Starting phenix.real_space_refine on Fri Mar 15 16:31:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9y_36119/03_2024/8j9y_36119.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9y_36119/03_2024/8j9y_36119.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9y_36119/03_2024/8j9y_36119.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9y_36119/03_2024/8j9y_36119.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9y_36119/03_2024/8j9y_36119.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9y_36119/03_2024/8j9y_36119.pdb" } resolution = 3.16 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= 0.045 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 7818 2.51 5 N 2086 2.21 5 O 2200 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 543": "OD1" <-> "OD2" Residue "B TYR 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 663": "OE1" <-> "OE2" Residue "B PHE 710": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 817": "OE1" <-> "OE2" Residue "B TYR 916": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 936": "OE1" <-> "OE2" Residue "B GLU 961": "OE1" <-> "OE2" Residue "B GLU 962": "OE1" <-> "OE2" Residue "B TYR 966": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 990": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 995": "OE1" <-> "OE2" Residue "B PHE 1015": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1024": "OE1" <-> "OE2" Residue "B TYR 1029": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1038": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1061": "OE1" <-> "OE2" Residue "B PHE 1094": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1132": "OE1" <-> "OE2" Residue "A ASP 543": "OD1" <-> "OD2" Residue "A TYR 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 663": "OE1" <-> "OE2" Residue "A PHE 710": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 817": "OE1" <-> "OE2" Residue "A TYR 916": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 936": "OE1" <-> "OE2" Residue "A GLU 961": "OE1" <-> "OE2" Residue "A GLU 962": "OE1" <-> "OE2" Residue "A TYR 966": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 990": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 995": "OE1" <-> "OE2" Residue "A PHE 1015": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1024": "OE1" <-> "OE2" Residue "A TYR 1029": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1038": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1061": "OE1" <-> "OE2" Residue "A PHE 1094": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1132": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12154 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 6077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 6077 Classifications: {'peptide': 747} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 716} Chain breaks: 1 Chain: "A" Number of atoms: 6077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 6077 Classifications: {'peptide': 747} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 716} Chain breaks: 1 Time building chain proxies: 6.20, per 1000 atoms: 0.51 Number of scatterers: 12154 At special positions: 0 Unit cell: (114.95, 109.25, 111.15, 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 2200 8.00 N 2086 7.00 C 7818 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: 4.61 Conformation dependent library (CDL) restraints added in 2.3 seconds 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2812 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 16 sheets defined 53.7% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'B' and resid 428 through 432 Processing helix chain 'B' and resid 439 through 451 Processing helix chain 'B' and resid 503 through 513 Processing helix chain 'B' and resid 522 through 527 Processing helix chain 'B' and resid 541 through 546 Processing helix chain 'B' and resid 547 through 560 Processing helix chain 'B' and resid 560 through 567 removed outlier: 3.879A pdb=" N ILE B 564 " --> pdb=" O TRP B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 602 removed outlier: 3.721A pdb=" N LYS B 602 " --> pdb=" O ALA B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.705A pdb=" N HIS B 620 " --> pdb=" O LEU B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 631 removed outlier: 3.541A pdb=" N HIS B 631 " --> pdb=" O SER B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 635 Processing helix chain 'B' and resid 642 through 654 removed outlier: 4.062A pdb=" N LYS B 646 " --> pdb=" O ASP B 642 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLU B 647 " --> pdb=" O ASP B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 664 Processing helix chain 'B' and resid 672 through 683 Processing helix chain 'B' and resid 687 through 707 removed outlier: 3.748A pdb=" N THR B 695 " --> pdb=" O LEU B 691 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LYS B 696 " --> pdb=" O GLN B 692 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN B 706 " --> pdb=" O ALA B 702 " (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 766 Processing helix chain 'B' and resid 806 through 814 removed outlier: 3.951A pdb=" N THR B 812 " --> pdb=" O GLU B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 877 Processing helix chain 'B' and resid 882 through 893 Processing helix chain 'B' and resid 942 through 953 removed outlier: 3.586A pdb=" N SER B 953 " --> pdb=" O SER B 949 " (cutoff:3.500A) Processing helix chain 