resid 502 through 513 Processing helix chain 'A' and resid 522 through 527 Processing helix chain 'A' and resid 547 through 560 Processing helix chain 'A' and resid 560 through 566 removed outlier: 3.972A pdb=" N ILE A 564 " --> pdb=" O TRP A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 602 removed outlier: 3.535A pdb=" N PHE A 596 " --> pdb=" O TYR A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.535A pdb=" N HIS A 620 " --> pdb=" O LEU A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 631 removed outlier: 3.629A pdb=" N HIS A 631 " --> pdb=" O SER A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 634 No H-bonds generated for 'chain 'A' and resid 632 through 634' Processing helix chain 'A' and resid 642 through 653 removed outlier: 3.863A pdb=" N LYS A 646 " --> pdb=" O ASP A 642 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLU A 647 " --> pdb=" O ASP A 643 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N HIS A 650 " --> pdb=" O LYS A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 664 removed outlier: 3.921A pdb=" N LYS A 661 " --> pdb=" O SER A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 682 Processing helix chain 'A' and resid 687 through 705 removed outlier: 3.628A pdb=" N THR A 695 " --> pdb=" O LEU A 691 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LYS A 696 " --> pdb=" O GLN A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 729 Processing helix chain 'A' and resid 738 through 749 Processing helix chain 'A' and resid 754 through 767 Processing helix chain 'A' and resid 806 through 814 removed outlier: 3.756A pdb=" N THR A 812 " --> pdb=" O GLU A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 877 Processing helix chain 'A' and resid 882 through 893 removed outlier: 3.941A pdb=" N LYS A 891 " --> pdb=" O HIS A 887 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N HIS A 892 " --> pdb=" O TYR A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 952 Processing helix chain 'A' and resid 953 through 958 Processing helix chain 'A' and resid 982 through 991 removed outlier: 3.983A pdb=" N VAL A 987 " --> pdb=" O LEU A 983 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU A 988 " --> pdb=" O ASN A 984 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU A 989 " --> pdb=" O ARG A 985 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1003 Processing helix chain 'A' and resid 1027 through 1068 removed outlier: 3.692A pdb=" N ILE A1031 " --> pdb=" O SER A1027 " (cutoff:3.500A) Proline residue: A1037 - end of helix Processing helix chain 'A' and resid 1109 through 1119 Processing helix chain 'A' and resid 1137 through 1158 Processing helix chain 'A' and resid 1166 through 1187 Processing helix chain 'B' and resid 428 through 431 Processing helix chain 'B' and resid 439 through 451 Processing helix chain 'B' and resid 452 through 456 Processing helix chain 'B' and resid 502 through 513 Processing helix chain 'B' and resid 522 through 527 Processing helix chain 'B' and resid 547 through 560 Processing helix chain 'B' and resid 560 through 566 removed outlier: 3.973A pdb=" N ILE B 564 " --> pdb=" O TRP B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 602 removed outlier: 3.534A pdb=" N PHE B 596 " --> pdb=" O TYR B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.537A pdb=" N HIS B 620 " --> pdb=" O LEU B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 631 removed outlier: 3.629A pdb=" N HIS B 631 " --> pdb=" O SER B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 634 No H-bonds generated for 'chain 'B' and resid 632 through 634' Processing helix chain 'B' and resid 642 through 653 removed outlier: 3.863A pdb=" N LYS B 646 " --> pdb=" O ASP B 642 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLU B 647 " --> pdb=" O ASP B 643 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS B 650 " --> pdb=" O LYS B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 664 removed outlier: 3.921A pdb=" N LYS B 661 " --> pdb=" O SER B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 682 Processing helix chain 'B' and resid 687 through 705 removed outlier: 3.626A pdb=" N THR B 695 " --> pdb=" O LEU B 691 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LYS B 696 " --> pdb=" O GLN B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 729 Processing helix chain 'B' and resid 738 through 749 Processing helix chain 'B' and resid 754 through 767 Processing helix chain 'B' and resid 806 through 814 