Starting phenix.real_space_refine on Thu Sep 26 07:00:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ygh_39250/09_2024/8ygh_39250.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ygh_39250/09_2024/8ygh_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ygh_39250/09_2024/8ygh_39250.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ygh_39250/09_2024/8ygh_39250.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ygh_39250/09_2024/8ygh_39250.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ygh_39250/09_2024/8ygh_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-5461/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: 7.47, per 1000 atoms: 0.61 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: 3.18 Conformation dependent library (CDL) restraints added in 1.6 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: 1.47 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: 3.96 Time building geometry restraints manager: 3.70 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 30.010 Find NCS groups from input model: 0.320 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: 0.010 Load rotamer database and sin/cos tables:13.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.520 ------------------------------------------------------------------------------- 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= 0.180 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 *********************** 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 fitting. rotamer outliers: 23 poor density : 70 time to evaluate : 1.595 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: 1.2939 time to fit residues: 128.7920 Evaluate side-chains 82 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 66 time to evaluate : 1.475 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 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= 0.262 Angle : 0.542 7.888 16932 Z= 0.285 Chirality : 0.042 0.170 1830 Planarity : 0.004 0.047 2166 Dihedral : 5.618 68.139 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 *********************** 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 fitting. rotamer outliers: 41 poor density : 67 time to evaluate : 1.497 Fit side-chains REVERT: A 1066 ARG cc_start: 0.9031 (ttt-90) cc_final: 0.8814 (ttt180) REVERT: B 688 SER cc_start: 0.9372 (OUTLIER) cc_final: 0.9017 (m) REVERT: B 929 ARG cc_start: 0.9232 (ptm-80) cc_final: 0.8804 (ptm-80) REVERT: B 957 MET cc_start: 0.9153 (mmm) cc_final: 0.8302 (mpp) outliers start: 41 outliers final: 15 residues processed: 100 average time/residue: 1.2357 time to fit residues: 136.1186 Evaluate side-chains 74 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 58 time to evaluate : 1.563 ------------------------------------------------------------------------------- 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 75 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 92 optimal weight: 0.0050 chunk 37 optimal weight: 0.1980 chunk 136 optimal weight: 0.8980 chunk 147 optimal weight: 0.0980 chunk 121 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 12532 Z= 0.154 Angle : 0.512 7.387 16932 Z= 0.265 Chirality : 0.040 0.149 1830 Planarity : 0.003 0.042 2166 Dihedral : 5.432 69.941 1689 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.65 % Allowed : 17.65 % Favored : 79.70 % 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: 1.51 (0.21), residues: 660 sheet: -0.53 (0.39), residues: 188 loop : -0.71 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1189 HIS 0.002 0.000 HIS B1092 PHE 0.008 0.001 PHE B 632 TYR 0.010 0.001 TYR B 520 ARG 0.011 0.000 ARG B1131 *********************** 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 99 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 64 time to evaluate : 1.449 Fit side-chains REVERT: A 1066 ARG cc_start: 0.9066 (ttt-90) cc_final: 0.8725 (ttt180) REVERT: B 524 GLU cc_start: 0.9010 (OUTLIER) cc_final: 0.8702 (pp20) REVERT: B 688 SER cc_start: 0.9389 (OUTLIER) cc_final: 0.9112 (m) REVERT: B 749 MET cc_start: 0.9390 (mmm) cc_final: 0.9163 (mmp) REVERT: B 957 MET cc_start: 0.9190 (mmm) cc_final: 0.8278 (mpp) outliers start: 35 outliers final: 13 residues processed: 