'B' and resid 953 through 958 Processing helix chain 'B' and resid 982 through 990 Processing helix chain 'B' and resid 997 through 1004 Processing helix chain 'B' and resid 1027 through 1075 removed outlier: 3.571A pdb=" N ILE B1031 " --> pdb=" O THR B1027 " (cutoff:3.500A) Proline residue: B1037 - end of helix removed outlier: 3.513A pdb=" N LEU B1042 " --> pdb=" O TYR B1038 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR B1043 " --> pdb=" O ARG B1039 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLN B1044 " --> pdb=" O ARG B1040 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS B1045 " --> pdb=" O GLU B1041 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ALA B1072 " --> pdb=" O ILE B1068 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N GLU B1073 " --> pdb=" O ASN B1069 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1079 Processing helix chain 'B' and resid 1081 through 1092 Processing helix chain 'B' and resid 1098 through 1104 Processing helix chain 'B' and resid 1109 through 1117 Processing helix chain 'B' and resid 1122 through 1127 Processing helix chain 'B' and resid 1129 through 1133 Processing helix chain 'B' and resid 1134 through 1160 Processing helix chain 'B' and resid 1166 through 1187 Processing helix chain 'A' and resid 428 through 432 Processing helix chain 'A' and resid 439 through 451 Processing helix chain 'A' and resid 503 through 513 Processing helix chain 'A' and resid 522 through 527 Processing helix chain 'A' and resid 541 through 546 Processing helix chain 'A' and resid 547 through 560 Processing helix chain 'A' and resid 560 through 567 removed outlier: 3.878A pdb=" N ILE A 564 " --> pdb=" O TRP A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 602 removed outlier: 3.721A pdb=" N LYS A 602 " --> pdb=" O ALA A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.705A pdb=" N HIS A 620 " --> pdb=" O LEU A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 631 removed outlier: 3.540A pdb=" N HIS A 631 " --> pdb=" O SER A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 635 Processing helix chain 'A' and resid 642 through 654 removed outlier: 4.062A pdb=" N LYS A 646 " --> pdb=" O ASP A 642 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLU A 647 " --> pdb=" O ASP A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 664 Processing helix chain 'A' and resid 672 through 683 Processing helix chain 'A' and resid 687 through 707 removed outlier: 3.748A pdb=" N THR A 695 " --> pdb=" O LEU A 691 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LYS A 696 " --> pdb=" O GLN A 692 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN A 706 " --> pdb=" O ALA A 702 " (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 766 Processing helix chain 'A' and resid 806 through 814 removed outlier: 3.950A pdb=" N THR A 812 " --> pdb=" O GLU A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 877 Processing helix chain 'A' and resid 882 through 893 Processing helix chain 'A' and resid 942 through 953 removed outlier: 3.585A pdb=" N SER A 953 " --> pdb=" O SER A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 958 Processing helix chain 'A' and resid 982 through 990 Processing helix chain 'A' and resid 997 through 1004 Processing helix chain 'A' and resid 1027 through 1075 removed outlier: 3.570A pdb=" N ILE A1031 " --> pdb=" O THR A1027 " (cutoff:3.500A) Proline residue: A1037 - end of helix removed outlier: 3.512A pdb=" N LEU A1042 " --> pdb=" O TYR A1038 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR A1043 " --> pdb=" O ARG A1039 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLN A1044 " --> pdb=" O ARG A1040 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS A1045 " --> pdb=" O GLU A1041 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N ALA A1072 " --> pdb=" O ILE A1068 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N GLU A1073 " --> pdb=" O ASN A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1079 Processing helix chain 'A' and resid 1081 through 1092 Processing helix chain 'A' and resid 1098 through 1104 Processing helix chain 'A' and resid 1109 through 1117 Processing helix chain 'A' and resid 1122 through 1127 Processing helix chain 'A' and resid 1129 through 1133 Processing helix chain 'A' and resid 1134 through 1160 Processing helix chain 'A' and resid 1166 through 1187 Processing sheet with id=AA1, first strand: chain 'B' and resid 418 through 419 removed outlier: 6.358A pdb=" N LEU B 434 " --> pdb=" O VAL B 535 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N CYS B 537 " --> pdb=" O LEU B 434 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ALA B 436 " --> pdb=" O CYS B 537 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ILE B 534 " --> pdb=" O LYS B 570 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N LEU B 572 " --> pdb=" O ILE B 534 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ALA B 536 " --> pdb=" O LEU B 572 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N VAL B 569 " --> pdb=" O PHE B 639 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 588 through 590 Processing sheet with id=AA3, first strand: chain 'B' and resid 736 through 737 Processing sheet with id=AA4, first strand: chain 'B' and resid 824 through 827 removed outlier: 4.181A pdb=" N VAL B 825 " --> pdb=" O ALA B 832 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 849 through 852 Processing sheet