Starting phenix.real_space_refine on Thu Sep 18 00:07:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ygh_39250/09_2025/8ygh_39250.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ygh_39250/09_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_39250/09_2025/8ygh_39250.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ygh_39250/09_2025/8ygh_39250.map" model { file = "/net/cci-nas-00/data/ceres_data/8ygh_39250/09_2025/8ygh_39250.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ygh_39250/09_2025/8ygh_39250.cif" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.88, per 1000 atoms: 0.24 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: 0.98 Conformation dependent library (CDL) restraints added in 586.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.49 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: 2.17 Time building geometry restraints manager: 1.33 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: 0.02 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: 1.170 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: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.430 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 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:6.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.480 ------------------------------------------------------------------------------- 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 : 9.89 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.018 0.000 ARG B1131 TYR 0.007 0.001 TYR B 520 PHE 0.011 0.001 PHE B 629 TRP 0.004 0.001 TRP A1189 HIS 0.003 0.000 HIS A 690 Details of bonding type rmsd covalent geometry : bond 0.00274 (12532) covalent geometry : angle 0.64409 (16932) hydrogen bonds : bond 0.13210 ( 574) hydrogen bonds : angle 5.69296 ( 1623) *********************** 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 : 0.541 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: 0.6733 time to fit residues: 66.5064 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 : 0.476 ------------------------------------------------------------------------------- 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 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.0470 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.0270 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.1940 ------------------------------------------------------------------------------- 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 = 0.063941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.045024 restraints weight = 38503.266| |-----------------------------------------------------------------------------| r_work (start): 0.2753 rms_B_bonded: 3.45 r_work: 0.2595 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.0919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 12532 Z= 0.142 Angle : 0.528 8.052 16932 Z= 0.277 Chirality : 0.041 0.165 1830 Planarity : 0.003 0.047 2166 Dihedral : 5.581 70.196 1698 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.26 % Allowed : 16.67 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.22), residues: 1502 helix: 1.52 (0.21), residues: 664 sheet: -0.49 (0.39), residues: 188 loop : -0.68 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 734 TYR 0.010 0.001 TYR B 520 PHE 0.010 0.001 PHE B1094 TRP 0.008 0.001 TRP B 820 HIS 0.004 0.001 HIS B 789 Details of bonding type rmsd covalent geometry : bond 0.00326 (12532) covalent geometry : angle 0.52815 (16932) hydrogen bonds : bond 0.03224 ( 574) hydrogen bonds : angle 4.56289 ( 1623) *********************** 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 110 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 67 time to evaluate : 0.502 Fit side-chains REVERT: A 1066 ARG cc_start: 0.9103 (ttt-90) cc_final: 0.8714 (ttt-90) REVERT: B 688 SER cc_start: 0.9343 (OUTLIER) cc_final: 0.9005 (m) REVERT: B 929 ARG cc_start: 0.9336 (ptm-80) cc_final: 0.9119 (ptm-80) REVERT: B 948 GLU cc_start: 0.8939 (pp20) cc_final: 0.8681 (pp20) REVERT: B 957 MET cc_start: 0.9123 (mmm) cc_final: 0.8250 (mpp) REVERT: B 1066 ARG cc_start: 0.9240 (ttt90) cc_final: 0.8955 (ttp-170) outliers start: 43 outliers final: 15 residues processed: 101 average time/residue: 0.6238 time to fit residues: 68.8440 Evaluate side-chains 75 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 0.537 ------------------------------------------------------------------------------- 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 1169 VAL 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 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 136 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 83 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 80 optimal weight: 6.