Starting phenix.real_space_refine on Wed Jul 30 13:54:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ygh_39250/07_2025/8ygh_39250.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ygh_39250/07_2025/8ygh_39250.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ygh_39250/07_2025/8ygh_39250.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ygh_39250/07_2025/8ygh_39250.map" model { file = "/net/cci-nas-00/data/ceres_data/8ygh_39250/07_2025/8ygh_39250.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ygh_39250/07_2025/8ygh_39250.cif" } resolution = 2.77 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= 0.041 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 52 5.16 5 C 7856 2.51 5 N 2104 2.21 5 O 2232 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12244 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 755, 6122 Classifications: {'peptide': 755} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 724} Chain breaks: 1 Chain: "B" Number of atoms: 6122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 755, 6122 Classifications: {'peptide': 755} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 724} Chain breaks: 1 Time building chain proxies: 8.29, per 1000 atoms: 0.68 Number of scatterers: 12244 At special positions: 0 Unit cell: (116.64, 110.16, 116.64, 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 52 16.00 O 2232 8.00 N 2104 7.00 C 7856 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: 3.22 Conformation dependent library (CDL) restraints added in 1.7 seconds 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2836 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 16 sheets defined 51.5% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 439 through 451 Processing helix chain 'A' and resid 496 through 501 Processing helix chain 'A' and resid 502 through 513 Processing helix chain 'A' and resid 522 through 527 Processing helix chain 'A' and resid 548 through 560 Processing helix chain 'A' and resid 560 through 565 removed outlier: 4.074A pdb=" N ILE A 564 " --> pdb=" O TRP A 560 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL A 565 " --> pdb=" O PRO A 561 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 560 through 565' Processing helix chain 'A' and resid 592 through 602 removed outlier: 3.815A pdb=" N LYS A 602 " --> pdb=" O ALA A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 621 through 631 removed outlier: 3.731A 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 645 through 654 Processing helix chain 'A' and resid 657 through 664 removed outlier: 3.501A pdb=" N LEU A 664 " --> pdb=" O ARG A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 683 Processing helix chain 'A' and resid 686 through 705 removed outlier: 4.597A pdb=" N LYS A 696 " --> pdb=" O GLN A 692 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA A 697 " --> pdb=" O VAL A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 729 Processing helix chain 'A' and resid 738 through 750 removed outlier: 3.564A pdb=" N PHE A 750 " --> pdb=" O ALA A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 767 Processing helix chain 'A' and resid 809 through 814 Processing helix chain 'A' and resid 817 through 821 removed outlier: 3.605A pdb=" N TRP A 820 " --> pdb=" O GLU A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 878 removed outlier: 4.448A pdb=" N LYS A 878 " --> pdb=" O ALA A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 882 through 892 Processing helix chain 'A' and resid 942 through 953 removed outlier: 3.598A pdb=" N SER A 953 " --> pdb=" O SER A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 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: 3.514A pdb=" N ILE A1031 " --> pdb=" O SER A1027 " (cutoff:3.500A) Proline residue: A1037 - end of helix removed outlier: 6.030A pdb=" N ALA A1072 " --> pdb=" O ILE A1068 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ASP A1073 " --> pdb=" O ASN A1069 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU A1074 " --> pdb=" O GLU A1070 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1092 removed outlier: 3.872A pdb=" N GLY A1086 " --> pdb=" O GLU A1082 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N HIS A1092 " --> pdb=" O ILE A1088 " (cutoff:3.500A) Processing helix chain 'A' and resid 1098 through 1104 Processing helix chain 'A' and resid 1109 through 1118 removed outlier: 4.573A pdb=" N LEU A1118 " --> pdb=" O ASN A1114 " (cutoff:3.500A) 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 1159 removed outlier: 4.195A pdb=" N ARG A1140 " --> pdb=" O ALA A1136 " (cutoff:3.500A) 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 453 Processing helix chain 'B' and resid 502 through 513 Processing helix chain 'B' and resid 522 through 528 Processing helix chain 'B' and resid 546 through 560 Processing helix chain 'B' and resid 560 through 565 removed outlier: 4.054A pdb=" N ILE B 564 " --> pdb=" O TRP B 560 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL B 565 " --> pdb=" O PRO B 561 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 