93 average time/residue: 1.3440 time to fit residues: 136.2852 Evaluate side-chains 77 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 62 time to evaluate : 1.585 ------------------------------------------------------------------------------- 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 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 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 134 optimal weight: 0.0670 chunk 102 optimal weight: 0.0970 chunk 70 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 65 optimal weight: 30.0000 chunk 91 optimal weight: 8.9990 chunk 136 optimal weight: 5.9990 chunk 144 optimal weight: 8.9990 chunk 71 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 overall best weight: 1.8322 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.1370 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= 0.291 Angle : 0.557 8.651 16932 Z= 0.288 Chirality : 0.042 0.152 1830 Planarity : 0.003 0.039 2166 Dihedral : 5.308 65.048 1688 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.89 % Allowed : 18.86 % Favored : 79.24 % 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: 674 sheet: -0.33 (0.41), residues: 176 loop : -0.77 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1189 HIS 0.004 0.001 HIS B 892 PHE 0.009 0.001 PHE B 596 TYR 0.012 0.001 TYR B 520 ARG 0.007 0.000 ARG B1140 *********************** 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 91 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 66 time to evaluate : 1.160 Fit side-chains REVERT: A 994 GLU cc_start: 0.8453 (tm-30) cc_final: 0.8222 (pp20) REVERT: A 1042 LEU cc_start: 0.9636 (OUTLIER) cc_final: 0.9412 (tm) REVERT: A 1066 ARG cc_start: 0.9085 (ttt-90) cc_final: 0.8852 (ttt180) REVERT: A 1111 GLU cc_start: 0.9342 (OUTLIER) cc_final: 0.9095 (pm20) REVERT: B 749 MET cc_start: 0.9466 (mmm) cc_final: 0.9134 (mmp) REVERT: B 957 MET cc_start: 0.9223 (mmm) cc_final: 0.8360 (mpp) REVERT: B 1094 PHE cc_start: 0.7916 (m-80) cc_final: 0.7593 (m-80) outliers start: 25 outliers final: 15 residues processed: 89 average time/residue: 1.1597 time to fit residues: 112.7411 Evaluate side-chains 75 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 58 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 659 LEU 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 1111 GLU 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 1118 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 123 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 74 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 915 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12532 Z= 0.188 Angle : 0.542 8.695 16932 Z= 0.276 Chirality : 0.041 0.175 1830 Planarity : 0.003 0.038 2166 Dihedral : 5.246 67.018 1687 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.12 % Allowed : 18.94 % Favored : 78.94 % 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: 0.41 (0.22), residues: 1502 helix: 1.49 (0.21), residues: 666 sheet: -0.29 (0.41), residues: 176 loop : -0.81 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1189 HIS 0.002 0.001 HIS B 789 PHE 0.008 0.001 PHE A 710 TYR 0.011 0.001 TYR B 520 ARG 0.013 0.000 ARG B1131 *********************** 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 94 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 66 time to evaluate : 1.455 Fit side-chains REVERT: A 662 ARG cc_start: 0.8234 (tmm160) cc_final: 0.7990 (tmm160) REVERT: A 994 GLU cc_start: 0.8448 (tm-30) cc_final: 0.8220 (pp20) REVERT: A 1042 LEU cc_start: 0.9607 (OUTLIER) cc_final: 0.9388 (tm) REVERT: B 524 GLU cc_start: 0.9031 (OUTLIER) cc_final: 0.8755 (pp20) REVERT: B 749 MET cc_start: 0.9389 (mmm) cc_final: 0.9096 (mmp) REVERT: B 957 MET cc_start: 0.9228 (mmm) cc_final: 0.8358 (mpp) REVERT: B 1094 PHE cc_start: 0.8035 (m-80) cc_final: 0.7702 (m-80) REVERT: B 1151 ARG cc_start: 0.9492 (OUTLIER) cc_final: 0.9272 (tmt-80) outliers start: 28 outliers final: 16 residues processed: 90 average time/residue: 1.1294 time to fit residues: 110.8570 Evaluate side-chains 83 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 64 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 845 ILE 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 