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.063041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.044209 restraints weight = 39160.982| |-----------------------------------------------------------------------------| r_work (start): 0.2730 rms_B_bonded: 3.44 r_work: 0.2569 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 12532 Z= 0.152 Angle : 0.526 7.352 16932 Z= 0.274 Chirality : 0.041 0.148 1830 Planarity : 0.003 0.042 2166 Dihedral : 5.319 67.295 1688 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.65 % Allowed : 17.73 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.22), residues: 1502 helix: 1.55 (0.21), residues: 660 sheet: -0.53 (0.40), residues: 188 loop : -0.74 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B1131 TYR 0.011 0.001 TYR B 520 PHE 0.008 0.001 PHE B 632 TRP 0.008 0.001 TRP A1189 HIS 0.003 0.001 HIS A 690 Details of bonding type rmsd covalent geometry : bond 0.00349 (12532) covalent geometry : angle 0.52616 (16932) hydrogen bonds : bond 0.03184 ( 574) hydrogen bonds : angle 4.45625 ( 1623) *********************** 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 100 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 65 time to evaluate : 0.590 Fit side-chains REVERT: A 1066 ARG cc_start: 0.9108 (ttt-90) cc_final: 0.8767 (ttt-90) REVERT: B 524 GLU cc_start: 0.9046 (OUTLIER) cc_final: 0.8713 (pp20) REVERT: B 688 SER cc_start: 0.9325 (OUTLIER) cc_final: 0.9027 (m) REVERT: B 749 MET cc_start: 0.9436 (mmm) cc_final: 0.9155 (mmp) REVERT: B 957 MET cc_start: 0.9150 (mmm) cc_final: 0.8295 (mpp) outliers start: 35 outliers final: 15 residues processed: 94 average time/residue: 0.6790 time to fit residues: 69.2064 Evaluate side-chains 75 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 0.507 ------------------------------------------------------------------------------- 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 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 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 62 optimal weight: 0.9980 chunk 47 optimal weight: 7.9990 chunk 130 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 chunk 118 optimal weight: 0.7980 chunk 5 optimal weight: 7.9990 chunk 142 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 915 GLN B1010 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.062634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.043852 restraints weight = 38951.419| |-----------------------------------------------------------------------------| r_work (start): 0.2716 rms_B_bonded: 3.42 r_work: 0.2553 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 12532 Z= 0.169 Angle : 0.546 7.953 16932 Z= 0.282 Chirality : 0.042 0.148 1830 Planarity : 0.003 0.040 2166 Dihedral : 5.274 65.505 1688 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.89 % Allowed : 18.64 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.22), residues: 1502 helix: 1.50 (0.21), residues: 664 sheet: -0.49 (0.40), residues: 188 loop : -0.71 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1140 TYR 0.012 0.001 TYR B 520 PHE 0.008 0.001 PHE B 596 TRP 0.009 0.001 TRP A1189 HIS 0.004 0.001 HIS B 892 Details of bonding type rmsd covalent geometry : bond 0.00390 (12532) covalent geometry : angle 0.54611 (16932) hydrogen bonds : bond 0.03163 ( 574) hydrogen bonds : angle 4.43854 ( 1623) *********************** 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 90 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 65 time to evaluate : 0.554 Fit side-chains REVERT: A 994 GLU cc_start: 0.8539 (tm-30) cc_final: 0.8308 (pp20) REVERT: A 1042 LEU cc_start: 0.9650 (OUTLIER) cc_final: 0.9413 (tm) REVERT: A 1066 ARG cc_start: 0.9136 (ttt-90) cc_final: 0.8914 (ttt180) REVERT: B 749 MET cc_start: 0.9443 (mmm) cc_final: 0.9115 (mmp) REVERT: B 929 ARG cc_start: 0.9366 (OUTLIER) cc_final: 0.9026 (ptm-80) REVERT: B 931 MET cc_start: 0.8883 (ttt) cc_final: 0.8670 (ttt) REVERT: B 957 