560 through 565' Processing helix chain 'B' and resid 592 through 603 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 621 through 631 removed outlier: 3.973A 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 644 through 653 removed outlier: 3.568A pdb=" N LEU B 648 " --> pdb=" O SER B 644 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE B 653 " --> pdb=" O PHE B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 658 through 665 Processing helix chain 'B' and resid 672 through 683 removed outlier: 3.694A pdb=" N VAL B 682 " --> pdb=" O SER B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 705 removed outlier: 3.979A pdb=" N THR B 695 " --> pdb=" O LEU B 691 " (cutoff:3.500A) removed outlier: 4.700A 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 750 removed outlier: 3.599A pdb=" N PHE B 750 " --> pdb=" O ALA B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 754 through 767 Processing helix chain 'B' and resid 787 through 791 removed outlier: 3.660A pdb=" N LEU B 790 " --> pdb=" O SER B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 806 through 814 Processing helix chain 'B' and resid 815 through 822 removed outlier: 4.064A pdb=" N TRP B 820 " --> pdb=" O THR B 816 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N LEU B 821 " --> pdb=" O GLU B 817 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B 822 " --> pdb=" O ASP B 818 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 878 removed outlier: 4.382A pdb=" N LYS B 878 " --> pdb=" O ALA B 874 " (cutoff:3.500A) Processing helix chain 'B' and resid 882 through 892 Processing helix chain 'B' and resid 942 through 953 removed outlier: 3.592A 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 1069 removed outlier: 3.595A pdb=" N ILE B1031 " --> pdb=" O SER B1027 " (cutoff:3.500A) Proline residue: B1037 - end of helix Processing helix chain 'B' and resid 1070 through 1075 Processing helix chain 'B' and resid 1084 through 1092 removed outlier: 3.884A pdb=" N ILE B1088 " --> pdb=" O GLU B1084 " (cutoff:3.500A) 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 1159 removed outlier: 3.568A pdb=" N LYS B1138 " --> pdb=" O LEU B1134 " (cutoff:3.500A) Processing helix chain 'B' and resid 1166 through 1187 removed outlier: 3.680A pdb=" N TRP B1170 " --> pdb=" O GLY B1166 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 465 through 469 removed outlier: 6.066A pdb=" N LEU A 434 " --> pdb=" O VAL A 535 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N CYS A 537 " --> pdb=" O LEU A 434 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ALA A 436 " --> pdb=" O CYS A 537 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE A 534 " --> pdb=" O LYS A 570 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N LEU A 572 " --> pdb=" O ILE A 534 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ALA A 536 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N VAL A 569 " --> pdb=" O PHE A 639 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N ILE A 685 " --> pdb=" O VAL A 636 " (cutoff:3.500A) removed outlier: 6.152A 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 Processing sheet with id=AA4, first strand: chain 'A' and resid 824 through 827 removed outlier: 4.724A 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 912 Processing sheet with id=AA7, first strand: chain 'A' and resid 923 through 926 removed outlier: 3.608A pdb=" N MET A 931 " --> pdb=" O SER A 926 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1013 through 1016 removed outlier: 4.292A pdb=" N LEU A1013 " --> pdb=" O PHE A1025 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 465 through 469 removed outlier: 6.118A pdb=" N ILE B 534 " --> pdb=" O LYS B 570 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU B 572 " --> pdb=" O ILE B 534 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ALA B 536 " --> pdb=" O LEU B 572 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N VAL B 569 " --> pdb=" O PHE B 639 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE B 639 " --> pdb=" O VAL B 569 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N ILE B 685 " --> pdb=" O VAL B 636 " (cutoff:3.500A) removed outlier: 5.922A 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 Processing sheet with id=AB3, first strand: chain 'B' and resid 824 through 827 removed outlier: 4.813A 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: 5.852A pdb=" N THR B 922 " --> pdb=" O THR B 935 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1013 through 1016 removed outlier: 4.403A pdb=" N LEU B1013 " --> pdb=" O PHE B1025 " (cutoff:3.500A) 574 hydrogen bonds defined for protein. 1623 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: 4.00 Time building geometry restraints manager: 3.