Starting phenix.real_space_refine on Thu Jun 12 05:49:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yge_39245/06_2025/8yge_39245.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yge_39245/06_2025/8yge_39245.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yge_39245/06_2025/8yge_39245.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yge_39245/06_2025/8yge_39245.map" model { file = "/net/cci-nas-00/data/ceres_data/8yge_39245/06_2025/8yge_39245.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yge_39245/06_2025/8yge_39245.cif" } resolution = 2.76 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= 0.038 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: 6 Type Number sf(0) Gaussians P 38 5.49 5 Mg 3 5.21 5 S 60 5.16 5 C 8509 2.51 5 N 2329 2.21 5 O 2540 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 13479 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6303 Classifications: {'peptide': 779} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 748} Chain: "B" Number of atoms: 6303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6303 Classifications: {'peptide': 779} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 748} Chain: "C" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 411 Classifications: {'DNA': 20} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 19} Chain: "D" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 161 Classifications: {'DNA': 8} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 7} Chain: "E" Number of atoms: 242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 242 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {' MG': 1, 'ASW': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'ASW': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.24, per 1000 atoms: 0.69 Number of scatterers: 13479 At special positions: 0 Unit cell: (100.3, 124.1, 126.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 60 16.00 P 38 15.00 Mg 3 11.99 O 2540 8.00 N 2329 7.00 C 8509 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: 3.51 Conformation dependent library (CDL) restraints added in 1.7 seconds 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2924 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 18 sheets defined 53.0% alpha, 11.0% beta 20 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 4.97 Creating SS restraints... Processing helix chain 'A' and resid 439 through 451 Processing helix chain 'A' and resid 476 through 479 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 541 through 560 removed outlier: 3.842A pdb=" N ILE A 548 " --> pdb=" O GLY A 544 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU A 549 " --> pdb=" O CYS A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 566 removed outlier: 3.908A pdb=" N ILE A 564 " --> pdb=" O TRP A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 603 Processing helix chain 'A' and resid 621 through 631 Processing helix chain 'A' and resid 632 through 634 No H-bonds generated for 'chain 'A' and resid 632 through 634' Processing helix chain 'A' and resid 644 through 654 removed outlier: 4.199A pdb=" N HIS A 650 " --> pdb=" O LYS A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 664 removed outlier: 4.051A pdb=" N ARG A 660 " --> pdb=" O GLU A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 683 Processing helix chain 'A' and resid 687 through 707 removed outlier: 3.703A pdb=" N THR A 695 " --> pdb=" O LEU A 691 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N LYS A 696 " --> pdb=" O GLN A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 729 Processing helix chain 'A' and resid 738 through 749 Processing helix chain 'A' and resid 754 through 767 removed outlier: 3.676A pdb=" N LEU A 758 " --> pdb=" O GLY A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 793 removed outlier: 3.501A pdb=" N GLY A 791 " --> pdb=" O ARG A 788 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY A 792 " --> pdb=" O HIS A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 814 Processing helix chain 'A' and resid 816 through 822 removed outlier: 3.895A pdb=" N LEU A 822 " --> pdb=" O SER A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 846 removed outlier: 3.565A pdb=" N ILE A 845 " --> pdb=" O PRO A 842 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET A 846 " --> pdb=" O LEU A 843 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 842 through 846' Processing helix chain 'A' and resid 864 through 877 Processing helix chain 'A' and resid 882 through 887 Processing helix chain 'A' and resid 942 through 953 