removed outlier: 3.756A pdb=" N THR B 812 " --> pdb=" O GLU B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 877 Processing helix chain 'B' and resid 882 through 893 removed outlier: 3.941A pdb=" N LYS B 891 " --> pdb=" O HIS B 887 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N HIS B 892 " --> pdb=" O TYR B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 952 Processing helix chain 'B' and resid 953 through 958 Processing helix chain 'B' and resid 982 through 991 removed outlier: 3.983A pdb=" N VAL B 987 " --> pdb=" O LEU B 983 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU B 988 " --> pdb=" O ASN B 984 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU B 989 " --> pdb=" O ARG B 985 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 997 through 1003 Processing helix chain 'B' and resid 1027 through 1068 removed outlier: 3.692A pdb=" N ILE B1031 " --> pdb=" O SER B1027 " (cutoff:3.500A) Proline residue: B1037 - end of helix Processing helix chain 'B' and resid 1109 through 1119 Processing helix chain 'B' and resid 1137 through 1158 Processing helix chain 'B' and resid 1166 through 1187 Processing sheet with id=AA1, first strand: chain 'A' and resid 418 through 419 removed outlier: 6.103A pdb=" N ILE A 534 " --> pdb=" O LYS A 570 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N LEU A 572 " --> pdb=" O ILE A 534 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ALA A 536 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N VAL A 569 " --> pdb=" O PHE A 639 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ILE A 685 " --> pdb=" O VAL A 636 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N THR A 638 " --> pdb=" O ILE A 685 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 588 through 590 Processing sheet with id=AA3, first strand: chain 'A' and resid 736 through 737 removed outlier: 3.575A pdb=" N ILE A 782 " --> pdb=" O SER A 802 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 824 through 827 removed outlier: 4.464A pdb=" N VAL A 825 " --> pdb=" O ALA A 832 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 849 through 850 Processing sheet with id=AA6, first strand: chain 'A' and resid 909 through 913 Processing sheet with id=AA7, first strand: chain 'A' and resid 922 through 926 removed outlier: 5.852A pdb=" N THR A 922 " --> pdb=" O THR A 935 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU A 975 " --> pdb=" O ILE A 963 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ILE A 963 " --> pdb=" O LEU A 975 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N LYS A 977 " --> pdb=" O GLU A 961 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1014 through 1016 Processing sheet with id=AA9, first strand: chain 'B' and resid 418 through 419 removed outlier: 6.102A pdb=" N ILE B 534 " --> pdb=" O LYS B 570 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU B 572 " --> pdb=" O ILE B 534 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ALA B 536 " --> pdb=" O LEU B 572 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N VAL B 569 " --> pdb=" O PHE B 639 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ILE B 685 " --> pdb=" O VAL B 636 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N THR B 638 " --> pdb=" O ILE B 685 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 588 through 590 Processing sheet with id=AB2, first strand: chain 'B' and resid 736 through 737 removed outlier: 3.575A pdb=" N ILE B 782 " --> pdb=" O SER B 802 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 824 through 827 removed outlier: 4.465A pdb=" N VAL B 825 " --> pdb=" O ALA B 832 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 849 through 850 Processing sheet with id=AB5, first strand: chain 'B' and resid 909 through 913 Processing sheet with id=AB6, first strand: chain 'B' and resid 922 through 926 removed outlier: 5.851A pdb=" N THR B 922 " --> pdb=" O THR B 935 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU B 975 " --> pdb=" O ILE B 963 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ILE B 963 " --> pdb=" O LEU B 975 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N LYS B 977 " --> pdb=" O GLU B 961 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1014 through 1016 528 hydrogen bonds defined for protein. 1500 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: 4.53 Time building geometry restraints manager: 3.