524 GLU Chi-restraints excluded: chain B residue 534 ILE 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 1151 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 85 optimal weight: 0.0060 chunk 35 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 76 optimal weight: 6.9990 chunk 139 optimal weight: 0.4980 overall best weight: 0.5596 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 12532 Z= 0.155 Angle : 0.530 9.067 16932 Z= 0.270 Chirality : 0.040 0.161 1830 Planarity : 0.003 0.036 2166 Dihedral : 5.202 71.023 1687 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.50 % Allowed : 19.70 % Favored : 77.80 % 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: 0.48 (0.22), residues: 1502 helix: 1.56 (0.21), residues: 664 sheet: -0.25 (0.41), residues: 176 loop : -0.79 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1189 HIS 0.002 0.000 HIS B 892 PHE 0.008 0.001 PHE A 559 TYR 0.010 0.001 TYR B 520 ARG 0.008 0.000 ARG B 662 *********************** 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 106 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 73 time to evaluate : 1.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 662 ARG cc_start: 0.8258 (tmm160) cc_final: 0.7926 (tmm160) REVERT: A 991 LYS cc_start: 0.8776 (mmmt) cc_final: 0.8572 (mmmt) REVERT: A 994 GLU cc_start: 0.8443 (tm-30) cc_final: 0.8166 (pp20) REVERT: A 1042 LEU cc_start: 0.9608 (OUTLIER) cc_final: 0.9380 (tm) REVERT: A 1111 GLU cc_start: 0.9334 (OUTLIER) cc_final: 0.9111 (pm20) REVERT: B 524 GLU cc_start: 0.9073 (OUTLIER) cc_final: 0.8797 (pp20) REVERT: B 749 MET cc_start: 0.9349 (mmm) cc_final: 0.8980 (mmp) REVERT: B 929 ARG cc_start: 0.9206 (OUTLIER) cc_final: 0.8590 (ptm-80) REVERT: B 957 MET cc_start: 0.9241 (mmm) cc_final: 0.8363 (mpp) REVERT: B 1151 ARG cc_start: 0.9495 (OUTLIER) cc_final: 0.9268 (tmt-80) outliers start: 33 outliers final: 18 residues processed: 103 average time/residue: 1.4213 time to fit residues: 159.1070 Evaluate side-chains 85 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 62 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 845 ILE 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 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 714 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 0.0010 chunk 82 optimal weight: 0.5980 chunk 105 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 144 optimal weight: 10.0000 chunk 90 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 overall best weight: 0.8988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12532 Z= 0.191 Angle : 0.558 9.553 16932 Z= 0.283 Chirality : 0.041 0.167 1830 Planarity : 0.004 0.055 2166 Dihedral : 5.194 70.832 1687 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.20 % Allowed : 21.06 % Favored : 76.74 % 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: 0.49 (0.22), residues: 1502 helix: 1.63 (0.21), residues: 656 sheet: -0.44 (0.39), residues: 188 loop : -0.76 (0.24), residues: 658 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 0.011 0.001 TYR B 520 ARG 0.015 0.000 ARG B1131 *********************** 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 fitting. rotamer outliers: 29 poor density : 66 time to evaluate : 1.633 Fit side-chains revert: symmetry clash REVERT: A 662 ARG cc_start: 0.8304 (tmm160) cc_final: 0.7957 (tmm160) REVERT: A 991 LYS cc_start: 0.8782 (mmmt) cc_final: 0.8573 (mmmt) REVERT: A 994 GLU cc_start: 0.8461 (tm-30) cc_final: 0.8190 (pp20) REVERT: A 1042 LEU cc_start: 0.9611 (OUTLIER) cc_final: 0.9367 (tm) REVERT: A 1066 ARG cc_start: 0.9116 (ttt180) cc_final: 0.8873 (ttt180) REVERT: A 1111 GLU cc_start: 0.9335 (OUTLIER) cc_final: 0.9102 (pm20) REVERT: B 524 GLU cc_start: 0.9063 (OUTLIER) cc_final: 0.8780 (pp20) REVERT: B 749 MET cc_start: 0.9379 (mmm) cc_final: 0.9075 (mmp) REVERT: B 929 ARG cc_start: 0.9192 (OUTLIER) cc_final: 0.8601 (ptm-80) REVERT: B 957 MET cc_start: 0.9250 (mmm) cc_final: 0.8448 (mpp) REVERT: B 1094 PHE cc_start: 0.8113 (m-80) cc_final: 0.7194 (m-80) REVERT: B 1151 ARG cc_start: 0.9493 (OUTLIER) cc_final: 0.9272 (tmt-80) outliers start: 29 outliers final: 17 residues processed: 91 average time/residue: 1.2809 