MET cc_start: 0.9182 (mmm) cc_final: 0.8291 (mpp) REVERT: B 1094 PHE cc_start: 0.7931 (m-80) cc_final: 0.7609 (m-80) outliers start: 25 outliers final: 16 residues processed: 86 average time/residue: 0.7273 time to fit residues: 67.7472 Evaluate side-chains 76 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.507 ------------------------------------------------------------------------------- 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 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 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 929 ARG 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 73 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 141 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3241 r_free = 0.3241 target = 0.063455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.044777 restraints weight = 38888.811| |-----------------------------------------------------------------------------| r_work (start): 0.2742 rms_B_bonded: 3.43 r_work: 0.2587 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1294 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= 0.119 Angle : 0.542 9.363 16932 Z= 0.275 Chirality : 0.041 0.169 1830 Planarity : 0.003 0.037 2166 Dihedral : 5.232 67.913 1687 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.20 % Allowed : 19.17 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.22), residues: 1502 helix: 1.59 (0.21), residues: 658 sheet: -0.47 (0.40), residues: 188 loop : -0.76 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B1131 TYR 0.010 0.001 TYR B 520 PHE 0.008 0.001 PHE A 710 TRP 0.008 0.001 TRP A1189 HIS 0.002 0.001 HIS B 789 Details of bonding type rmsd covalent geometry : bond 0.00272 (12532) covalent geometry : angle 0.54167 (16932) hydrogen bonds : bond 0.02923 ( 574) hydrogen bonds : angle 4.32113 ( 1623) *********************** 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 95 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 66 time to evaluate : 0.654 Fit side-chains REVERT: A 994 GLU cc_start: 0.8532 (tm-30) cc_final: 0.8280 (pp20) REVERT: A 1042 LEU cc_start: 0.9632 (OUTLIER) cc_final: 0.9396 (tm) REVERT: A 1111 GLU cc_start: 0.9381 (OUTLIER) cc_final: 0.9160 (pm20) REVERT: B 524 GLU cc_start: 0.9075 (OUTLIER) cc_final: 0.8825 (pp20) REVERT: B 749 MET cc_start: 0.9384 (mmm) cc_final: 0.9130 (mmp) REVERT: B 957 MET cc_start: 0.9202 (mmm) cc_final: 0.8304 (mpp) REVERT: B 1066 ARG cc_start: 0.9131 (ttt90) cc_final: 0.8808 (ttt90) REVERT: B 1094 PHE cc_start: 0.8025 (m-80) cc_final: 0.7156 (m-80) REVERT: B 1151 ARG cc_start: 0.9460 (OUTLIER) cc_final: 0.9223 (tmt-80) outliers start: 29 outliers final: 14 residues processed: 91 average time/residue: 0.7233 time to fit residues: 71.3438 Evaluate side-chains 81 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.523 ------------------------------------------------------------------------------- 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 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 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 64 optimal weight: 7.9990 chunk 69 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 110 optimal weight: 4.9990 chunk 136 optimal weight: 5.9990 chunk 2 optimal weight: 0.5980 chunk 104 optimal weight: 5.9990 chunk 92 optimal weight: 0.8980 chunk 83 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- 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 = 0.3202 r_free = 0.3202 target = 0.061769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.042943 restraints weight = 39035.762| |-----------------------------------------------------------------------------| r_work (start): 0.2694 rms_B_bonded: 3.42 r_work: 0.2528 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 12532 Z= 0.209 Angle : 0.577 10.045 16932 Z= 0.295 Chirality : 0.043 0.159 1830 Planarity : 0.004 0.036 2166 Dihedral : 5.313 63.311 1687 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.42 % Allowed : 19.77 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.22), residues: 1502 helix: 1.45 (0.21), residues: 674 sheet: -0.33 (0.41), residues: 176 loop : -0.79 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 662 TYR 0.014 0.001 TYR B 520 PHE 0.009 0.001 PHE B 596 TRP 0.010 0.001 TRP B1189 HIS 0.004 0.001 HIS B 789 Details of bonding type rmsd covalent geometry : bond 0.00486 (12532) covalent geometry : angle 0.57730 (16932) hydrogen bonds : bond 0.03280 ( 574) hydrogen bonds : angle 4.44277 ( 1623) *********************** 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 96 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 64 time to evaluate : 0.503 Fit side-chains REVERT: A 994 GLU cc_start: 0.8620 (tm-30) cc_final: 0.8392 (pp20) REVERT: A 1042 LEU cc_start: 0.9655 (OUTLIER) cc_final: 0.9386 (tm) REVERT: A 1066 ARG cc_start: 0.9139 (ttt180) cc_final: 0.8910 (ttt180) REVERT: A 1111 GLU cc_start: 0.9367 (OUTLIER) cc_final: 0.9156 (pm20) REVERT: B 524 GLU cc_start: 0.9087 (OUTLIER) cc_final: 0.8815 (pp20) REVERT: B 929 ARG cc_start: 0.9364 (ptm-80) cc_final: 0.8664 (ptm-80) REVERT: B 957 MET cc_start: 0.9203 (mmm) cc_final: 0.8459 (mpp) REVERT: B 1066 ARG cc_start: 0.9105 (ttt90) cc_final: 0.8695 (ttt90) REVERT: B 1094 PHE cc_start: 0.8034 (m-80) cc_final: 0.7107 (m-80) REVERT: B 1151 ARG cc_start: 0.9450 (OUTLIER) cc_final: 0.9107 (mmm160) outliers start: 32 outliers final: 18 residues processed: 94 average time/residue: 0.6650 time to fit residues: 68.1219 Evaluate side-chains 83 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 61 time to evaluate : 0.515 ------------------------------------------------------------------------------- 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 714 MET 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 501 ASN 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 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 6 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 45 optimal weight: 0.0980 chunk 48 optimal weight: 0.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- 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 = 0.3218 r_free = 0.3218 target = 0.062475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.043572 restraints weight = 38642.221| |-----------------------------------------------------------------------------| r_work (start): 0.2713 rms_B_bonded: 3.43 r_work: 0.2549 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 12532 Z= 0.157 Angle : 0.565 10.960 16932 Z= 0.288 Chirality : 0.042 0.157 1830 Planarity : 0.003 0.034 2166 Dihedral : 5.271 64.396 1687 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.12 % Allowed : 20.38 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.22), residues: 1502 helix: 1.43 (0.21), residues: 672 sheet: -0.33 (0.41), residues: 176 loop : -0.77 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 662 TYR 0.012 0.001 TYR B 520 PHE 0.008 0.001 PHE B 632 TRP 0.009 0.001 TRP A1189 HIS 0.003 0.001 HIS B 789 Details of bonding type rmsd covalent geometry : bond 0.00366 (12532) covalent geometry : angle 0.56510 (16932) hydrogen bonds : bond 0.03095 ( 574) hydrogen bonds : angle 4.37967 ( 1623) *********************** 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 94 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 66 time to evaluate : 0.567 Fit side-chains REVERT: A 994 GLU cc_start: 0.8634 (tm-30) cc_final: 0.8393 (pp20) REVERT: A 1042 LEU cc_start: 0.9638 (OUTLIER) cc_final: 0.9351 (tm) REVERT: B 524 GLU cc_start: 0.9107 (OUTLIER) cc_final: 0.8850 (pp20) REVERT: B 929 ARG cc_start: 0.9388 (ptm-80) cc_final: 0.8798 (ptm-80) REVERT: B 957 MET cc_start: 0.9201 (mmm) cc_final: 0.8472 (mpp) outliers start: 28 outliers final: 17 residues processed: 91 average time/residue: 0.6908 time to fit residues: 68.4510 Evaluate side-chains 78 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 59 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 586 VAL 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 501 ASN 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 964 VAL Chi-restraints excluded: chain B residue 1118 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 112 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 136 optimal weight: 0.7980 chunk 68 optimal weight: 7.9990 chunk 16 optimal weight: 8.