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3746 1.34 - 1.46: 2716 1.46 - 1.58: 5384 1.58 - 1.69: 0 1.69 - 1.81: 78 Bond restraints: 11924 Sorted by residual: bond pdb=" C SER A1162 " pdb=" N PRO A1163 " ideal model delta sigma weight residual 1.334 1.354 -0.020 2.34e-02 1.83e+03 7.18e-01 bond pdb=" CB ILE A 801 " pdb=" CG2 ILE A 801 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 7.11e-01 bond pdb=" CB ILE B 801 " pdb=" CG2 ILE B 801 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.83e-01 bond pdb=" C SER B1162 " pdb=" N PRO B1163 " ideal model delta sigma weight residual 1.334 1.353 -0.019 2.34e-02 1.83e+03 6.68e-01 bond pdb=" N ASN B 732 " pdb=" CA ASN B 732 " ideal model delta sigma weight residual 1.457 1.467 -0.010 1.29e-02 6.01e+03 5.91e-01 ... (remaining 11919 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 15966 1.78 - 3.56: 114 3.56 - 5.34: 18 5.34 - 7.12: 0 7.12 - 8.90: 2 Bond angle restraints: 16100 Sorted by residual: angle pdb=" N ILE A 845 " pdb=" CA ILE A 845 " pdb=" C ILE A 845 " ideal model delta sigma weight residual 112.96 109.38 3.58 1.00e+00 1.00e+00 1.28e+01 angle pdb=" N ILE B 845 " pdb=" CA ILE B 845 " pdb=" C ILE B 845 " ideal model delta sigma weight residual 112.96 109.39 3.57 1.00e+00 1.00e+00 1.27e+01 angle pdb=" CA LEU A1159 " pdb=" CB LEU A1159 " pdb=" CG LEU A1159 " ideal model delta sigma weight residual 116.30 125.20 -8.90 3.50e+00 8.16e-02 6.47e+00 angle pdb=" CA LEU B1159 " pdb=" CB LEU B1159 " pdb=" CG LEU B1159 " ideal model delta sigma weight residual 116.30 125.19 -8.89 3.50e+00 8.16e-02 6.45e+00 angle pdb=" N LYS B 991 " pdb=" CA LYS B 991 " pdb=" CB LYS B 991 " ideal model delta sigma weight residual 113.65 109.93 3.72 1.47e+00 4.63e-01 6.40e+00 ... (remaining 16095 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.56: 6589 10.56 - 21.12: 400 21.12 - 31.67: 125 31.67 - 42.23: 20 42.23 - 52.79: 12 Dihedral angle restraints: 7146 sinusoidal: 2952 harmonic: 4194 Sorted by residual: dihedral pdb=" CA SER A 731 " pdb=" C SER A 731 " pdb=" N ASN A 732 " pdb=" CA ASN A 732 " ideal model delta harmonic sigma weight residual 180.00 152.03 27.97 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA SER B 731 " pdb=" C SER B 731 " pdb=" N ASN B 732 " pdb=" CA ASN B 732 " ideal model delta harmonic sigma weight residual 180.00 152.13 27.87 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" CA PRO B 938 " pdb=" C PRO B 938 " pdb=" N LEU B 939 " pdb=" CA LEU B 939 " ideal model delta harmonic sigma weight residual 180.00 -162.01 -17.99 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 7143 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1044 0.026 - 0.051: 396 0.051 - 0.077: 193 0.077 - 0.103: 66 0.103 - 0.128: 43 Chirality restraints: 1742 Sorted by residual: chirality pdb=" CA ILE A 685 " pdb=" N ILE A 685 " pdb=" C ILE A 685 " pdb=" CB ILE A 685 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.12e-01 chirality pdb=" CA ILE B 685 " pdb=" N ILE B 685 " pdb=" C ILE B 685 " pdb=" CB ILE B 685 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.11e-01 chirality pdb=" CA ILE B 707 " pdb=" N ILE B 707 " pdb=" C ILE B 707 " pdb=" CB ILE B 707 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.97e-01 ... (remaining 1739 not shown) Planarity restraints: 2048 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 937 " -0.029 5.00e-02 4.00e+02 4.38e-02 3.07e+00 pdb=" N PRO A 938 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 938 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 938 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 937 " 0.029 5.00e-02 4.00e+02 4.38e-02 3.06e+00 pdb=" N PRO B 938 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 938 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 938 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B1164 " -0.021 5.00e-02 4.00e+02 3.18e-02 1.62e+00 pdb=" N PRO B1165 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO B1165 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B1165 " -0.018 5.00e-02 4.00e+02 ... (remaining 2045 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2468 2.78 - 3.31: 11011 3.31 - 3.84: 18886 3.84 - 4.37: 23500 4.37 - 4.90: 40102 Nonbonded interactions: 95967 Sorted by model distance: nonbonded pdb=" OH TYR B1043 " pdb=" OE1 GLU B1173 " model vdw 2.250 3.040 nonbonded pdb=" OH TYR A1043 " pdb=" OE1 GLU A1173 " model vdw 2.250 3.040 nonbonded pdb=" OG SER B 919 " pdb=" ND2 ASN B1007 " model vdw 2.281 3.120 nonbonded pdb=" OG SER B 787 " pdb=" OD2 ASP B 794 " model vdw 2.285 3.040 nonbonded pdb=" OG SER A 787 " pdb=" OD2 ASP A 794 " model vdw 2.286 3.040 ... (remaining 95962 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 'B' } 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 individual isotropic 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: 7.620 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: 0.480 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 29.670 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 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:15.