time to fit residues: 127.5655 Evaluate side-chains 84 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 62 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 845 ILE 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 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 931 MET Chi-restraints excluded: chain B residue 1118 LEU Chi-restraints excluded: chain B residue 1151 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 91 optimal weight: 7.9990 chunk 98 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 chunk 138 optimal weight: 10.0000 chunk 126 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12532 Z= 0.188 Angle : 0.559 10.034 16932 Z= 0.281 Chirality : 0.041 0.163 1830 Planarity : 0.003 0.034 2166 Dihedral : 5.154 70.542 1687 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.97 % Allowed : 21.36 % Favored : 76.67 % 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: 0.50 (0.22), residues: 1502 helix: 1.57 (0.21), residues: 664 sheet: -0.24 (0.41), residues: 176 loop : -0.77 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1189 HIS 0.004 0.001 HIS B 892 PHE 0.008 0.001 PHE A 559 TYR 0.011 0.001 TYR A1043 ARG 0.006 0.000 ARG A1141 *********************** 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 fitting. rotamer outliers: 26 poor density : 62 time to evaluate : 1.563 Fit side-chains REVERT: A 662 ARG cc_start: 0.8343 (tmm160) cc_final: 0.8036 (tmm160) REVERT: A 991 LYS cc_start: 0.8782 (mmmt) cc_final: 0.8568 (mmmt) REVERT: A 994 GLU cc_start: 0.8462 (tm-30) cc_final: 0.8168 (pp20) REVERT: A 1042 LEU cc_start: 0.9609 (OUTLIER) cc_final: 0.9362 (tm) REVERT: A 1066 ARG cc_start: 0.9125 (ttt180) cc_final: 0.8876 (ttt180) REVERT: A 1111 GLU cc_start: 0.9331 (OUTLIER) cc_final: 0.9114 (pm20) REVERT: B 749 MET cc_start: 0.9387 (mmm) cc_final: 0.9064 (mmp) REVERT: B 929 ARG cc_start: 0.9204 (OUTLIER) cc_final: 0.8356 (ptm-80) REVERT: B 931 MET cc_start: 0.9041 (OUTLIER) cc_final: 0.7715 (ttt) REVERT: B 957 MET cc_start: 0.9253 (mmm) cc_final: 0.8441 (mpp) REVERT: B 1094 PHE cc_start: 0.8140 (m-80) cc_final: 0.7219 (m-80) REVERT: B 1151 ARG cc_start: 0.9491 (OUTLIER) cc_final: 0.9264 (tmt-80) outliers start: 26 outliers final: 16 residues processed: 84 average time/residue: 1.2862 time to fit residues: 118.6169 Evaluate side-chains 81 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 60 time to evaluate : 1.441 ------------------------------------------------------------------------------- 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 822 LEU Chi-restraints excluded: chain A residue 845 ILE 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 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 931 MET Chi-restraints excluded: chain B residue 964 VAL 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 134 optimal weight: 4.9990 chunk 138 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 121 optimal weight: 9.9990 chunk 127 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 12532 Z= 0.354 Angle : 0.616 11.830 16932 Z= 0.313 Chirality : 0.043 0.174 1830 Planarity : 0.004 0.034 2166 Dihedral : 5.261 61.668 1687 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.74 % Allowed : 21.74 % Favored : 76.52 % 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: 0.38 (0.22), residues: 1502 helix: 1.39 (0.21), residues: 674 sheet: -0.33 (0.41), residues: 176 loop : -0.76 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 820 HIS 0.004 0.001 HIS B 789 PHE 0.010 0.001 PHE A 629 TYR 0.015 0.001 TYR B 520 ARG 0.005 0.000 ARG A1141 *********************** 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 fitting. rotamer outliers: 23 poor density : 63 time to evaluate : 1.713 Fit side-chains revert: symmetry clash REVERT: A 662 ARG cc_start: 0.8355 (tmm160) cc_final: 0.8044 (tmm160) REVERT: A 994 GLU cc_start: 0.8594 (tm-30) cc_final: 0.8289 (pp20) REVERT: A 1042 LEU cc_start: 0.9611 (OUTLIER) cc_final: 0.9340 (tm) REVERT: A 1131 ARG cc_start: 0.8783 (tpm-80) cc_final: 0.8327 (tpm170) REVERT: B 957 MET cc_start: 0.9237 (mmm) cc_final: 0.8427 (mpp) REVERT: B 1066 ARG cc_start: 0.9068 (ttt90) cc_final: 0.8685 (ttt90) REVERT: B 1094 PHE cc_start: 0.8148 (m-80) cc_final: 0.7180 (m-80) outliers start: 23 outliers final: 14 residues processed: 82 average time/residue: 1.3944 time to fit residues: 124.9305 Evaluate side-chains 77 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 62 time to evaluate : 1.332 ------------------------------------------------------------------------------- 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 845 ILE Chi-restraints excluded: chain A residue 1042 LEU 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 929 ARG Chi-restraints excluded: chain B residue 964 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 149 optimal weight: 0.8980 chunk 137 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 12 optimal weight: 0.0070 chunk 91 optimal weight: 4.9990 chunk 72 optimal weight: 0.3980 chunk 94 optimal weight: 0.6980 chunk 126 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.5598 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 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 : 0.003 0.047 12532 Z= 0.169 Angle : 0.587 12.283 16932 Z= 0.291 Chirality : 0.041 0.189 1830 Planarity : 0.003 0.057 2166 Dihedral : 5.087 68.284 1687 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.29 % Allowed : 22.12 % Favored : 76.59 % 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: 0.43 (0.22), residues: 1502 helix: 1.50 (0.21), residues: 664 sheet: -0.30 (0.41), residues: 176 loop : -0.77 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1189 HIS 0.004 0.001 HIS B 892 PHE 0.008 0.001 PHE A 559 TYR 0.010 0.001 TYR B 888 ARG 0.015 0.000 ARG B1131 ********************** 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 81 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 64 time to evaluate : 1.515 Fit side-chains revert: symmetry clash REVERT: A 662 ARG cc_start: 0.8393 (tmm160) cc_final: 0.8059 (tmm160) REVERT: A 994 GLU cc_start: 0.8485 (tm-30) cc_final: 0.8183 (pp20) REVERT: A 1076 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8274 (mp) REVERT: A 1131 ARG cc_start: 0.8721 (tpm-80) cc_final: 0.8255 (tpm170) REVERT: B 524 GLU cc_start: 0.9087 (OUTLIER) cc_final: 0.8848 (pp20) REVERT: B 749 MET cc_start: 0.9421 (mmm) cc_final: 0.9011 (mmp) REVERT: B 957 MET cc_start: 0.9237 (mmm) cc_final: 0.8534 (mpp) outliers start: 17 outliers final: 13 residues processed: 80 average time/residue: 1.3342 time to fit residues: 116.7171 Evaluate side-chains 74 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 59 time to evaluate : 1.448 ------------------------------------------------------------------------------- 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 845 ILE Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain B residue 524 GLU 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 1118 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 33 optimal weight: 0.0270 chunk 119 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 21 optimal weight: 0.5980 chunk 104 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 86 optimal weight: 5.9990 overall best weight: 1.6642 ------------------------------------------------------------------------------- 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 = 0.3214 r_free = 0.3214 target = 0.062269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.043521 restraints weight = 38687.835| |-----------------------------------------------------------------------------| r_work (start): 0.2710 rms_B_bonded: 3.42 r_work: 0.2549 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 12532 Z= 0.275 Angle : 0.620 13.140 16932 Z= 0.310 Chirality : 0.043 0.183 1830 Planarity : 0.003 0.034 2166 Dihedral : 5.106 65.741 1687 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.21 % Allowed : 22.35 % Favored : 76.44 % 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: 0.38 (0.22), residues: 1502 helix: 1.42 (0.21), residues: 666 sheet: -0.35 (0.41), residues: 176 loop : -0.75 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1189 HIS 0.006 0.001 HIS B 892 PHE 0.008 0.001 PHE B 596 TYR 0.019 0.001 TYR A1043 ARG 0.005 0.000 ARG A1141 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3230.62 seconds wall clock time: 58 minutes 50.23 seconds (3530.23 seconds total)