removed outlier: 3.600A pdb=" N SER A 953 " --> pdb=" O SER A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 958 removed outlier: 3.539A pdb=" N MET A 957 " --> pdb=" O SER A 953 " (cutoff:3.500A) 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: 3.536A pdb=" N ILE A1031 " --> pdb=" O SER A1027 " (cutoff:3.500A) Proline residue: A1037 - end of helix removed outlier: 5.709A pdb=" N ALA A1072 " --> pdb=" O ILE A1068 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ASP A1073 " --> pdb=" O ASN A1069 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU A1074 " --> pdb=" O GLU A1070 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1093 Processing helix chain 'A' and resid 1098 through 1104 Processing helix chain 'A' and resid 1109 through 1118 removed outlier: 3.604A pdb=" N ASN A1114 " --> pdb=" O ILE A1110 " (cutoff:3.500A) removed outlier: 4.051A 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 1160 removed outlier: 3.764A pdb=" N GLN A1160 " --> pdb=" O GLU A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1187 Processing helix chain 'B' and resid 428 through 431 removed outlier: 3.580A pdb=" N ASP B 431 " --> pdb=" O LYS B 428 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 428 through 431' Processing helix chain 'B' and resid 440 through 451 Processing helix chain 'B' and resid 476 through 481 removed outlier: 3.862A pdb=" N LYS B 480 " --> pdb=" O ASN B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 501 Processing helix chain 'B' and resid 502 through 513 Processing helix chain 'B' and resid 522 through 527 Processing helix chain 'B' and resid 541 through 547 Processing helix chain 'B' and resid 547 through 560 Processing helix chain 'B' and resid 560 through 566 removed outlier: 4.153A pdb=" N ILE B 564 " --> pdb=" O TRP B 560 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL B 565 " --> pdb=" O PRO B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 603 Processing helix chain 'B' and resid 621 through 631 removed outlier: 3.620A 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 654 removed outlier: 3.561A pdb=" N ILE B 651 " --> pdb=" O GLU B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 664 removed outlier: 4.073A pdb=" N ARG B 660 " --> pdb=" O GLU B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 683 Processing helix chain 'B' and resid 687 through 707 removed outlier: 3.784A pdb=" N THR B 695 " --> pdb=" O LEU B 691 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LYS B 696 " --> pdb=" O GLN B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 730 Processing helix chain 'B' and resid 738 through 749 Processing helix chain 'B' and resid 754 through 767 removed outlier: 3.680A pdb=" N LEU B 758 " --> pdb=" O GLY B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 793 removed outlier: 3.742A pdb=" N GLY B 791 " --> pdb=" O ARG B 788 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY B 792 " --> pdb=" O HIS B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 806 through 814 removed outlier: 3.918A pdb=" N THR B 812 " --> pdb=" O GLU B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 815 through 822 removed outlier: 4.004A pdb=" N TRP B 820 " --> pdb=" O GLU B 817 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU B 822 " --> pdb=" O SER B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 878 removed outlier: 4.697A pdb=" N LYS B 878 " --> pdb=" O ALA B 874 " (cutoff:3.500A) Processing helix chain 'B' and resid 882 through 887 Processing helix chain 'B' and resid 942 through 953 removed outlier: 3.597A 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 1070 removed outlier: 3.551A 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 1076 through 1079 Processing helix chain 'B' and resid 1081 through 1092 Processing helix chain 'B' and resid 1098 through 1103 Processing helix chain 'B' and resid 1109 through 1119 removed outlier: 3.821A pdb=" N GLN B1119 " --> pdb=" O GLN B1115 " (cutoff:3.500A) Processing helix chain 'B' and resid 1122 through 1127 Processing helix chain 'B' and resid 1129 through 1133 Processing helix chain 'B' and resid 1134 through 1160 removed outlier: 3.637A pdb=" N LYS B1138 " --> pdb=" O LEU B1134 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLN B1160 " --> pdb=" O GLU B1156 " (cutoff:3.500A) Processing helix chain 'B' and resid 1166 through 1187 Processing sheet with id=AA1, first strand: chain 'A' and resid 468 through 469 removed outlier: 6.086A pdb=" N LEU A 434 " --> pdb=" O VAL A 535 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N CYS