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 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 : 0.002 0.028 11924 Z= 0.148 Angle : 0.416 8.903 16100 Z= 0.225 Chirality : 0.039 0.128 1742 Planarity : 0.003 0.044 2048 Dihedral : 8.078 52.788 4458 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.48 % Allowed : 2.15 % Favored : 97.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.23), residues: 1418 helix: 1.28 (0.21), residues: 626 sheet: 0.10 (0.42), residues: 178 loop : 0.17 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 856 HIS 0.002 0.000 HIS A1051 PHE 0.008 0.001 PHE A 990 TYR 0.006 0.001 TYR A 837 ARG 0.003 0.000 ARG A 863 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 115 time to evaluate : 1.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 662 ARG cc_start: 0.8168 (mmp-170) cc_final: 0.7890 (mmp-170) REVERT: A 714 MET cc_start: 0.9088 (ptp) cc_final: 0.8862 (ptp) REVERT: A 846 MET cc_start: 0.8910 (mtm) cc_final: 0.8709 (mtp) REVERT: A 1060 MET cc_start: 0.8047 (ttt) cc_final: 0.7617 (tpt) REVERT: A 1148 MET cc_start: 0.8463 (ptp) cc_final: 0.8184 (ptt) REVERT: B 433 MET cc_start: 0.8082 (ptp) cc_final: 0.7811 (ptp) REVERT: B 662 ARG cc_start: 0.8113 (mmp-170) cc_final: 0.7844 (mmp-170) REVERT: B 714 MET cc_start: 0.9055 (ptp) cc_final: 0.8798 (ptp) REVERT: B 846 MET cc_start: 0.8928 (mtm) cc_final: 0.8717 (mtp) REVERT: B 988 GLU cc_start: 0.8633 (tt0) cc_final: 0.8404 (mm-30) REVERT: B 1041 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7856 (mm-30) outliers start: 6 outliers final: 2 residues processed: 121 average time/residue: 1.8786 time to fit residues: 241.8261 Evaluate side-chains 64 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain B residue 549 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 82 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1051 HIS B1007 ASN B1051 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11924 Z= 0.273 Angle : 0.528 9.936 16100 Z= 0.282 Chirality : 0.043 0.142 1742 Planarity : 0.004 0.044 2048 Dihedral : 4.466 52.833 1592 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.91 % Allowed : 5.10 % Favored : 92.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.23), residues: 1418 helix: 1.47 (0.21), residues: 640 sheet: -0.09 (0.41), residues: 186 loop : 0.10 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B1189 HIS 0.005 0.001 HIS B1051 PHE 0.015 0.001 PHE B 990 TYR 0.013 0.001 TYR A 555 ARG 0.005 0.000 ARG A 929 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 68 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 658 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7437 (tm-30) REVERT: A 1060 MET cc_start: 0.7831 (ttt) cc_final: 0.7409 (tpt) REVERT: B 988 GLU cc_start: 0.8675 (tt0) cc_final: 0.8409 (mm-30) REVERT: B 1147 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8387 (mtmm) outliers start: 24 outliers final: 5 residues processed: 84 average time/residue: 1.1594 time to fit residues: 105.0835 Evaluate side-chains 63 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 1147 LYS Chi-restraints excluded: chain B residue 1151 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 71 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 139 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- 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: 0.8423 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11924 Z= 0.234 Angle : 0.499 10.014 16100 Z= 0.264 Chirality : 0.042 0.139 1742 Planarity : 0.003 0.044 2048 Dihedral : 4.529 52.725 1592 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.91 % Allowed : 5.89 % Favored : 92.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.23), residues: 1418 helix: 1.49 (0.21), residues: 640 sheet: -0.29 (0.39), residues: 192 loop : 0.01 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1189 HIS 0.003 0.001 HIS A1051 PHE 0.013 0.001 PHE A 990 TYR 0.013 0.001 TYR A1122 ARG 0.007 0.000 ARG B 929 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 58 time to evaluate : 1.