with id=AA6, first strand: chain 'B' and resid 910 through 913 Processing sheet with id=AA7, first strand: chain 'B' and resid 922 through 926 removed outlier: 6.250A pdb=" N THR B 922 " --> pdb=" O THR B 935 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LEU B 975 " --> pdb=" O ILE B 963 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ILE B 963 " --> pdb=" O LEU B 975 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LYS B 977 " --> pdb=" O GLU B 961 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1013 through 1016 removed outlier: 4.320A pdb=" N LEU B1013 " --> pdb=" O PHE B1025 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 418 through 419 removed outlier: 6.358A pdb=" N LEU A 434 " --> pdb=" O VAL A 535 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N CYS A 537 " --> pdb=" O LEU A 434 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ALA A 436 " --> pdb=" O CYS A 537 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ILE A 534 " --> pdb=" O LYS A 570 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N LEU A 572 " --> pdb=" O ILE A 534 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ALA A 536 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N VAL A 569 " --> pdb=" O PHE A 639 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 588 through 590 Processing sheet with id=AB2, first strand: chain 'A' and resid 736 through 737 Processing sheet with id=AB3, first strand: chain 'A' and resid 824 through 827 removed outlier: 4.181A pdb=" N VAL A 825 " --> pdb=" O ALA A 832 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 849 through 852 Processing sheet with id=AB5, first strand: chain 'A' and resid 910 through 913 Processing sheet with id=AB6, first strand: chain 'A' and resid 922 through 926 removed outlier: 6.251A pdb=" N THR A 922 " --> pdb=" O THR A 935 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LEU A 975 " --> pdb=" O ILE A 963 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ILE A 963 " --> pdb=" O LEU A 975 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LYS A 977 " --> pdb=" O GLU A 961 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1013 through 1016 removed outlier: 4.321A pdb=" N LEU A1013 " --> pdb=" O PHE A1025 " (cutoff:3.500A) 598 hydrogen bonds defined for protein. 1704 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: 3.53 Time building geometry restraints manager: 4.94 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: 3910 1.34 - 1.46: 2690 1.46 - 1.58: 5768 1.58 - 1.69: 0 1.69 - 1.81: 78 Bond restraints: 12446 Sorted by residual: bond pdb=" CB PRO A 881 " pdb=" CG PRO A 881 " ideal model delta sigma weight residual 1.492 1.557 -0.065 5.00e-02 4.00e+02 1.68e+00 bond pdb=" CB PRO B 881 " pdb=" CG PRO B 881 " ideal model delta sigma weight residual 1.492 1.557 -0.065 5.00e-02 4.00e+02 1.68e+00 bond pdb=" C ILE B 896 " pdb=" N LEU B 897 " ideal model delta sigma weight residual 1.331 1.354 -0.023 2.07e-02 2.33e+03 1.20e+00 bond pdb=" C ILE A 896 " pdb=" N LEU A 897 " ideal model delta sigma weight residual 1.331 1.353 -0.022 2.07e-02 2.33e+03 1.17e+00 bond pdb=" N LYS A 882 " pdb=" CA LYS A 882 " ideal model delta sigma weight residual 1.457 1.469 -0.012 1.29e-02 6.01e+03 8.52e-01 ... (remaining 12441 not shown) Histogram of bond angle deviations from ideal: 99.93 - 106.74: 322 106.74 - 113.55: 6631 113.55 - 120.35: 4644 120.35 - 127.16: 5087 127.16 - 133.97: 132 Bond angle restraints: 16816 Sorted by residual: angle pdb=" N ASN B 930 " pdb=" CA ASN B 930 " pdb=" C ASN B 930 " ideal model delta sigma weight residual 111.02 107.36 3.66 1.25e+00 6.40e-01 8.59e+00 angle pdb=" N ASN A 930 " pdb=" CA ASN A 930 " pdb=" C ASN A 930 " ideal model delta sigma weight residual 111.02 107.39 3.63 1.25e+00 6.40e-01 8.41e+00 angle pdb=" C HIS A 631 " pdb=" N PHE A 632 " pdb=" CA PHE A 632 " ideal model delta sigma weight residual 120.82 124.91 -4.09 1.50e+00 4.44e-01 7.42e+00 angle pdb=" C SER A 455 " pdb=" N ASN A 456 " pdb=" CA ASN A 456 " ideal model delta sigma weight residual 121.80 126.86 -5.06 2.44e+00 1.68e-01 4.31e+00 angle pdb=" CA LEU A 452 " pdb=" CB LEU A 452 " pdb=" CG LEU A 452 " ideal model delta sigma weight residual 116.30 123.54 -7.24 3.50e+00 8.16e-02 4.28e+00 ... (remaining 16811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.96: 6496 16.96 - 33.91: 738 33.91 - 50.87: 210 50.87 - 67.82: 24 67.82 - 84.78: 6 Dihedral angle restraints: 7474 sinusoidal: 3088 harmonic: 4386 Sorted by residual: dihedral pdb=" CG ARG A 873 " pdb=" CD ARG A 873 " pdb=" NE ARG A 873 " pdb=" CZ ARG A 873 " ideal model delta sinusoidal sigma weight residual 180.00 137.17 42.83 2 1.50e+01 4.44e-03 9.86e+00 dihedral pdb=" CG ARG B 873 " pdb=" CD ARG B 873 " pdb=" NE ARG B 873 " pdb=" CZ ARG B 873 " ideal model delta sinusoidal sigma weight residual 180.00 137.18 42.82 2 1.50e+01 4.44e-03 9.86e+00 dihedral pdb=" CA GLY A 453 " pdb=" C GLY A 453 " pdb=" N LYS A 454 " pdb=" CA LYS A 454 " ideal model delta harmonic sigma weight residual 180.00 164.39 15.61 0 5.00e+00 4.00e-02 9.75e+00 ... (remaining 7471 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1066 0.025 - 0.049: 432 0.049 - 0.074: 212 0.074 - 0.099: 57 0.099 - 0.124: 53 Chirality restraints: 1820 Sorted by residual: 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 -0.12 2.00e-01 2.50e+01 3.82e-01 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 -0.12 2.00e-01 