A 537 " --> pdb=" O LEU A 434 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ALA A 436 " --> pdb=" O CYS A 537 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ILE A 534 " --> pdb=" O LYS A 570 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N LEU A 572 " --> pdb=" O ILE A 534 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ALA A 536 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N VAL A 569 " --> pdb=" O PHE A 639 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N ILE A 685 " --> pdb=" O VAL A 636 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N THR A 638 " --> pdb=" O ILE A 685 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 481 through 485 Processing sheet with id=AA3, first strand: chain 'A' and resid 588 through 590 Processing sheet with id=AA4, first strand: chain 'A' and resid 736 through 737 Processing sheet with id=AA5, first strand: chain 'A' and resid 824 through 827 removed outlier: 4.968A pdb=" N VAL A 825 " --> pdb=" O ALA A 832 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 849 through 853 Processing sheet with id=AA7, first strand: chain 'A' and resid 909 through 913 Processing sheet with id=AA8, first strand: chain 'A' and resid 923 through 926 removed outlier: 4.047A pdb=" N ILE A 932 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1014 through 1016 Processing sheet with id=AB1, first strand: chain 'B' and resid 468 through 469 removed outlier: 6.092A pdb=" N LEU B 434 " --> pdb=" O VAL B 535 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N CYS B 537 " --> pdb=" O LEU B 434 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ALA B 436 " --> pdb=" O CYS B 537 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ILE B 534 " --> pdb=" O LYS B 570 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N LEU B 572 " --> pdb=" O ILE B 534 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ALA B 536 " --> pdb=" O LEU B 572 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N VAL B 569 " --> pdb=" O PHE B 639 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 482 through 485 Processing sheet with id=AB3, first strand: chain 'B' and resid 588 through 590 Processing sheet with id=AB4, first strand: chain 'B' and resid 736 through 737 Processing sheet with id=AB5, first strand: chain 'B' and resid 824 through 827 removed outlier: 4.742A pdb=" N VAL B 825 " --> pdb=" O ALA B 832 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 849 through 852 Processing sheet with id=AB7, first strand: chain 'B' and resid 909 through 913 Processing sheet with id=AB8, first strand: chain 'B' and resid 922 through 926 removed outlier: 6.113A pdb=" N THR B 922 " --> pdb=" O THR B 935 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 1014 through 1016 605 hydrogen bonds defined for protein. 1701 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 49 hydrogen bonds 98 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 30 stacking parallelities Total time for adding SS restraints: 5.55 Time building geometry restraints manager: 4.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3596 1.33 - 1.45: 2778 1.45 - 1.57: 7324 1.57 - 1.69: 79 1.69 - 1.81: 96 Bond restraints: 13873 Sorted by residual: bond pdb=" O9 ASW A1202 " pdb=" S7 ASW A1202 " ideal model delta sigma weight residual 1.453 1.651 -0.198 2.00e-02 2.50e+03 9.81e+01 bond pdb=" O9 ASW C 101 " pdb=" S7 ASW C 101 " ideal model delta sigma weight residual 1.453 1.650 -0.197 2.00e-02 2.50e+03 9.69e+01 bond pdb=" O10 ASW C 101 " pdb=" S7 ASW C 101 " ideal model delta sigma weight residual 1.453 1.646 -0.193 2.00e-02 2.50e+03 9.29e+01 bond pdb=" O10 ASW A1202 " pdb=" S7 ASW A1202 " ideal model delta sigma weight residual 1.453 1.644 -0.191 2.00e-02 2.50e+03 9.14e+01 bond pdb=" C15 ASW A1202 " pdb=" N14 ASW A1202 " ideal model delta sigma weight residual 1.376 1.461 -0.085 2.00e-02 2.50e+03 1.81e+01 ... (remaining 13868 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 18648 2.14 - 4.28: 234 4.28 - 6.42: 28 6.42 - 8.57: 5 8.57 - 10.71: 5 Bond angle restraints: 18920 Sorted by residual: angle pdb=" CA ARG A 929 " pdb=" CB ARG A 929 " pdb=" CG ARG A 929 " ideal model delta sigma weight residual 114.10 123.65 -9.55 2.00e+00 2.50e-01 2.28e+01 angle pdb=" CA ARG B 929 " pdb=" CB ARG B 929 " pdb=" CG ARG B 929 " ideal model delta sigma weight residual 114.10 122.74 -8.64 2.00e+00 2.50e-01 1.87e+01 angle pdb=" CA GLN A 928 " pdb=" CB GLN A 928 " pdb=" CG GLN A 928 " ideal model delta sigma weight residual 114.10 121.28 -7.18 2.00e+00 2.50e-01 1.29e+01 angle