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3949 1.34 - 1.46: 2597 1.46 - 1.58: 5904 1.58 - 1.70: 0 1.70 - 1.82: 82 Bond restraints: 12532 Sorted by residual: bond pdb=" C ILE A 685 " pdb=" N PRO A 686 " ideal model delta sigma weight residual 1.331 1.375 -0.044 1.31e-02 5.83e+03 1.15e+01 bond pdb=" C ILE B 685 " pdb=" N PRO B 686 " ideal model delta sigma weight residual 1.332 1.372 -0.040 1.32e-02 5.74e+03 9.39e+00 bond pdb=" CA GLU A1112 " pdb=" C GLU A1112 " ideal model delta sigma weight residual 1.522 1.557 -0.035 1.39e-02 5.18e+03 6.30e+00 bond pdb=" CA VAL A 569 " pdb=" C VAL A 569 " ideal model delta sigma weight residual 1.523 1.497 0.026 1.26e-02 6.30e+03 4.12e+00 bond pdb=" CA VAL B 569 " pdb=" C VAL B 569 " ideal model delta sigma weight residual 1.522 1.500 0.022 1.21e-02 6.83e+03 3.24e+00 ... (remaining 12527 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 16723 2.47 - 4.95: 162 4.95 - 7.42: 30 7.42 - 9.90: 12 9.90 - 12.37: 5 Bond angle restraints: 16932 Sorted by residual: angle pdb=" N SER A 605 " pdb=" CA SER A 605 " pdb=" C SER A 605 " ideal model delta sigma weight residual 111.28 120.90 -9.62 1.09e+00 8.42e-01 7.79e+01 angle pdb=" N LEU A1113 " pdb=" CA LEU A1113 " pdb=" C LEU A1113 " ideal model delta sigma weight residual 110.97 102.31 8.66 1.09e+00 8.42e-01 6.31e+01 angle pdb=" N THR A 604 " pdb=" CA THR A 604 " pdb=" C THR A 604 " ideal model delta sigma weight residual 111.28 119.68 -8.40 1.09e+00 8.42e-01 5.93e+01 angle pdb=" N GLU A1111 " pdb=" CA GLU A1111 " pdb=" C GLU A1111 " ideal model delta sigma weight residual 110.97 117.68 -6.71 1.09e+00 8.42e-01 3.79e+01 angle pdb=" C ILE B 685 " pdb=" N PRO B 686 " pdb=" CA PRO B 686 " ideal model delta sigma weight residual 119.76 114.27 5.49 1.00e+00 1.00e+00 3.01e+01 ... (remaining 16927 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 6576 17.40 - 34.80: 706 34.80 - 52.20: 184 52.20 - 69.60: 43 69.60 - 87.00: 21 Dihedral angle restraints: 7530 sinusoidal: 3104 harmonic: 4426 Sorted by residual: dihedral pdb=" CA LYS B 893 " pdb=" C LYS B 893 " pdb=" N ILE B 894 " pdb=" CA ILE B 894 " ideal model delta harmonic sigma weight residual 180.00 161.90 18.10 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA GLN A1157 " pdb=" C GLN A1157 " pdb=" N LEU A1158 " pdb=" CA LEU A1158 " ideal model delta harmonic sigma weight residual 180.00 163.01 16.99 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA THR B1109 " pdb=" C THR B1109 " pdb=" N ILE B1110 " pdb=" CA ILE B1110 " ideal model delta harmonic sigma weight residual 180.00 -163.37 -16.63 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 7527 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1669 0.072 - 0.144: 153 0.144 - 0.216: 5 0.216 - 0.288: 2 0.288 - 0.361: 1 Chirality restraints: 1830 Sorted by residual: chirality pdb=" CA GLU A1111 " pdb=" N GLU A1111 " pdb=" C GLU A1111 " pdb=" CB GLU A1111 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" CA SER A 605 " pdb=" N SER A 605 " pdb=" C SER A 605 " pdb=" CB SER A 605 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CA THR A 604 " pdb=" N THR A 604 " pdb=" C THR A 604 " pdb=" CB THR A 604 " both_signs ideal model delta sigma weight residual False 2.53 2.29 0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 1827 not shown) Planarity restraints: 2166 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B1095 " -0.038 5.00e-02 4.00e+02 5.82e-02 5.42e+00 pdb=" N PRO B1096 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO B1096 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B1096 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B1131 " -0.140 9.50e-02 1.11e+02 6.33e-02 3.47e+00 pdb=" NE ARG B1131 " 0.014 2.00e-02 2.50e+03 pdb=" CZ ARG B1131 " -0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG B1131 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG B1131 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 568 " 0.008 2.00e-02 2.50e+03 1.74e-02 3.01e+00 pdb=" C PHE A 568 " -0.030 2.00e-02 2.50e+03 pdb=" O PHE A 568 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL A 569 " 0.010 2.00e-02 2.50e+03 ... (remaining 2163 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2213 2.76 - 3.30: 11943 3.30 - 3.83: 21327 3.83 - 4.37: 25391 4.37 - 4.90: 42639 Nonbonded interactions: 103513 Sorted by model distance: nonbonded pdb=" O TYR A1067 " pdb=" OG SER A1071 " model vdw 2.230 3.040 nonbonded pdb=" O THR B1123 " pdb=" OG SER B1127 " model vdw 2.246 3.040 nonbonded pdb=" OH TYR A1043 " pdb=" OE1 GLU A1173 " model vdw 2.260 3.040 nonbonded pdb=" OH TYR A 614 " pdb=" OE2 GLU A 624 " model vdw 2.263 3.040 nonbonded pdb=" OG SER B 787 " pdb=" OD2 ASP B 794 " model vdw 2.291 3.040 ... (remaining 103508 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: 0.06 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=0.00 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: 0.730 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: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 32.380 Find NCS groups from input model: 0.410 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:10.