2.50e+01 3.76e-01 chirality pdb=" CA ILE B 963 " pdb=" N ILE B 963 " pdb=" C ILE B 963 " pdb=" CB ILE B 963 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.42e-01 ... (remaining 1817 not shown) Planarity restraints: 2142 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 880 " -0.051 5.00e-02 4.00e+02 7.64e-02 9.34e+00 pdb=" N PRO A 881 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 881 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 881 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 880 " 0.051 5.00e-02 4.00e+02 7.62e-02 9.28e+00 pdb=" N PRO B 881 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO B 881 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 881 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 930 " -0.008 2.00e-02 2.50e+03 1.59e-02 2.53e+00 pdb=" C ASN B 930 " 0.028 2.00e-02 2.50e+03 pdb=" O ASN B 930 " -0.010 2.00e-02 2.50e+03 pdb=" N ILE B 931 " -0.009 2.00e-02 2.50e+03 ... (remaining 2139 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 254 2.71 - 3.26: 11750 3.26 - 3.81: 19267 3.81 - 4.35: 24778 4.35 - 4.90: 42209 Nonbonded interactions: 98258 Sorted by model distance: nonbonded pdb=" O LYS A 979 " pdb=" OG SER A 982 " model vdw 2.167 2.440 nonbonded pdb=" O LYS B 979 " pdb=" OG SER B 982 " model vdw 2.169 2.440 nonbonded pdb=" O VAL B 838 " pdb=" NH2 ARG B1039 " model vdw 2.205 2.520 nonbonded pdb=" O VAL A 838 " pdb=" NH2 ARG A1039 " model vdw 2.205 2.520 nonbonded pdb=" OD1 ASP A 997 " pdb=" N SER A 998 " model vdw 2.226 2.520 ... (remaining 98253 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 '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: 0.000 Normalize map: mean=0, sd=1: 1.660 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: 6.390 Check model and map are aligned: 0.180 Set scattering table: 0.100 Process input model: 33.670 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 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 0.065 12446 Z= 0.149 Angle : 0.498 7.241 16816 Z= 0.275 Chirality : 0.037 0.124 1820 Planarity : 0.004 0.076 2142 Dihedral : 15.113 84.780 4662 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.76 % Allowed : 11.91 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.63 (0.22), residues: 1486 helix: 1.47 (0.19), residues: 680 sheet: -0.64 (0.38), residues: 212 loop : -0.31 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B1189 HIS 0.005 0.001 HIS A 650 PHE 0.007 0.001 PHE B 629 TYR 0.008 0.001 TYR A1079 ARG 0.007 0.000 ARG A1004 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 142 time to evaluate : 1.537 Fit side-chains REVERT: B 663 GLU cc_start: 0.6940 (tp30) cc_final: 0.6522 (tp30) REVERT: A 663 GLU cc_start: 0.6923 (tp30) cc_final: 0.6504 (tp30) outliers start: 10 outliers final: 2 residues processed: 146 average time/residue: 0.2707 time to fit residues: 55.8986 Evaluate side-chains 135 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 133 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain A residue 982 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 38 optimal weight: 0.0980 chunk 75 optimal weight: 8.9990 chunk 59 optimal weight: 0.8980 chunk 116 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 70 optimal weight: 6.9990 chunk 86 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 887 HIS B 892 HIS A 887 HIS A 892 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12446 Z= 0.222 Angle : 0.496 8.070 16816 Z= 0.255 Chirality : 0.040 0.141 1820 Planarity : 0.004 0.053 2142 Dihedral : 3.608 14.896 1664 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.22 % Allowed : 12.67 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 (0.22), residues: 1486 helix: 1.78 (0.19), residues: 704 sheet: -0.77 (0.37), residues: 224 loop : -0.22 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 820 HIS 0.003 0.001 HIS B1051 PHE 0.009 0.001 PHE A 629 TYR 0.011 0.001 TYR B 837 ARG 0.004 0.001 ARG A1004 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 128 time to evaluate : 1.496 Fit side-chains REVERT: B 851 ASN cc_start: 0.6565 (m-40) cc_final: 0.6346 (m-40) REVERT: B 1080 GLU cc_start: 0.7712 (tt0) cc_final: 0.7123 (tp30) REVERT: A 582 LYS cc_start: 0.7912 (mtpp) cc_final: 0.7688 (mtmm) REVERT: A 851 ASN cc_start: 0.6555 (m-40) cc_final: 0.6340 (m-40) REVERT: A 1080 GLU cc_start: 0.7687 (tt0) cc_final: 0.7108 (tp30) outliers start: 16 outliers final: 12 residues processed: 138 average time/residue: 0.2607 time to fit residues: 51.8543 Evaluate side-chains 127 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 115 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 571 ARG Chi-restraints excluded: chain B residue 634 ASN Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 735 GLU Chi-restraints excluded: chain B residue 773 SER Chi-restraints excluded: chain B residue 964 ILE Chi-restraints excluded: chain A residue 571 ARG Chi-restraints excluded: chain A residue 634 ASN Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 964 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 91 optimal weight: 0.0670 chunk 37 optimal weight: 0.0670 chunk 134 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 119 optimal weight: 0.0070 chunk 133 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 overall best weight: 0.3874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 892 HIS A 892 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12446 Z= 0.129 