pdb=" O10 ASW C 101 " pdb=" S7 ASW C 101 " pdb=" O9 ASW C 101 " ideal model delta sigma weight residual 119.56 108.85 10.71 3.00e+00 1.11e-01 1.27e+01 angle pdb=" CB GLN A 928 " pdb=" CG GLN A 928 " pdb=" CD GLN A 928 " ideal model delta sigma weight residual 112.60 118.47 -5.87 1.70e+00 3.46e-01 1.19e+01 ... (remaining 18915 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.54: 7784 32.54 - 65.08: 383 65.08 - 97.62: 25 97.62 - 130.16: 0 130.16 - 162.70: 5 Dihedral angle restraints: 8197 sinusoidal: 3633 harmonic: 4564 Sorted by residual: dihedral pdb=" CA GLU B1106 " pdb=" C GLU B1106 " pdb=" N PHE B1107 " pdb=" CA PHE B1107 " ideal model delta harmonic sigma weight residual 180.00 153.22 26.78 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA SER B1104 " pdb=" C SER B1104 " pdb=" N PRO B1105 " pdb=" CA PRO B1105 " ideal model delta harmonic sigma weight residual -180.00 -156.12 -23.88 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" C5 ASW C 101 " pdb=" N6 ASW C 101 " pdb=" S7 ASW C 101 " pdb=" O10 ASW C 101 " ideal model delta sinusoidal sigma weight residual 185.69 31.73 153.96 1 3.00e+01 1.11e-03 2.03e+01 ... (remaining 8194 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1686 0.053 - 0.106: 322 0.106 - 0.159: 39 0.159 - 0.212: 2 0.212 - 0.265: 1 Chirality restraints: 2050 Sorted by residual: chirality pdb=" CA GLN A1115 " pdb=" N GLN A1115 " pdb=" C GLN A1115 " pdb=" CB GLN A1115 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CB VAL B 964 " pdb=" CA VAL B 964 " pdb=" CG1 VAL B 964 " pdb=" CG2 VAL B 964 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.52e-01 chirality pdb=" CA ILE B 974 " pdb=" N ILE B 974 " pdb=" C ILE B 974 " pdb=" CB ILE B 974 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.09e-01 ... (remaining 2047 not shown) Planarity restraints: 2272 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 929 " 0.009 2.00e-02 2.50e+03 1.77e-02 3.15e+00 pdb=" C ARG A 929 " -0.031 2.00e-02 2.50e+03 pdb=" O ARG A 929 " 0.011 2.00e-02 2.50e+03 pdb=" N ASN A 930 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 929 " 0.008 2.00e-02 2.50e+03 1.68e-02 2.83e+00 pdb=" C ARG B 929 " -0.029 2.00e-02 2.50e+03 pdb=" O ARG B 929 " 0.011 2.00e-02 2.50e+03 pdb=" N ASN B 930 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 456 " 0.025 5.00e-02 4.00e+02 3.80e-02 2.31e+00 pdb=" N PRO A 457 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 457 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 457 " 0.021 5.00e-02 4.00e+02 ... (remaining 2269 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.16: 3 2.16 - 2.85: 4657 2.85 - 3.53: 18349 3.53 - 4.22: 31303 4.22 - 4.90: 54789 Nonbonded interactions: 109101 Sorted by model distance: nonbonded pdb=" OH TYR A 800 " pdb=" P DA E 14 " model vdw 1.476 3.400 nonbonded pdb=" O ARG B 929 " pdb=" NH1 ARG B 929 " model vdw 2.067 3.120 nonbonded pdb=" O ARG A 929 " pdb=" NH1 ARG A 929 " model vdw 2.133 3.120 nonbonded pdb=" OG SER B 461 " pdb=" OD1 ASP B 463 " model vdw 2.172 3.040 nonbonded pdb=" OG SER A 984 " pdb=" OE2 GLU A 988 " model vdw 2.176 3.040 ... (remaining 109096 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' and (resid 416 through 1194 or resid 1201)) selection = (chain 'B' and (resid 416 through 1194 or resid 1201)) } 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: 1.790 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: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 38.720 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 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 : 0.006 0.198 13873 Z= 0.263 Angle : 0.589 10.707 18920 Z= 0.308 Chirality : 0.041 0.265 2050 Planarity : 0.003 0.038 2272 Dihedral : 17.865 162.703 5273 Min Nonbonded Distance : 1.476 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.70 % Favored : 95.24 % Rotamer: Outliers : 1.62 % Allowed : 15.79 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.22), residues: 1554 helix: 2.03 (0.21), residues: 648 sheet: -1.15 (0.35), residues: 232 loop : -0.57 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 820 HIS 0.002 0.001 HIS B 566 PHE 0.013 0.001 PHE A 959 TYR 0.011 0.001 TYR B 698 ARG 0.005 0.000 ARG B 929 Details of bonding type rmsd hydrogen bonds : bond 0.13780 ( 654) hydrogen bonds : angle 5.53699 ( 1799) covalent geometry : bond 0.00556 (13873) covalent geometry : angle 0.58888 (18920) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 63 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 458 SER cc_start: 0.9324 (t) cc_final: 0.9082 (p) REVERT: A 948 GLU cc_start: 