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 524 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8492 (pp20) REVERT: A 658 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7405 (tm-30) REVERT: A 735 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8314 (mt-10) REVERT: A 1060 MET cc_start: 0.7848 (ttt) cc_final: 0.7407 (tpt) REVERT: B 524 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8511 (pp20) REVERT: B 1103 ILE cc_start: 0.7370 (pp) cc_final: 0.7106 (pp) REVERT: B 1147 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8433 (mtmm) outliers start: 24 outliers final: 6 residues processed: 75 average time/residue: 1.6272 time to fit residues: 131.4257 Evaluate side-chains 66 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 735 GLU Chi-restraints excluded: chain B residue 1147 LYS Chi-restraints excluded: chain B residue 1151 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 127 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 67 optimal weight: 7.9990 chunk 14 optimal weight: 0.4980 chunk 61 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 36 optimal weight: 0.0770 chunk 114 optimal weight: 0.0470 overall best weight: 0.7038 ------------------------------------------------------------------------------- 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: 0.8414 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11924 Z= 0.193 Angle : 0.485 10.222 16100 Z= 0.253 Chirality : 0.041 0.137 1742 Planarity : 0.003 0.046 2048 Dihedral : 4.449 52.401 1592 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.67 % Allowed : 6.61 % Favored : 91.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.23), residues: 1418 helix: 1.50 (0.21), residues: 644 sheet: -0.41 (0.39), residues: 192 loop : -0.04 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1189 HIS 0.003 0.001 HIS B1051 PHE 0.013 0.001 PHE B 990 TYR 0.012 0.001 TYR A 920 ARG 0.007 0.000 ARG A 929 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 63 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 524 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8491 (pp20) REVERT: A 606 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.9069 (mm) REVERT: A 735 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8255 (mt-10) REVERT: A 1060 MET cc_start: 0.7869 (ttt) cc_final: 0.7409 (tpt) REVERT: B 658 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7769 (tm-30) REVERT: B 659 LEU cc_start: 0.8378 (mm) cc_final: 0.8032 (mt) REVERT: B 1103 ILE cc_start: 0.7433 (OUTLIER) cc_final: 0.7172 (pp) REVERT: B 1147 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8424 (mtmm) outliers start: 21 outliers final: 5 residues processed: 79 average time/residue: 1.6107 time to fit residues: 137.2182 Evaluate side-chains 68 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 658 GLU Chi-restraints excluded: chain B residue 1103 ILE Chi-restraints excluded: chain B residue 1147 LYS Chi-restraints excluded: chain B residue 1151 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 77 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 117 optimal weight: 0.0060 chunk 94 optimal weight: 0.0870 chunk 0 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 overall best weight: 0.5374 ------------------------------------------------------------------------------- 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: 0.8404 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11924 Z= 0.166 Angle : 0.476 10.529 16100 Z= 0.247 Chirality : 0.041 0.134 1742 Planarity : 0.003 0.046 2048 Dihedral : 4.353 52.185 1592 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.91 % Allowed : 7.25 % Favored : 90.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.23), residues: 1418 helix: 1.54 (0.21), residues: 644 sheet: -0.43 (0.39), residues: 192 loop : -0.06 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1189 HIS 0.003 0.001 HIS A1051 PHE 0.013 0.001 PHE B 990 TYR 0.012 0.001 TYR B1122 ARG 0.008 0.000 ARG B 929 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 61 time to evaluate : 1.555 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 524 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8504 (pp20) REVERT: A 606 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.9067 (mm) REVERT: A 735 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8220 (mt-10) REVERT: A 1060 MET cc_start: 0.7881 (ttt) cc_final: 0.7343 (tpt) REVERT: B 524 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8534 (pp20) REVERT: B 659 LEU cc_start: 0.8377 (mm) cc_final: 0.8147 (mt) REVERT: B 1103 ILE cc_start: 0.7432 (OUTLIER) cc_final: 0.7198 (pp) REVERT: B 1147 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8411 (mtmm) outliers start: 24 outliers final: 6 residues processed: 79 average time/residue: 1.5747 time to fit residues: 134.4654 Evaluate side-chains 66 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 1103 ILE Chi-restraints excluded: chain B residue 1122 TYR Chi-restraints excluded: chain B residue 1147 LYS Chi-restraints excluded: chain B residue 1151 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 123 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 137 optimal weight: 0.7980 chunk 114 optimal weight: 0.0050 chunk 63 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- 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: 0.8409 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11924 Z= 0.185 Angle : 0.482 10.703 16100 Z= 0.249 Chirality : 0.041 0.145 1742 Planarity : 0.003 0.046 2048 Dihedral : 4.399 51.994 1592 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.51 % Allowed : 7.88 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.87 (0.23), residues: 1418 helix: 1.55 (0.21), residues: 644 sheet: -0.45 (0.39), residues: 192 loop : -0.05 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1189 HIS 0.003 0.001 HIS B1051 PHE 0.013 0.001 PHE B 990 TYR 0.013 0.001 TYR B1122 ARG 0.010 0.000 ARG B 929 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 58 time to evaluate : 1.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 524 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8504 (pp20) REVERT: A 606 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9080 (mm) REVERT: A 658 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7612 (tm-30) REVERT: A 659 LEU cc_start: 0.8368 (mm) cc_final: 0.7966 (mt) REVERT: A 735 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8218 (mt-10) REVERT: A 1060 MET cc_start: 0.7870 (ttt) cc_final: 0.7340 (tpt) REVERT: B 524 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8515 (pp20) REVERT: B 659 LEU cc_start: 0.8384 (mm) cc_final: 0.8104 (mt) REVERT: B 1048 MET cc_start: 0.8074 (mtp) cc_final: 0.7642 (mtm) REVERT: B 1103 ILE cc_start: 0.7460 (OUTLIER) cc_final: 0.7219 (pp) REVERT: B 1147 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8382 (mtmm) outliers start: 19 outliers final: 5 residues processed: 73 average time/residue: 1.6528 time to fit residues: 129.9055 Evaluate side-chains 68 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 1103 ILE Chi-restraints excluded: chain B residue 1147 LYS Chi-restraints excluded: chain B residue 1151 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 15 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 100 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 136 optimal weight: 8.9990 chunk 85 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 chunk 63 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11924 Z= 0.206 Angle : 0.499 10.890 16100 Z= 0.257 Chirality : 0.042 0.146 1742 Planarity : 0.004 0.047 2048 Dihedral : 4.419 51.982 1592 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.51 % Allowed : 8.60 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.23), residues: 1418 helix: 1.56 (0.21), residues: 644 sheet: -0.61 (0.39), residues: 196 loop : -0.01 (0.27), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1189 HIS 0.003 0.001 HIS B1051 PHE 0.013 0.001 PHE B 990 TYR 0.011 0.001 TYR A 920 ARG 0.009 0.000 ARG B 929 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 56 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 524 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8503 (pp20) REVERT: A 606 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9076 (mm) REVERT: A 658 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7648 (tm-30) REVERT: A 659 LEU cc_start: 0.8368 (mm) cc_final: 0.8019 (mt) REVERT: A 735 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8212 (mt-10) REVERT: A 1048 MET cc_start: 0.8017 (mtm) cc_final: 0.7191 (mtm) REVERT: A 1060 MET cc_start: 0.7855 (ttt) cc_final: 0.7356 (tpt) REVERT: B 524 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8525 (pp20) REVERT: B 1103 ILE cc_start: 0.7486 (OUTLIER) cc_final: 0.7236 (pp) REVERT: B 1147 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8394 (mtmm) outliers start: 19 outliers final: 6 residues processed: 71 average time/residue: 1.6459 time to fit residues: 125.9482 Evaluate side-chains 68 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 960 ILE Chi-restraints excluded: chain B residue 1103 ILE Chi-restraints excluded: chain B residue 1147 LYS Chi-restraints excluded: chain B residue 1151 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 54 optimal weight: 0.8980 chunk 81 optimal weight: 0.0770 chunk 41 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 87 optimal weight: 0.2980 chunk 93 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 124 optimal weight: 0.0670 chunk 131 optimal weight: 1.