Angle : 0.426 6.458 16816 Z= 0.220 Chirality : 0.038 0.142 1820 Planarity : 0.003 0.048 2142 Dihedral : 3.409 15.014 1662 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.60 % Allowed : 12.67 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.26 (0.23), residues: 1486 helix: 2.16 (0.20), residues: 692 sheet: -0.63 (0.37), residues: 226 loop : -0.13 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1189 HIS 0.002 0.001 HIS B1092 PHE 0.008 0.001 PHE A 710 TYR 0.010 0.001 TYR B 920 ARG 0.003 0.000 ARG B1004 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 137 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 851 ASN cc_start: 0.6488 (m-40) cc_final: 0.6215 (m-40) REVERT: B 1073 GLU cc_start: 0.7922 (tt0) cc_final: 0.7621 (mt-10) REVERT: B 1080 GLU cc_start: 0.7656 (tt0) cc_final: 0.7077 (tp30) REVERT: A 582 LYS cc_start: 0.7919 (mtpp) cc_final: 0.7628 (mtmm) REVERT: A 851 ASN cc_start: 0.6484 (m-40) cc_final: 0.6212 (m-40) REVERT: A 1073 GLU cc_start: 0.7912 (tt0) cc_final: 0.7608 (mt-10) REVERT: A 1080 GLU cc_start: 0.7632 (tt0) cc_final: 0.7094 (tp30) outliers start: 21 outliers final: 16 residues processed: 155 average time/residue: 0.2940 time to fit residues: 62.7928 Evaluate side-chains 137 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 121 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 571 ARG Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 735 GLU Chi-restraints excluded: chain B residue 773 SER Chi-restraints excluded: chain B residue 857 LYS Chi-restraints excluded: chain B residue 964 ILE Chi-restraints excluded: chain B residue 1046 ARG Chi-restraints excluded: chain B residue 1127 SER Chi-restraints excluded: chain A residue 571 ARG Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 857 LYS Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 1046 ARG Chi-restraints excluded: chain A residue 1127 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 135 optimal weight: 0.7980 chunk 143 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 128 optimal weight: 7.9990 chunk 38 optimal weight: 0.0060 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 623 HIS B 892 HIS A 623 HIS A 892 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12446 Z= 0.186 Angle : 0.449 6.622 16816 Z= 0.233 Chirality : 0.039 0.140 1820 Planarity : 0.003 0.047 2142 Dihedral : 3.515 14.822 1662 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.98 % Allowed : 12.44 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.33 (0.23), residues: 1486 helix: 2.23 (0.20), residues: 692 sheet: -0.59 (0.37), residues: 226 loop : -0.12 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B1189 HIS 0.003 0.001 HIS B1051 PHE 0.009 0.001 PHE A 739 TYR 0.012 0.001 TYR A 418 ARG 0.002 0.000 ARG B1057 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 132 time to evaluate : 1.399 Fit side-chains revert: symmetry clash REVERT: B 420 ARG cc_start: 0.7620 (ptm160) cc_final: 0.7225 (ptm-80) REVERT: B 928 GLN cc_start: 0.8067 (mp10) cc_final: 0.7789 (mp10) REVERT: B 1073 GLU cc_start: 0.7962 (tt0) cc_final: 0.7557 (mt-10) REVERT: B 1080 GLU cc_start: 0.7631 (tt0) cc_final: 0.7107 (tp30) REVERT: A 928 GLN cc_start: 0.8055 (mp10) cc_final: 0.7787 (mp10) REVERT: A 1046 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.6693 (ttt180) REVERT: A 1073 GLU cc_start: 0.7949 (tt0) cc_final: 0.7560 (mt-10) REVERT: A 1080 GLU cc_start: 0.7624 (tt0) cc_final: 0.7099 (tp30) outliers start: 26 outliers final: 20 residues processed: 154 average time/residue: 0.2851 time to fit residues: 61.0683 Evaluate side-chains 138 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 117 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 571 ARG Chi-restraints excluded: chain B residue 634 ASN Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 735 GLU Chi-restraints excluded: chain B residue 773 SER Chi-restraints excluded: chain B residue 790 LEU Chi-restraints excluded: chain B residue 964 ILE Chi-restraints excluded: chain B residue 1046 ARG Chi-restraints excluded: chain B residue 1097 LEU Chi-restraints excluded: chain B residue 1127 SER Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 571 ARG Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 1046 ARG Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1127 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 122 optimal weight: 0.5980 chunk 98 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 73 optimal weight: 0.9990 chunk 128 optimal weight: 7.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 892 HIS A 892 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12446 Z= 0.191 Angle : 0.446 6.327 16816 Z= 0.232 Chirality : 0.039 0.140 1820 Planarity : 0.003 0.049 2142 Dihedral : 3.552 14.940 1662 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.91 % Allowed : 13.13 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.32 (0.23), residues: 1486 helix: 2.21 (0.19), residues: 704 sheet: -0.70 (0.36), residues: 236 loop : -0.07 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B1189 HIS 0.006 0.001 HIS A 609 PHE 0.008 0.001 PHE A 710 TYR 0.016 0.001 TYR A 418 ARG 0.003 0.000 ARG A1057 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 124 time to evaluate : 1.373 Fit side-chains revert: symmetry clash REVERT: B 928 GLN cc_start: 0.8070 (mp10) cc_final: 0.7824 (mp10) REVERT: B 1073 GLU cc_start: 0.8002 (tt0) cc_final: 0.7579 (mt-10) REVERT: B 1080 