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 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 : 0.003 0.044 12532 Z= 0.142 Angle : 0.644 12.373 16932 Z= 0.353 Chirality : 0.043 0.361 1830 Planarity : 0.004 0.063 2166 Dihedral : 16.161 87.004 4694 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.74 % Allowed : 19.55 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.23), residues: 1502 helix: 1.56 (0.21), residues: 656 sheet: -0.41 (0.41), residues: 178 loop : -0.61 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A1189 HIS 0.003 0.000 HIS A 690 PHE 0.011 0.001 PHE B 629 TYR 0.007 0.001 TYR B 520 ARG 0.018 0.000 ARG B1131 Details of bonding type rmsd hydrogen bonds : bond 0.13210 ( 574) hydrogen bonds : angle 5.69296 ( 1623) covalent geometry : bond 0.00274 (12532) covalent geometry : angle 0.64409 (16932) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 70 time to evaluate : 1.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 970 GLU cc_start: 0.9089 (mt-10) cc_final: 0.8844 (mm-30) REVERT: B 688 SER cc_start: 0.9222 (OUTLIER) cc_final: 0.8997 (m) outliers start: 23 outliers final: 15 residues processed: 91 average time/residue: 1.2794 time to fit residues: 127.4542 Evaluate side-chains 82 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 853 SER Chi-restraints excluded: chain A residue 933 THR Chi-restraints excluded: chain B residue 456 ASN Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 688 SER Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 1121 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 117 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 87 optimal weight: 0.0980 chunk 136 optimal weight: 4.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 915 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.063195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.044347 restraints weight = 38592.041| |-----------------------------------------------------------------------------| r_work (start): 0.2729 rms_B_bonded: 3.41 r_work: 0.2569 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 12532 Z= 0.174 Angle : 0.542 7.888 16932 Z= 0.285 Chirality : 0.042 0.170 1830 Planarity : 0.004 0.047 2166 Dihedral : 5.618 68.140 1698 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.11 % Allowed : 17.05 % Favored : 79.85 % 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: 0.44 (0.22), residues: 1502 helix: 1.47 (0.21), residues: 666 sheet: -0.53 (0.39), residues: 188 loop : -0.66 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 820 HIS 0.005 0.001 HIS B 789 PHE 0.011 0.001 PHE B1094 TYR 0.011 0.001 TYR B 520 ARG 0.004 0.000 ARG A 734 Details of bonding type rmsd hydrogen bonds : bond 0.03293 ( 574) hydrogen bonds : angle 4.60103 ( 1623) covalent geometry : bond 0.00402 (12532) covalent geometry : angle 0.54241 (16932) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 67 time to evaluate : 1.485 Fit side-chains REVERT: A 1066 ARG cc_start: 0.9079 (ttt-90) cc_final: 0.8867 (ttt180) REVERT: B 688 SER cc_start: 0.9331 (OUTLIER) cc_final: 0.8973 (m) REVERT: B 929 ARG cc_start: 0.9359 (ptm-80) cc_final: 0.8956 (ptm-80) REVERT: B 957 MET cc_start: 0.9127 (mmm) cc_final: 0.8239 (mpp) outliers start: 41 outliers final: 15 residues processed: 100 average time/residue: 1.1608 time to fit residues: 127.8627 Evaluate side-chains 74 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 571 ARG Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 933 THR Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 688 SER Chi-restraints excluded: chain B residue 797 SER Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 1118 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 128 optimal weight: 0.9980 chunk 63 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 64 optimal weight: 8.9990 chunk 51 optimal weight: 0.9980 chunk 129 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 92 optimal weight: 0.0570 chunk 12 optimal weight: 0.0670 chunk 18 optimal weight: 2.9990 overall best weight: 1.0238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 915 GLN B 623 HIS B 887 HIS B1010 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.063538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.044690 restraints weight = 38970.061| |-----------------------------------------------------------------------------| r_work (start): 0.2744 rms_B_bonded: 3.44 r_work: 0.2585 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12532 Z= 0.129 Angle : 0.519 7.200 16932 Z= 0.270 Chirality : 0.041 0.149 1830 Planarity : 0.003 0.045 2166 Dihedral : 5.465 68.069 1689 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.58 % Allowed : 17.80 % Favored : 79.62 % 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: 0.42 (0.22), residues: 1502 helix: 1.50 (0.21), residues: 660 sheet: -0.54 (0.39), residues: 188 loop : -0.70 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B1189 HIS 0.003 0.001 HIS B1092 PHE 0.008 0.001 PHE B 632 TYR 0.010 0.001 TYR B 520 ARG 0.009 0.000 ARG B1131 Details of bonding type rmsd hydrogen bonds : bond 0.03105 ( 574) hydrogen bonds : angle 4.44757 ( 1623) covalent geometry : bond 0.00294 (12532) covalent geometry : angle 0.51941 (16932) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 63 time to