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- 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 = 0.3203 r_free = 0.3203 target = 0.061785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.042988 restraints weight = 38952.570| |-----------------------------------------------------------------------------| r_work (start): 0.2694 rms_B_bonded: 3.42 r_work: 0.2530 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 12532 Z= 0.198 Angle : 0.598 11.493 16932 Z= 0.305 Chirality : 0.043 0.197 1830 Planarity : 0.003 0.034 2166 Dihedral : 5.314 63.061 1687 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.05 % Allowed : 20.98 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.22), residues: 1502 helix: 1.40 (0.21), residues: 672 sheet: -0.35 (0.41), residues: 176 loop : -0.76 (0.25), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 662 TYR 0.013 0.001 TYR B 520 PHE 0.009 0.001 PHE B 596 TRP 0.009 0.001 TRP B1189 HIS 0.009 0.001 HIS B 892 Details of bonding type rmsd covalent geometry : bond 0.00463 (12532) covalent geometry : angle 0.59836 (16932) hydrogen bonds : bond 0.03237 ( 574) hydrogen bonds : angle 4.43057 ( 1623) *********************** 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 87 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 60 time to evaluate : 0.514 Fit side-chains revert: symmetry clash REVERT: A 994 GLU cc_start: 0.8686 (tm-30) cc_final: 0.8437 (pp20) REVERT: A 1042 LEU cc_start: 0.9636 (OUTLIER) cc_final: 0.9347 (tm) REVERT: A 1076 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8324 (mp) REVERT: B 524 GLU cc_start: 0.9113 (OUTLIER) cc_final: 0.8860 (pp20) REVERT: B 929 ARG cc_start: 0.9431 (ptm-80) cc_final: 0.8894 (ptm-80) REVERT: B 957 MET cc_start: 0.9205 (mmm) cc_final: 0.8345 (mpp) REVERT: B 1094 PHE cc_start: 0.8007 (m-80) cc_final: 0.7001 (m-80) outliers start: 27 outliers final: 20 residues processed: 86 average time/residue: 0.6302 time to fit residues: 59.5230 Evaluate side-chains 82 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 59 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 586 VAL 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 845 ILE Chi-restraints excluded: chain A residue 987 MET Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain B residue 501 ASN 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 964 VAL Chi-restraints excluded: chain B residue 1118 LEU Chi-restraints excluded: chain B residue 1169 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 28 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 122 optimal weight: 4.9990 chunk 143 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 1 optimal weight: 0.0470 chunk 46 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 overall best weight: 1.7682 ------------------------------------------------------------------------------- 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 = 0.3205 r_free = 0.3205 target = 0.061873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.043069 restraints weight = 38915.388| |-----------------------------------------------------------------------------| r_work (start): 0.2697 rms_B_bonded: 3.41 r_work: 0.2536 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1680 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= 0.186 Angle : 0.599 12.056 16932 Z= 0.304 Chirality : 0.043 0.182 1830 Planarity : 0.003 0.033 2166 Dihedral : 5.289 63.628 1687 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.74 % Allowed : 21.52 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.22), residues: 1502 helix: 1.36 (0.21), residues: 674 sheet: -0.37 (0.41), residues: 176 loop : -0.72 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 662 TYR 0.013 0.001 TYR B 520 PHE 0.008 0.001 PHE B 596 TRP 0.009 0.001 TRP A1189 HIS 0.008 0.001 HIS B 892 Details of bonding type rmsd covalent geometry : bond 0.00436 (12532) covalent geometry : angle 0.59912 (16932) hydrogen bonds : bond 0.03199 ( 574) hydrogen bonds : angle 4.42748 ( 1623) *********************** 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 85 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 62 time to evaluate : 0.497 Fit side-chains REVERT: A 994 GLU cc_start: 0.8677 (tm-30) cc_final: 0.8427 (pp20) REVERT: A 1042 LEU cc_start: 0.9626 (OUTLIER) cc_final: 0.9335 (tm) REVERT: A 1131 ARG cc_start: 0.8847 (tpm-80) cc_final: 0.8404 (tpm170) REVERT: B 524 GLU cc_start: 0.9111 (OUTLIER) cc_final: 0.8861 (pp20) REVERT: B 929 ARG cc_start: 0.9435 (ptm-80) cc_final: 0.8890 (ptm-80) REVERT: B 957 MET cc_start: 0.9202 (mmm) cc_final: 0.8332 (mpp) REVERT: B 1094 PHE cc_start: 0.8054 (m-80) cc_final: 0.7459 (m-80) outliers start: 23 outliers final: 18 residues processed: 85 average time/residue: 0.6139 time