GLU cc_start: 0.7631 (tt0) cc_final: 0.7140 (tp30) REVERT: A 928 GLN cc_start: 0.8066 (mp10) cc_final: 0.7820 (mp10) REVERT: A 1046 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.6787 (ttt180) REVERT: A 1073 GLU cc_start: 0.7997 (tt0) cc_final: 0.7578 (mt-10) REVERT: A 1080 GLU cc_start: 0.7640 (tt0) cc_final: 0.7138 (tp30) outliers start: 25 outliers final: 24 residues processed: 144 average time/residue: 0.2670 time to fit residues: 55.4786 Evaluate side-chains 138 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 113 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 571 ARG Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 735 GLU Chi-restraints excluded: chain B residue 773 SER Chi-restraints excluded: chain B residue 790 LEU Chi-restraints excluded: chain B residue 964 ILE Chi-restraints excluded: chain B residue 1046 ARG Chi-restraints excluded: chain B residue 1097 LEU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1127 SER Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 571 ARG Chi-restraints excluded: chain A residue 634 ASN Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 1046 ARG Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1127 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 0.7980 chunk 128 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 118 optimal weight: 0.2980 chunk 66 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 75 optimal weight: 0.4980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 892 HIS A 892 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12446 Z= 0.212 Angle : 0.456 6.344 16816 Z= 0.237 Chirality : 0.039 0.140 1820 Planarity : 0.003 0.051 2142 Dihedral : 3.613 15.202 1662 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.14 % Allowed : 12.60 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.27 (0.23), residues: 1486 helix: 2.18 (0.19), residues: 704 sheet: -0.76 (0.36), residues: 236 loop : -0.10 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1189 HIS 0.008 0.001 HIS A 609 PHE 0.009 0.001 PHE B 739 TYR 0.015 0.001 TYR A 418 ARG 0.003 0.000 ARG A1057 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 128 time to evaluate : 1.480 Fit side-chains REVERT: B 416 ASP cc_start: 0.7830 (OUTLIER) cc_final: 0.7618 (p0) REVERT: B 997 ASP cc_start: 0.7860 (t0) cc_final: 0.7329 (t0) REVERT: B 1046 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.6807 (ttt180) REVERT: B 1073 GLU cc_start: 0.7993 (tt0) cc_final: 0.7557 (mt-10) REVERT: B 1080 GLU cc_start: 0.7587 (tt0) cc_final: 0.7179 (tp30) REVERT: A 997 ASP cc_start: 0.7874 (t0) cc_final: 0.7343 (t0) REVERT: A 1046 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.6795 (ttt180) REVERT: A 1073 GLU cc_start: 0.8018 (tt0) cc_final: 0.7557 (mt-10) REVERT: A 1080 GLU cc_start: 0.7574 (tt0) cc_final: 0.7175 (tp30) outliers start: 28 outliers final: 22 residues processed: 149 average time/residue: 0.2724 time to fit residues: 57.8566 Evaluate side-chains 146 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 121 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 571 ARG Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 735 GLU Chi-restraints excluded: chain B residue 773 SER Chi-restraints excluded: chain B residue 790 LEU Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 1046 ARG Chi-restraints excluded: chain B residue 1097 LEU Chi-restraints excluded: chain B residue 1127 SER Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 571 ARG Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 1046 ARG Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1127 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 81 optimal weight: 0.1980 chunk 104 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 142 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 892 HIS A 892 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12446 Z= 0.168 Angle : 0.438 5.859 16816 Z= 0.229 Chirality : 0.038 0.139 1820 Planarity : 0.003 0.053 2142 Dihedral : 3.536 15.157 1662 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.29 % Allowed : 12.52 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 (0.23), residues: 1486 helix: 2.24 (0.19), residues: 704 sheet: -0.74 (0.36), residues: 236 loop : -0.05 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B1189 HIS 0.003 0.001 HIS A 609 PHE 0.009 0.001 PHE A 710 TYR 0.011 0.001 TYR A 418 ARG 0.003 0.000 ARG A1057 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 133 time to evaluate : 1.514 Fit side-chains REVERT: B 928 GLN cc_start: 0.8141 (mp10) cc_final: 0.7840 (mp10) REVERT: B 930 ASN cc_start: 0.8249 (t0) cc_final: 0.7816 (t0) REVERT: B 997 ASP cc_start: 0.7856 (t0) cc_final: 0.7294 (t0) REVERT: B 1046 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.6748 (ttt180) REVERT: B 1073 GLU cc_start: 0.8016 (tt0) cc_final: 0.7796 (tt0) REVERT: B 1080 GLU cc_start: 0.7549 (tt0) cc_final: 0.7198 (tp30) REVERT: A 928 GLN cc_start: 0.8151 (mp10) cc_final: 0.7851 (mp10) REVERT: A 930 ASN cc_start: 0.8260 (t0) cc_final: 0.7844 (t0) REVERT: A 997 ASP cc_start: 0.7839 (t0) cc_final: 0.7285 (t0) REVERT: A 1046 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.6754 (ttt180) REVERT: A 1073 GLU cc_start: 0.8010 (tt0) cc_final: 0.7787 (tt0) REVERT: A 1080 GLU cc_start: 0.7544 (tt0) cc_final: 0.7178 (tp30) outliers start: 30 outliers final: 28 residues processed: 158 average time/residue: 0.2683 time to fit residues: 60.0996 