evaluate : 1.432 Fit side-chains REVERT: A 1066 ARG cc_start: 0.9132 (ttt-90) cc_final: 0.8789 (ttt-90) REVERT: B 524 GLU cc_start: 0.9048 (OUTLIER) cc_final: 0.8735 (pp20) REVERT: B 688 SER cc_start: 0.9329 (OUTLIER) cc_final: 0.9041 (m) REVERT: B 749 MET cc_start: 0.9418 (mmm) cc_final: 0.9169 (mmp) REVERT: B 957 MET cc_start: 0.9148 (mmm) cc_final: 0.8317 (mpp) outliers start: 34 outliers final: 15 residues processed: 91 average time/residue: 1.4064 time to fit residues: 139.4946 Evaluate side-chains 77 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 933 THR Chi-restraints excluded: chain A residue 987 MET Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain B residue 467 MET Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 688 SER Chi-restraints excluded: chain B residue 797 SER Chi-restraints excluded: chain B residue 825 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 4 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 137 optimal weight: 3.9990 chunk 113 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 915 GLN B 879 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.062342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.043660 restraints weight = 38571.381| |-----------------------------------------------------------------------------| r_work (start): 0.2709 rms_B_bonded: 3.38 r_work: 0.2547 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 12532 Z= 0.183 Angle : 0.553 8.607 16932 Z= 0.286 Chirality : 0.042 0.147 1830 Planarity : 0.003 0.039 2166 Dihedral : 5.464 64.931 1689 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.05 % Allowed : 18.79 % Favored : 79.17 % 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: 0.42 (0.22), residues: 1502 helix: 1.48 (0.21), residues: 666 sheet: -0.49 (0.40), residues: 188 loop : -0.71 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1189 HIS 0.004 0.001 HIS B 892 PHE 0.008 0.001 PHE B 596 TYR 0.012 0.001 TYR B 520 ARG 0.006 0.000 ARG B1140 Details of bonding type rmsd hydrogen bonds : bond 0.03211 ( 574) hydrogen bonds : angle 4.48225 ( 1623) covalent geometry : bond 0.00425 (12532) covalent geometry : angle 0.55334 (16932) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 66 time to evaluate : 1.364 Fit side-chains REVERT: A 662 ARG cc_start: 0.8229 (tmm160) cc_final: 0.8023 (tmm160) REVERT: A 994 GLU cc_start: 0.8547 (tm-30) cc_final: 0.8316 (pp20) REVERT: A 1042 LEU cc_start: 0.9656 (OUTLIER) cc_final: 0.9423 (tm) REVERT: A 1066 ARG cc_start: 0.9131 (ttt-90) cc_final: 0.8905 (ttt180) REVERT: A 1111 GLU cc_start: 0.9378 (OUTLIER) cc_final: 0.9148 (pm20) REVERT: B 749 MET cc_start: 0.9444 (mmm) cc_final: 0.9172 (mmp) REVERT: B 957 MET cc_start: 0.9185 (mmm) cc_final: 0.8293 (mpp) outliers start: 27 outliers final: 18 residues processed: 89 average time/residue: 1.4127 time to fit residues: 137.5127 Evaluate side-chains 77 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 57 time to evaluate : 1.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 933 THR Chi-restraints excluded: chain A residue 987 MET Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain B residue 467 MET Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 797 SER Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 1118 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 53 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 7 optimal weight: 0.5980 chunk 3 optimal weight: 0.2980 chunk 113 optimal weight: 0.9980 chunk 138 optimal weight: 7.9990 chunk 104 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 127 optimal weight: 5.9990 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 915 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.063792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.045064 restraints weight = 38713.167| |-----------------------------------------------------------------------------| r_work (start): 0.2752 rms_B_bonded: 3.43 r_work: 0.2596 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 12532 Z= 0.110 Angle : 0.536 8.651 16932 Z= 0.273 Chirality : 0.041 0.169 1830 Planarity : 0.003 0.037 2166 Dihedral : 5.392 68.580 1688 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.35 % Allowed : 18.94 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.22), residues: 1502 helix: 1.58 (0.21), residues: 658 sheet: -0.44 (0.40), residues: 188 loop : -0.75 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1189 HIS 0.003 0.000 HIS B 892 PHE 0.008 0.001 PHE A 710 TYR 0.010 0.001 TYR B 520 ARG 0.012 0.000 ARG B1131 Details of bonding type rmsd hydrogen bonds : bond 0.02859 ( 574) hydrogen bonds : angle 4.33686 ( 1623) covalent geometry : bond 0.00250 (12532) covalent geometry : angle 0.53574 (16932) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 65 time to evaluate : 2.106 Fit side-chains REVERT: A 662 ARG cc_start: 0.8191 (tmm160) cc_final: 0.7969 (tmm160) REVERT: A 994 GLU cc_start: 0.8522 (tm-30) cc_final: 0.8286 (pp20) REVERT: A 1042 LEU cc_start: 0.9629 (OUTLIER) cc_final: 0.9399 (tm) REVERT: A 1066 ARG cc_start: 0.9153 (ttt-90) cc_final: 