to fit residues: 57.1597 Evaluate side-chains 80 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 60 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 586 VAL 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 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 964 VAL Chi-restraints excluded: chain B residue 1118 LEU Chi-restraints excluded: chain B residue 1169 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 23 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 110 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 116 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 147 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 915 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.063521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.044665 restraints weight = 38731.158| |-----------------------------------------------------------------------------| r_work (start): 0.2742 rms_B_bonded: 3.46 r_work: 0.2583 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12532 Z= 0.118 Angle : 0.578 12.350 16932 Z= 0.289 Chirality : 0.041 0.177 1830 Planarity : 0.003 0.033 2166 Dihedral : 5.137 68.938 1687 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.52 % Allowed : 21.74 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.22), residues: 1502 helix: 1.48 (0.21), residues: 666 sheet: -0.35 (0.41), residues: 176 loop : -0.77 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 662 TYR 0.010 0.001 TYR B 888 PHE 0.008 0.001 PHE A 559 TRP 0.008 0.001 TRP B1189 HIS 0.007 0.001 HIS B 892 Details of bonding type rmsd covalent geometry : bond 0.00270 (12532) covalent geometry : angle 0.57784 (16932) hydrogen bonds : bond 0.02854 ( 574) hydrogen bonds : angle 4.27288 ( 1623) ********************** 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 to be fit. rotamer outliers: 20 poor density : 61 time to evaluate : 0.528 Fit side-chains revert: symmetry clash REVERT: A 994 GLU cc_start: 0.8656 (tm-30) cc_final: 0.8383 (pp20) REVERT: A 1131 ARG cc_start: 0.8849 (tpm-80) cc_final: 0.8406 (tpm170) REVERT: B 524 GLU cc_start: 0.9122 (OUTLIER) cc_final: 0.8906 (pp20) REVERT: B 749 MET cc_start: 0.9403 (mmm) cc_final: 0.9056 (mmp) REVERT: B 929 ARG cc_start: 0.9434 (ptm-80) cc_final: 0.8898 (ptm-80) REVERT: B 957 MET cc_start: 0.9204 (mmm) cc_final: 0.8457 (mpp) REVERT: B 1094 PHE cc_start: 0.8088 (m-80) cc_final: 0.7451 (m-80) outliers start: 20 outliers final: 15 residues processed: 81 average time/residue: 0.6258 time to fit residues: 55.7161 Evaluate side-chains 76 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.533 ------------------------------------------------------------------------------- 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 987 MET Chi-restraints excluded: chain A residue 1169 VAL 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 1118 LEU Chi-restraints excluded: chain B residue 1169 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 11 optimal weight: 4.9990 chunk 23 optimal weight: 0.0980 chunk 98 optimal weight: 0.2980 chunk 57 optimal weight: 6.9990 chunk 82 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 38 optimal weight: 0.2980 chunk 102 optimal weight: 1.9990 chunk 128 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.3278 r_free = 0.3278 target = 0.064808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.046137 restraints weight = 38258.741| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 3.45 r_work: 0.2624 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1561 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= 0.106 Angle : 0.578 12.389 16932 Z= 0.289 Chirality : 0.041 0.177 1830 Planarity : 0.003 0.033 2166 Dihedral : 5.051 73.687 1687 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.22), residues: 1502 helix: 1.49 (0.21), residues: 670 sheet: -0.28 (0.41), residues: 176 loop : -0.77 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 662 TYR 0.010 0.001 TYR B 520 PHE 0.008 0.001 PHE B 710 TRP 0.008 0.001 TRP A1189 HIS 0.007 0.001 HIS B 892 Details of bonding type rmsd covalent geometry : bond 0.00242 (12532) covalent geometry : angle 0.57833 (16932) hydrogen bonds : bond 0.02705 ( 574) hydrogen bonds : angle 4.15427 ( 1623) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3665.71 seconds wall clock time: 63 minutes 39.18 seconds (3819.18 seconds total)