Evaluate side-chains 156 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 126 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 543 ASP Chi-restraints excluded: chain B residue 571 ARG Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 735 GLU Chi-restraints excluded: chain B residue 773 SER Chi-restraints excluded: chain B residue 790 LEU Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 909 HIS Chi-restraints excluded: chain B residue 1046 ARG Chi-restraints excluded: chain B residue 1097 LEU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1127 SER Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 571 ARG Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 909 HIS Chi-restraints excluded: chain A residue 1046 ARG Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1127 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 90 optimal weight: 0.1980 chunk 97 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 129 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 892 HIS A 892 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12446 Z= 0.182 Angle : 0.445 5.878 16816 Z= 0.232 Chirality : 0.038 0.140 1820 Planarity : 0.003 0.056 2142 Dihedral : 3.545 15.053 1662 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.52 % Allowed : 12.14 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 (0.23), residues: 1486 helix: 2.23 (0.19), residues: 704 sheet: -0.66 (0.36), residues: 230 loop : -0.07 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B1189 HIS 0.006 0.001 HIS B 566 PHE 0.009 0.001 PHE A 710 TYR 0.011 0.001 TYR A 418 ARG 0.004 0.000 ARG A1057 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 131 time to evaluate : 1.330 Fit side-chains REVERT: B 416 ASP cc_start: 0.7874 (OUTLIER) cc_final: 0.7640 (p0) REVERT: B 652 TYR cc_start: 0.8111 (m-80) cc_final: 0.7851 (m-80) REVERT: B 928 GLN cc_start: 0.8148 (mp10) cc_final: 0.7847 (mp10) REVERT: B 930 ASN cc_start: 0.8236 (t0) cc_final: 0.7795 (t0) REVERT: B 997 ASP cc_start: 0.7866 (t0) cc_final: 0.7310 (t0) REVERT: B 1046 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.6766 (ttt180) REVERT: B 1073 GLU cc_start: 0.8027 (tt0) cc_final: 0.7811 (tt0) REVERT: B 1080 GLU cc_start: 0.7542 (tt0) cc_final: 0.7207 (tp30) REVERT: A 530 ARG cc_start: 0.7259 (mtp-110) cc_final: 0.6952 (mtm180) REVERT: A 652 TYR cc_start: 0.8125 (m-80) cc_final: 0.7831 (m-80) REVERT: A 928 GLN cc_start: 0.8177 (mp10) cc_final: 0.7894 (mp10) REVERT: A 930 ASN cc_start: 0.8236 (t0) cc_final: 0.7814 (t0) REVERT: A 997 ASP cc_start: 0.7851 (t0) cc_final: 0.7297 (t0) REVERT: A 1046 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.6768 (ttt180) REVERT: A 1073 GLU cc_start: 0.8025 (tt0) cc_final: 0.7812 (tt0) REVERT: A 1080 GLU cc_start: 0.7529 (tt0) cc_final: 0.7181 (tp30) outliers start: 33 outliers final: 30 residues processed: 158 average time/residue: 0.2494 time to fit residues: 56.2804 Evaluate side-chains 162 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 129 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 543 ASP Chi-restraints excluded: chain B residue 571 ARG Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 735 GLU Chi-restraints excluded: chain B residue 773 SER Chi-restraints excluded: chain B residue 790 LEU Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 909 HIS Chi-restraints excluded: chain B residue 1046 ARG Chi-restraints excluded: chain B residue 1097 LEU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1127 SER Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 571 ARG Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 909 HIS Chi-restraints excluded: chain A residue 1046 ARG Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1127 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 3.9990 chunk 124 optimal weight: 0.6980 chunk 132 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 104 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 125 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 chunk 140 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 892 HIS A 892 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12446 Z= 0.188 Angle : 0.446 5.897 16816 Z= 0.233 Chirality : 0.038 0.140 1820 Planarity : 0.003 0.055 2142 Dihedral : 3.559 15.206 1662 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.52 % Allowed : 12.21 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 (0.23), residues: 1486 helix: 2.23 (0.19), residues: 704 sheet: -0.69 (0.36), residues: 230 loop : -0.06 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B1189 HIS 0.003 0.001 HIS B1051 PHE 0.009 0.001 PHE A 710 TYR 0.011 0.001 TYR A 418 ARG 0.003 0.000 ARG A1057 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 133 time to evaluate : 1.381 Fit side-chains REVERT: B 416 ASP cc_start: 0.7941 (OUTLIER) cc_final: 0.7687 (p0) REVERT: B 652 TYR cc_start: 0.8179 (m-80) cc_final: 0.7892 (m-80) REVERT: B 928 GLN cc_start: 0.8181 (mp10) cc_final: 0.7901 (mp10) REVERT: B 930 ASN cc_start: 0.8233 (t0) cc_final: 0.7807 (t0) REVERT: B 997 ASP cc_start: 0.7890 (t0) cc_final: 0.7431 (t0) REVERT: B 1046 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.6763 (ttt180) REVERT: B 1073 GLU cc_start: 0.8058 (tt0) cc_final: 0.7847 (tt0) REVERT: B 1080 GLU cc_start: 0.7632 (tt0) cc_final: 0.7231 (tp30) REVERT: A 530 ARG cc_start: 0.7238 (mtp-110) cc_final: 0.6928 (mtm180) REVERT: A 652 TYR cc_start: 0.8173 (m-80) cc_final: 0.7852 (m-80) REVERT: A 928 GLN cc_start: 0.8184 (mp10) cc_final: 0.7908 (mp10) REVERT: A 930 ASN cc_start: 0.8240 (t0) cc_final: 0.7829 (t0) REVERT: A 997 ASP cc_start: 0.7884 (t0) cc_final: 0.7460 (t0) REVERT: A 1046 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.6772 (ttt180) REVERT: A 1073 GLU cc_start: 0.8105 (tt0) cc_final: 0.7904 (tt0) REVERT: A 1080 GLU cc_start: 0.7623 (tt0) cc_final: 0.7220 (tp30) outliers start: 33 outliers final: 30 residues processed: 160 average time/residue: 0.2779 time to fit residues: 63.4276 Evaluate side-chains 159 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 126 time to evaluate : 1.