0.8928 (ttt180) REVERT: B 524 GLU cc_start: 0.9074 (OUTLIER) cc_final: 0.8801 (pp20) REVERT: B 749 MET cc_start: 0.9368 (mmm) cc_final: 0.9059 (mmp) REVERT: B 957 MET cc_start: 0.9205 (mmm) cc_final: 0.8307 (mpp) REVERT: B 1094 PHE cc_start: 0.7968 (m-80) cc_final: 0.7185 (m-80) REVERT: B 1151 ARG cc_start: 0.9459 (OUTLIER) cc_final: 0.9222 (tmt-80) outliers start: 31 outliers final: 15 residues processed: 90 average time/residue: 1.3102 time to fit residues: 129.4170 Evaluate side-chains 82 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 987 MET Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain B residue 467 MET Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 797 SER Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 1151 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 129 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 78 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 83 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 915 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.062096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.043212 restraints weight = 39387.870| |-----------------------------------------------------------------------------| r_work (start): 0.2701 rms_B_bonded: 3.44 r_work: 0.2540 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 12532 Z= 0.184 Angle : 0.558 8.959 16932 Z= 0.287 Chirality : 0.042 0.159 1830 Planarity : 0.003 0.035 2166 Dihedral : 5.293 65.096 1687 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.12 % Allowed : 20.00 % Favored : 77.88 % 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: 0.42 (0.22), residues: 1502 helix: 1.46 (0.21), residues: 674 sheet: -0.29 (0.41), residues: 176 loop : -0.79 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1189 HIS 0.004 0.001 HIS B 789 PHE 0.009 0.001 PHE B 596 TYR 0.013 0.001 TYR B 520 ARG 0.007 0.000 ARG A1141 Details of bonding type rmsd hydrogen bonds : bond 0.03164 ( 574) hydrogen bonds : angle 4.40511 ( 1623) covalent geometry : bond 0.00429 (12532) covalent geometry : angle 0.55825 (16932) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 66 time to evaluate : 1.421 Fit side-chains revert: symmetry clash REVERT: A 662 ARG cc_start: 0.8331 (tmm160) cc_final: 0.8057 (tmm160) REVERT: A 994 GLU cc_start: 0.8623 (tm-30) cc_final: 0.8347 (pp20) REVERT: A 1042 LEU cc_start: 0.9650 (OUTLIER) cc_final: 0.9399 (tm) REVERT: A 1066 ARG cc_start: 0.9134 (ttt-90) cc_final: 0.8911 (ttt180) REVERT: B 749 MET cc_start: 0.9462 (mmm) cc_final: 0.9256 (mmp) REVERT: B 929 ARG cc_start: 0.9257 (OUTLIER) cc_final: 0.8573 (ptm-80) REVERT: B 957 MET cc_start: 0.9215 (mmm) cc_final: 0.8373 (mpp) REVERT: B 1094 PHE cc_start: 0.8003 (m-80) cc_final: 0.7109 (m-80) REVERT: B 1151 ARG cc_start: 0.9455 (OUTLIER) cc_final: 0.9112 (mmm160) outliers start: 28 outliers final: 13 residues processed: 92 average time/residue: 1.2878 time to fit residues: 129.3476 Evaluate side-chains 77 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 797 SER Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 929 ARG Chi-restraints excluded: chain B residue 1118 LEU Chi-restraints excluded: chain B residue 1151 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 107 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 chunk 129 optimal weight: 0.9980 chunk 127 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 915 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.062265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.043381 restraints weight = 38984.587| |-----------------------------------------------------------------------------| r_work (start): 0.2706 rms_B_bonded: 3.45 r_work: 0.2545 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 12532 Z= 0.168 Angle : 0.570 9.665 16932 Z= 0.290 Chirality : 0.042 0.156 1830 Planarity : 0.003 0.035 2166 Dihedral : 5.287 64.667 1687 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.27 % Allowed : 20.38 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.22), residues: 1502 helix: 1.43 (0.21), residues: 672 sheet: -0.32 (0.41), residues: 176 loop : -0.76 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1189 HIS 0.008 0.001 HIS B 892 PHE 0.008 0.001 PHE B 632 TYR 0.012 0.001 TYR B 520 ARG 0.007 0.000 ARG A1141 Details of bonding type rmsd hydrogen bonds : bond 0.03110 ( 574) hydrogen bonds : angle 4.38207 ( 1623) covalent geometry : bond 0.00392 (12532) covalent geometry : angle 0.56979 (16932) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 65 time to evaluate : 1.451 Fit side-chains revert: symmetry clash REVERT: A 662 ARG cc_start: 0.8349 (tmm160) cc_final: 0.8088 (tmm160) REVERT: A 994 GLU cc_start: 0.8634 (tm-30) cc_final: 0.8374 (pp20) REVERT: A 1042 LEU cc_start: 0.9642 (OUTLIER) cc_final: 0.9365 (tm) REVERT: A 1060 MET cc_start: 0.7437 (pp-130) cc_final: 0.7185 (ttp) REVERT: A 1066 ARG cc_start: 0.9129 (ttt-90) cc_final: 0.8907 (ttt180) REVERT: A 1111 GLU cc_start: 0.9365 (OUTLIER) cc_final: 0.9156 (pm20) REVERT: B 524 GLU cc_start: 0.9114 (OUTLIER) cc_final: 0.8842 (pp20) REVERT: B 749 MET cc_start: 0.9458 (mmm) cc_final: 0.9250 (mmp) REVERT: B 957 MET cc_start: 0.9207 (mmm) cc_final: 0.8480 (mpp) REVERT: B 1094 PHE cc_start: 0.7959 (m-80) cc_final: 0.7172 (m-80) REVERT: B 1151 ARG cc_start: 0.9457 (OUTLIER) cc_final: 0.9106 (mmm160) outliers start: 30 outliers final: 16 residues processed: 91 average time/residue: 1.3117 time to fit residues: 131.8803 Evaluate side-chains 81 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 61 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 797 SER Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 929 ARG Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 1118 LEU Chi-restraints excluded: chain B residue 1151 ARG Chi-restraints excluded: chain B residue 1169 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 101 optimal weight: 0.9980 chunk 53 optimal weight: 0.0370 chunk 83 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 143 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 35 optimal weight: 0.0970 chunk 77 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 overall best weight: 0.5856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 915 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.063725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.045018 restraints weight = 38910.979| |-----------------------------------------------------------------------------| r_work (start): 0.2751 rms_B_bonded: 3.45 r_work: 0.2589 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 12532 Z= 0.110 Angle : 0.556 10.708 16932 Z= 0.281 Chirality : 0.041 0.192 1830 Planarity : 0.003 0.034 2166 Dihedral : 5.219 69.671 1687 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.89 % Allowed : 21.06 % Favored : 77.05 % 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: 0.46 (0.22), residues: 1502 helix: 1.52 (0.21), residues: 664 sheet: -0.30 (0.41), residues: 176 loop : -0.76 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1189 HIS 0.006 0.001 HIS B 892 PHE 0.008 0.001 PHE A 559 TYR 0.010 0.001 TYR B 520 ARG 0.005 0.000 ARG A1141 Details of bonding type rmsd hydrogen bonds : bond 0.02824 ( 574) hydrogen bonds : angle 4.25877 ( 1623) covalent geometry : bond 0.00250 (12532) covalent geometry : angle 0.55618 (16932) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 63 time to evaluate : 1.542 Fit side-chains REVERT: A 662 ARG cc_start: 0.8335 (tmm160) cc_final: 0.8067 (tmm160) REVERT: A 994 GLU cc_start: 0.8561 (tm-30) cc_final: 0.8272 (pp20) REVERT: A 1042 LEU cc_start: 0.9627 (OUTLIER) cc_final: 0.9339 (tm) REVERT: A 1066 ARG cc_start: 0.9138 (ttt-90) cc_final: 0.8781 (ttt-90) REVERT: A 1111 GLU cc_start: 0.9371 (OUTLIER) cc_final: 0.9157 (pm20) REVERT: A 1131 ARG cc_start: 0.8806 (tpm-80) cc_final: 0.8378 (tpm170) REVERT: B 524 GLU cc_start: 0.9130 (OUTLIER) cc_final: 0.8875 (pp20) REVERT: B 929 ARG cc_start: 0.9228 (OUTLIER) cc_final: 0.8744 (ptm-80) REVERT: B 957 MET cc_start: 0.9216 (mmm) cc_final: 0.8376 (mpp) REVERT: B 1094 PHE cc_start: 0.8028 (m-80) cc_final: 0.7269 (m-80) REVERT: B 1151 ARG cc_start: 0.9461 (OUTLIER) cc_final: 0.9226 (tmt-80) outliers start: 25 outliers final: 14 residues processed: 86 average time/residue: 1.4091 time to fit residues: 132.8307 Evaluate side-chains 80 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 61 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 797 SER Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 929 ARG Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 1118 LEU Chi-restraints excluded: chain B residue 1151 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 84 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 56 optimal weight: 0.0670 chunk 54 optimal weight: 0.7980 chunk 8 optimal weight: 9.9990 chunk 29 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 915 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.063878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.045089 restraints weight = 38896.061| |-----------------------------------------------------------------------------| r_work (start): 0.2755 rms_B_bonded: 3.46 r_work: 0.2595 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12532 Z= 0.113 Angle : 0.564 12.678 16932 Z= 0.281 Chirality : 0.041 0.172 1830 Planarity : 0.003 0.034 2166 Dihedral : 5.172 71.522 1687 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.89 % Allowed : 21.29 % Favored : 76.82 % 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: 0.47 (0.22), residues: 1502 helix: 1.53 (0.21), residues: 664 sheet: -0.31 (0.41), residues: 176 loop : -0.75 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1189 HIS 0.005 0.001 HIS B 892 PHE 0.008 0.001 PHE A 559 TYR 0.012 0.001 TYR A1043 ARG 0.005 0.000 ARG A1141 Details of bonding type rmsd hydrogen bonds : bond 0.02788 ( 574) hydrogen bonds : angle 4.20020 ( 1623) covalent geometry : bond 0.00259 (12532) covalent geometry : angle 0.56388 (16932) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 61 time to evaluate : 1.431 Fit side-chains REVERT: A 662 ARG cc_start: 0.8394 (tmm160) cc_final: 