0.9221 (OUTLIER) cc_final: 0.8753 (mp0) outliers start: 22 outliers final: 12 residues processed: 85 average time/residue: 1.2493 time to fit residues: 117.3181 Evaluate side-chains 66 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 948 GLU Chi-restraints excluded: chain A residue 1050 GLU Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 595 GLU Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 669 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 7.9990 chunk 118 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 80 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 47 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.063911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.044606 restraints weight = 42823.203| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 3.47 r_work: 0.2598 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.0981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 13873 Z= 0.182 Angle : 0.569 6.907 18920 Z= 0.305 Chirality : 0.041 0.173 2050 Planarity : 0.004 0.043 2272 Dihedral : 16.074 162.394 2191 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.18 % Favored : 95.75 % Rotamer: Outliers : 3.08 % Allowed : 14.39 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.54 (0.22), residues: 1554 helix: 1.86 (0.21), residues: 682 sheet: -1.21 (0.35), residues: 232 loop : -0.63 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 820 HIS 0.004 0.001 HIS B 566 PHE 0.015 0.001 PHE A1002 TYR 0.020 0.001 TYR A1067 ARG 0.004 0.000 ARG B 929 Details of bonding type rmsd hydrogen bonds : bond 0.04592 ( 654) hydrogen bonds : angle 4.59023 ( 1799) covalent geometry : bond 0.00416 (13873) covalent geometry : angle 0.56931 (18920) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 60 time to evaluate : 1.380 Fit side-chains REVERT: A 458 SER cc_start: 0.9320 (t) cc_final: 0.9073 (p) REVERT: A 916 TYR cc_start: 0.8841 (m-80) cc_final: 0.8629 (m-80) REVERT: A 929 ARG cc_start: 0.8102 (tpt90) cc_final: 0.7830 (tpt90) REVERT: A 931 MET cc_start: 0.7500 (mmm) cc_final: 0.7154 (mmm) REVERT: A 1115 GLN cc_start: 0.8714 (tm-30) cc_final: 0.8331 (tm-30) REVERT: B 988 GLU cc_start: 0.9355 (mm-30) cc_final: 0.9095 (mm-30) outliers start: 42 outliers final: 17 residues processed: 97 average time/residue: 1.1322 time to fit residues: 122.4800 Evaluate side-chains 70 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 53 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 890 ILE Chi-restraints excluded: chain B residue 1054 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 14 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 7 optimal weight: 20.0000 chunk 49 optimal weight: 10.0000 chunk 134 optimal weight: 9.9990 chunk 147 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 112 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 145 optimal weight: 0.9980 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 620 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.062249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.042885 restraints weight = 43466.552| |-----------------------------------------------------------------------------| r_work (start): 0.2707 rms_B_bonded: 3.51 r_work: 0.2543 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 13873 Z= 0.242 Angle : 0.589 7.271 18920 Z= 0.317 Chirality : 0.042 0.160 2050 Planarity : 0.004 0.049 2272 Dihedral : 16.118 161.835 2181 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.25 % Favored : 95.62 % Rotamer: Outliers : 3.38 % Allowed : 15.12 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.52 (0.22), residues: 1554 helix: 1.79 (0.21), residues: 688 sheet: -0.96 (0.36), residues: 222 loop : -0.72 (0.25), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 820 HIS 0.004 0.001 HIS A1092 PHE 0.015 0.001 PHE A1002 TYR 0.016 0.001 TYR A1067 ARG 0.005 0.000 ARG B 929 Details of bonding type rmsd hydrogen bonds : bond 0.05031 ( 654) hydrogen bonds : angle 4.56077 ( 1799) covalent geometry : bond 0.00561 (13873) covalent geometry : angle 0.58911 (18920) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 53 time to evaluate : 1.382 Fit side-chains revert: symmetry clash REVERT: A 666 THR cc_start: 0.8962 (OUTLIER) cc_final: 0.8750 (p) REVERT: A 1148 MET cc_start: 0.9242 (mtm) cc_final: 0.9037 (mtp) REVERT: B 983 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8725 (mm) outliers start: 46 outliers final: 16 residues processed: 95 average time/residue: 0.9961 time to fit residues: 106.7591 Evaluate side-chains 64 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 46 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 890 ILE Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 1054 LEU Chi-restraints excluded: chain B residue 1194 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 20 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 4 optimal weight: 0.0870 chunk 63 optimal weight: 6.9990 chunk 93 optimal weight: 8.9990 chunk 49 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 133 optimal weight: 9.9990 overall best weight: 2.