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 543 ASP Chi-restraints excluded: chain B residue 571 ARG Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 735 GLU Chi-restraints excluded: chain B residue 773 SER Chi-restraints excluded: chain B residue 790 LEU Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 909 HIS Chi-restraints excluded: chain B residue 1046 ARG Chi-restraints excluded: chain B residue 1097 LEU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1127 SER Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 571 ARG Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 909 HIS Chi-restraints excluded: chain A residue 1046 ARG Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1127 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 147 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 chunk 117 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 90 optimal weight: 0.5980 chunk 71 optimal weight: 0.5980 chunk 93 optimal weight: 0.7980 chunk 125 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 892 HIS A 892 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12446 Z= 0.183 Angle : 0.446 6.004 16816 Z= 0.233 Chirality : 0.038 0.140 1820 Planarity : 0.003 0.056 2142 Dihedral : 3.549 15.194 1662 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.60 % Allowed : 12.29 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.38 (0.23), residues: 1486 helix: 2.25 (0.19), residues: 704 sheet: -0.70 (0.36), residues: 230 loop : -0.03 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1189 HIS 0.007 0.001 HIS B 566 PHE 0.009 0.001 PHE B 710 TYR 0.010 0.001 TYR A 418 ARG 0.008 0.000 ARG B 428 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 128 time to evaluate : 1.479 Fit side-chains REVERT: B 652 TYR cc_start: 0.8190 (m-80) cc_final: 0.7893 (m-80) REVERT: B 928 GLN cc_start: 0.8175 (mp10) cc_final: 0.7911 (mp10) REVERT: B 930 ASN cc_start: 0.8230 (t0) cc_final: 0.7809 (t0) REVERT: B 1046 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.6756 (ttt180) REVERT: B 1073 GLU cc_start: 0.8102 (tt0) cc_final: 0.7895 (tt0) REVERT: B 1080 GLU cc_start: 0.7632 (tt0) cc_final: 0.7229 (tp30) REVERT: A 530 ARG cc_start: 0.7236 (mtp-110) cc_final: 0.6923 (mtm180) REVERT: A 652 TYR cc_start: 0.8188 (m-80) cc_final: 0.7856 (m-80) REVERT: A 928 GLN cc_start: 0.8185 (mp10) cc_final: 0.7927 (mp10) REVERT: A 930 ASN cc_start: 0.8217 (t0) cc_final: 0.7812 (t0) REVERT: A 1046 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.6764 (ttt180) REVERT: A 1073 GLU cc_start: 0.8106 (tt0) cc_final: 0.7900 (tt0) REVERT: A 1080 GLU cc_start: 0.7622 (tt0) cc_final: 0.7218 (tp30) outliers start: 34 outliers final: 32 residues processed: 155 average time/residue: 0.2795 time to fit residues: 61.2746 Evaluate side-chains 159 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 125 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 543 ASP Chi-restraints excluded: chain B residue 571 ARG Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 735 GLU Chi-restraints excluded: chain B residue 773 SER Chi-restraints excluded: chain B residue 790 LEU Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 909 HIS Chi-restraints excluded: chain B residue 1046 ARG Chi-restraints excluded: chain B residue 1097 LEU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1127 SER Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 571 ARG Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 909 HIS Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 1046 ARG Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1127 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 49 optimal weight: 0.0670 chunk 120 optimal weight: 0.0980 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 7.9990 chunk 103 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 892 HIS A 892 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.147711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.113209 restraints weight = 13370.144| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.13 r_work: 0.2853 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12446 Z= 0.165 Angle : 0.437 5.923 16816 Z= 0.229 Chirality : 0.038 0.139 1820 Planarity : 0.003 0.056 2142 Dihedral : 3.509 15.195 1662 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.52 % Allowed : 12.44 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.41 (0.23), residues: 1486 helix: 2.28 (0.19), residues: 704 sheet: -0.63 (0.37), residues: 218 loop : -0.07 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B1189 HIS 0.007 0.001 HIS B 566 PHE 0.009 0.001 PHE B 710 TYR 0.010 0.001 TYR A 418 ARG 0.008 0.000 ARG B 428 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2619.11 seconds wall clock time: 48 minutes 1.57 seconds (2881.57 seconds total)