0.8089 (tmm160) REVERT: A 970 GLU cc_start: 0.9180 (mt-10) cc_final: 0.8956 (mm-30) REVERT: A 994 GLU cc_start: 0.8545 (tm-30) cc_final: 0.8246 (pp20) REVERT: A 1042 LEU cc_start: 0.9622 (OUTLIER) cc_final: 0.9333 (tm) REVERT: A 1066 ARG cc_start: 0.9136 (ttt-90) cc_final: 0.8773 (ttt-90) REVERT: A 1076 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8260 (mp) REVERT: A 1111 GLU cc_start: 0.9373 (OUTLIER) cc_final: 0.9144 (pm20) REVERT: A 1131 ARG cc_start: 0.8859 (tpm-80) cc_final: 0.8460 (tpm170) REVERT: B 524 GLU cc_start: 0.9130 (OUTLIER) cc_final: 0.8872 (pp20) REVERT: B 957 MET cc_start: 0.9223 (mmm) cc_final: 0.8391 (mpp) REVERT: B 1094 PHE cc_start: 0.8030 (m-80) cc_final: 0.7253 (m-80) REVERT: B 1151 ARG cc_start: 0.9457 (OUTLIER) cc_final: 0.9220 (tmt-80) outliers start: 25 outliers final: 12 residues processed: 83 average time/residue: 1.2450 time to fit residues: 113.4591 Evaluate side-chains 77 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 797 SER Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 1151 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 119 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 64 optimal weight: 30.0000 chunk 84 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 915 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.061058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.042336 restraints weight = 39020.291| |-----------------------------------------------------------------------------| r_work (start): 0.2675 rms_B_bonded: 3.39 r_work: 0.2510 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 12532 Z= 0.260 Angle : 0.643 13.424 16932 Z= 0.323 Chirality : 0.044 0.191 1830 Planarity : 0.004 0.034 2166 Dihedral : 5.285 61.504 1687 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.67 % Allowed : 21.52 % Favored : 76.82 % 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: 0.35 (0.22), residues: 1502 helix: 1.34 (0.21), residues: 674 sheet: -0.39 (0.41), residues: 176 loop : -0.72 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 820 HIS 0.005 0.001 HIS B 789 PHE 0.010 0.001 PHE A 629 TYR 0.016 0.001 TYR B 520 ARG 0.005 0.000 ARG A1141 Details of bonding type rmsd hydrogen bonds : bond 0.03459 ( 574) hydrogen bonds : angle 4.51381 ( 1623) covalent geometry : bond 0.00606 (12532) covalent geometry : angle 0.64298 (16932) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3004 Ramachandran restraints generated. 1502 Oldfield, 0 Emsley, 1502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 62 time to evaluate : 1.524 Fit side-chains REVERT: A 662 ARG cc_start: 0.8407 (tmm160) cc_final: 0.8097 (tmm160) REVERT: A 994 GLU cc_start: 0.8688 (tm-30) cc_final: 0.8432 (pp20) REVERT: A 1042 LEU cc_start: 0.9630 (OUTLIER) cc_final: 0.9340 (tm) REVERT: A 1066 ARG cc_start: 0.9099 (ttt-90) cc_final: 0.8825 (ttt180) REVERT: A 1076 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8361 (mp) REVERT: A 1111 GLU cc_start: 0.9373 (OUTLIER) cc_final: 0.9159 (pm20) REVERT: A 1131 ARG cc_start: 0.8874 (tpm-80) cc_final: 0.8449 (tpm170) REVERT: B 957 MET cc_start: 0.9181 (mmm) cc_final: 0.8318 (mpp) REVERT: B 1094 PHE cc_start: 0.7979 (m-80) cc_final: 0.7131 (m-80) outliers start: 22 outliers final: 13 residues processed: 83 average time/residue: 1.3817 time to fit residues: 125.4976 Evaluate side-chains 77 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 586 VAL Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 797 SER Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 976 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 4 optimal weight: 0.3980 chunk 82 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 110 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 148 optimal weight: 0.8980 chunk 140 optimal weight: 7.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 915 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.063090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.044579 restraints weight = 38751.777| |-----------------------------------------------------------------------------| r_work (start): 0.2740 rms_B_bonded: 3.40 r_work: 0.2581 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 12532 Z= 0.122 Angle : 0.595 13.114 16932 Z= 0.296 Chirality : 0.042 0.213 1830 Planarity : 0.003 0.034 2166 Dihedral : 5.105 66.907 1687 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.21 % Allowed : 21.89 % Favored : 76.89 % 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: 0.37 (0.22), residues: 1502 helix: 1.42 (0.21), residues: 666 sheet: -0.41 (0.41), residues: 176 loop : -0.74 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1189 HIS 0.005 0.001 HIS B 892 PHE 0.008 0.001 PHE A 559 TYR 0.009 0.001 TYR B 520 ARG 0.005 0.000 ARG A1141 Details of bonding type rmsd hydrogen bonds : bond 0.02918 ( 574) hydrogen bonds : angle 4.32248 ( 1623) covalent geometry : bond 0.00282 (12532) covalent geometry : angle 0.59482 (16932) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7181.72 seconds wall clock time: 125 minutes 36.31 seconds (7536.31 seconds total)