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.062787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.043404 restraints weight = 42895.198| |-----------------------------------------------------------------------------| r_work (start): 0.2731 rms_B_bonded: 3.47 r_work: 0.2571 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 13873 Z= 0.191 Angle : 0.564 6.761 18920 Z= 0.303 Chirality : 0.041 0.262 2050 Planarity : 0.004 0.062 2272 Dihedral : 16.022 162.459 2178 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.05 % Favored : 95.82 % Rotamer: Outliers : 2.79 % Allowed : 16.81 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.61 (0.22), residues: 1554 helix: 1.88 (0.21), residues: 680 sheet: -0.91 (0.36), residues: 224 loop : -0.66 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 820 HIS 0.004 0.001 HIS A 620 PHE 0.014 0.001 PHE A1002 TYR 0.014 0.001 TYR B 698 ARG 0.006 0.000 ARG B 929 Details of bonding type rmsd hydrogen bonds : bond 0.04604 ( 654) hydrogen bonds : angle 4.44250 ( 1799) covalent geometry : bond 0.00438 (13873) covalent geometry : angle 0.56396 (18920) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 52 time to evaluate : 1.485 Fit side-chains revert: symmetry clash REVERT: A 1061 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8472 (mp0) outliers start: 38 outliers final: 18 residues processed: 87 average time/residue: 1.0925 time to fit residues: 106.9585 Evaluate side-chains 66 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 47 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 803 VAL Chi-restraints excluded: chain A residue 1061 GLU Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 890 ILE Chi-restraints excluded: chain B residue 1054 LEU Chi-restraints excluded: chain B residue 1194 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 138 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 80 optimal weight: 8.9990 chunk 120 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 584 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.063870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.044599 restraints weight = 43050.119| |-----------------------------------------------------------------------------| r_work (start): 0.2755 rms_B_bonded: 3.48 r_work: 0.2592 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13873 Z= 0.133 Angle : 0.528 8.246 18920 Z= 0.284 Chirality : 0.040 0.188 2050 Planarity : 0.003 0.051 2272 Dihedral : 15.864 162.489 2177 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.67 % Favored : 96.27 % Rotamer: Outliers : 2.42 % Allowed : 17.99 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.22), residues: 1554 helix: 2.13 (0.21), residues: 668 sheet: -1.04 (0.35), residues: 234 loop : -0.57 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 820 HIS 0.003 0.000 HIS B 566 PHE 0.013 0.001 PHE A1002 TYR 0.012 0.001 TYR B 698 ARG 0.010 0.000 ARG B 929 Details of bonding type rmsd hydrogen bonds : bond 0.04117 ( 654) hydrogen bonds : angle 4.28283 ( 1799) covalent geometry : bond 0.00297 (13873) covalent geometry : angle 0.52799 (18920) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 55 time to evaluate : 1.346 Fit side-chains revert: symmetry clash REVERT: A 1061 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8490 (mp0) REVERT: A 1148 MET cc_start: 0.9281 (mtm) cc_final: 0.9066 (mtp) REVERT: B 1076 LEU cc_start: 0.8842 (tp) cc_final: 0.8618 (tt) outliers start: 33 outliers final: 18 residues processed: 87 average time/residue: 1.1515 time to fit residues: 111.5869 Evaluate side-chains 68 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 49 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 803 VAL Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 1061 GLU Chi-restraints excluded: chain A residue 1074 LEU Chi-restraints excluded: chain A residue 1131 ARG Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 890 ILE Chi-restraints excluded: chain B residue 1123 THR Chi-restraints excluded: chain B residue 1194 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 