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 887 HIS A1099 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11924 Z= 0.185 Angle : 0.493 11.026 16100 Z= 0.253 Chirality : 0.041 0.134 1742 Planarity : 0.004 0.047 2048 Dihedral : 4.388 51.873 1592 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.67 % Allowed : 8.04 % Favored : 90.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.87 (0.23), residues: 1418 helix: 1.57 (0.21), residues: 644 sheet: -0.60 (0.39), residues: 196 loop : -0.01 (0.27), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1189 HIS 0.006 0.001 HIS A1099 PHE 0.013 0.001 PHE B 990 TYR 0.011 0.001 TYR A 920 ARG 0.010 0.000 ARG B 929 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 57 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 524 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8501 (pp20) REVERT: A 606 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.9064 (mm) REVERT: A 658 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7641 (tm-30) REVERT: A 659 LEU cc_start: 0.8311 (mm) cc_final: 0.8088 (mt) REVERT: A 1042 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.9004 (tt) REVERT: A 1060 MET cc_start: 0.7893 (ttt) cc_final: 0.7353 (tpt) REVERT: B 524 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8519 (pp20) REVERT: B 607 VAL cc_start: 0.9376 (OUTLIER) cc_final: 0.9162 (m) REVERT: B 692 GLN cc_start: 0.8365 (mm-40) cc_final: 0.7934 (pt0) REVERT: B 1103 ILE cc_start: 0.7491 (OUTLIER) cc_final: 0.7250 (pp) REVERT: B 1147 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8388 (mtmm) outliers start: 21 outliers final: 8 residues processed: 72 average time/residue: 1.6261 time to fit residues: 126.5278 Evaluate side-chains 74 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 803 VAL Chi-restraints excluded: chain A residue 960 ILE Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 803 VAL Chi-restraints excluded: chain B residue 960 ILE Chi-restraints excluded: chain B residue 1103 ILE Chi-restraints excluded: chain B residue 1147 LYS Chi-restraints excluded: chain B residue 1151 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 0.7980 chunk 127 optimal weight: 0.0270 chunk 131 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 100 optimal weight: 0.0470 chunk 39 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 120 optimal weight: 0.4980 chunk 83 optimal weight: 2.9990 chunk 134 optimal weight: 7.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 887 HIS A1099 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11924 Z= 0.155 Angle : 0.497 11.291 16100 Z= 0.251 Chirality : 0.041 0.139 1742 Planarity : 0.003 0.047 2048 Dihedral : 4.298 51.775 1592 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.51 % Allowed : 8.44 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.23), residues: 1418 helix: 1.63 (0.21), residues: 642 sheet: -0.56 (0.39), residues: 196 loop : -0.01 (0.27), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1189 HIS 0.010 0.001 HIS A1099 PHE 0.013 0.001 PHE A 990 TYR 0.020 0.001 TYR A1122 ARG 0.010 0.000 ARG B 929 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 65 time to evaluate : 1.790 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 606 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.9044 (mm) REVERT: A 607 VAL cc_start: 0.9382 (OUTLIER) cc_final: 0.9170 (m) REVERT: A 658 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7555 (tm-30) REVERT: A 659 LEU cc_start: 0.8298 (mm) cc_final: 0.8092 (mt) REVERT: A 692 GLN cc_start: 0.8350 (mm-40) cc_final: 0.7944 (pt0) REVERT: A 1042 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8965 (tt) REVERT: A 1060 MET cc_start: 0.7867 (ttt) cc_final: 0.7343 (tpt) REVERT: B 524 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8524 (pp20) REVERT: B 607 VAL cc_start: 0.9360 (OUTLIER) cc_final: 0.9151 (m) REVERT: B 692 GLN cc_start: 0.8341 (mm-40) cc_final: 0.7921 (pt0) REVERT: B 1103 ILE cc_start: 0.7500 (OUTLIER) cc_final: 0.7267 (pp) REVERT: B 1147 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8370 (mtmm) outliers start: 19 outliers final: 7 residues processed: 79 average time/residue: 1.5614 time to fit residues: 133.1112 Evaluate side-chains 76 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 803 VAL Chi-restraints excluded: chain A residue 960 ILE Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 803 VAL Chi-restraints excluded: chain B residue 960 ILE Chi-restraints excluded: chain B residue 1103 ILE Chi-restraints excluded: chain B residue 1147 LYS Chi-restraints excluded: chain B residue 1151 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 82 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 93 optimal weight: 0.9980 chunk 141 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 112 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 89 optimal weight: 0.6980 chunk 120 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1099 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11924 Z= 0.230 Angle : 0.530 11.196 16100 Z= 0.270 Chirality : 0.042 0.137 1742 Planarity : 0.004 0.047 2048 Dihedral : 4.461 51.854 1592 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.35 % Allowed : 8.92 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.23), residues: 1418 helix: 1.56 (0.21), residues: 644 sheet: -0.63 (0.39), residues: 196 loop : -0.01 (0.27), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1189 HIS 0.011 0.001 HIS A1099 PHE 0.013 0.001 PHE B 990 TYR 0.011 0.001 TYR B 555 ARG 0.010 0.000 ARG A 929 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 1.246 Fit side-chains revert: symmetry clash REVERT: A 606 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.9057 (mm) REVERT: A 607 VAL cc_start: 0.9388 (OUTLIER) cc_final: 0.9183 (m) REVERT: A 658 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7649 (tm-30) REVERT: A 659 LEU cc_start: 0.8356 (mm) cc_final: 0.7975 (mm) REVERT: A 662 ARG cc_start: 0.7521 (ttp-110) cc_final: 0.7284 (ttp80) REVERT: A 734 ARG cc_start: 0.6903 (ptp90) cc_final: 0.6407 (pmt170) REVERT: A 1060 MET cc_start: 0.7843 (ttt) cc_final: 0.7337 (tpt) REVERT: B 524 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8504 (pp20) REVERT: B 607 VAL cc_start: 0.9387 (OUTLIER) cc_final: 0.9183 (m) REVERT: B 662 ARG cc_start: 0.7590 (ttp-110) cc_final: 0.7253 (ptm-80) REVERT: B 692 GLN cc_start: 0.8365 (mm-40) cc_final: 0.7962 (pt0) REVERT: B 1103 ILE cc_start: 0.7497 (OUTLIER) cc_final: 0.7266 (pp) REVERT: B 1147 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8375 (mtmm) outliers start: 17 outliers final: 8 residues processed: 70 average time/residue: 1.5559 time to fit residues: 118.2672 Evaluate side-chains 73 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 803 VAL Chi-restraints excluded: chain A residue 960 ILE Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 803 VAL Chi-restraints excluded: chain B residue 960 ILE Chi-restraints excluded: chain B residue 1103 ILE Chi-restraints excluded: chain B residue 1147 LYS Chi-restraints excluded: chain B residue 1151 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 34 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 112 optimal weight: 0.2980 chunk 47 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 6 optimal weight: 8.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 887 HIS B1099 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.086359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.064383 restraints weight = 23317.108| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 3.09 r_work: 0.2803 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11924 Z= 0.189 Angle : 0.519 11.415 16100 Z= 0.262 Chirality : 0.042 0.160 1742 Planarity : 0.004 0.047 2048 Dihedral : 4.393 51.822 1592 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.51 % Allowed : 8.68 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.23), residues: 1418 helix: 1.58 (0.21), residues: 644 sheet: -0.61 (0.39), residues: 196 loop : 0.00 (0.27), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1189 HIS 0.003 0.001 HIS A1051 PHE 0.013 0.001 PHE A 990 TYR 0.011 0.001 TYR A 920 ARG 0.010 0.000 ARG A 929 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3451.59 seconds wall clock time: 68 minutes 11.83 seconds (4091.83 seconds total)