10 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 156 optimal weight: 4.9990 chunk 133 optimal weight: 7.9990 chunk 84 optimal weight: 20.0000 chunk 95 optimal weight: 8.9990 chunk 116 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 740 GLN B 996 GLN 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 = 0.061063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.041710 restraints weight = 43881.822| |-----------------------------------------------------------------------------| r_work (start): 0.2672 rms_B_bonded: 3.50 r_work: 0.2507 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.108 13873 Z= 0.348 Angle : 0.660 11.793 18920 Z= 0.351 Chirality : 0.045 0.194 2050 Planarity : 0.004 0.045 2272 Dihedral : 16.275 163.022 2177 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.70 % Favored : 95.17 % Rotamer: Outliers : 3.23 % Allowed : 17.55 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1554 helix: 1.67 (0.20), residues: 688 sheet: -0.88 (0.36), residues: 224 loop : -0.77 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 820 HIS 0.005 0.001 HIS A 789 PHE 0.017 0.001 PHE A1002 TYR 0.018 0.002 TYR B 698 ARG 0.009 0.000 ARG B 929 Details of bonding type rmsd hydrogen bonds : bond 0.05494 ( 654) hydrogen bonds : angle 4.64710 ( 1799) covalent geometry : bond 0.00804 (13873) covalent geometry : angle 0.66013 (18920) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 49 time to evaluate : 1.492 Fit side-chains REVERT: A 666 THR cc_start: 0.8936 (OUTLIER) cc_final: 0.8736 (p) REVERT: A 1061 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8520 (mp0) REVERT: A 1116 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8408 (mtmp) REVERT: B 1050 GLU cc_start: 0.8758 (tp30) cc_final: 0.8538 (tp30) outliers start: 44 outliers final: 23 residues processed: 89 average time/residue: 1.0805 time to fit residues: 107.9092 Evaluate side-chains 73 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 47 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 803 VAL Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 1061 GLU Chi-restraints excluded: chain A residue 1074 LEU Chi-restraints excluded: chain A residue 1116 LYS Chi-restraints excluded: chain A residue 1131 ARG Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 890 ILE Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1123 THR Chi-restraints excluded: chain B residue 1194 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 2 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 108 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 136 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.063185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.043927 restraints weight = 43480.443| |-----------------------------------------------------------------------------| r_work (start): 0.2736 rms_B_bonded: 3.50 r_work: 0.2572 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13873 Z= 0.143 Angle : 0.561 9.528 18920 Z= 0.297 Chirality : 0.040 0.166 2050 Planarity : 0.003 0.047 2272 Dihedral : 15.963 161.717 2177 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.28 % Favored : 96.65 % Rotamer: Outliers : 2.57 % Allowed : 18.72 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.22), residues: 1554 helix: 2.01 (0.21), residues: 678 sheet: -1.06 (0.35), residues: 234 loop : -0.60 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1189 HIS 0.003 0.000 HIS A 620 PHE 0.014 0.001 PHE A 959 TYR 0.014 0.001 TYR B 966 ARG 0.016 0.000 ARG B 929 Details of bonding type rmsd hydrogen bonds : bond 0.04354 ( 654) hydrogen bonds : angle 4.34058 ( 1799) covalent geometry : bond 0.00319 (13873) covalent geometry : angle 0.56088 (18920) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 50 time to evaluate : 1.578 Fit side-chains REVERT: A 1061 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8519 (mp0) REVERT: A 1116 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8385 (mtmp) REVERT: A 1148 MET cc_start: 0.9298 (mtm) cc_final: 0.9078 (mtp) REVERT: B 929 ARG cc_start: 0.9082 (tmt-80) cc_final: 0.8635 (tpt90) REVERT: B 1050 GLU cc_start: 0.8736 (tp30) cc_final: 0.8536 (tp30) REVERT: B 1121 CYS cc_start: 0.7043 (OUTLIER) cc_final: 0.6619 (p) outliers start: 35 outliers final: 18 residues processed: 84 average time/residue: 1.0791 time to fit residues: 101.9251 Evaluate side-chains 68 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 47 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 803 VAL Chi-restraints excluded: chain A residue 1061 GLU Chi-restraints excluded: chain A residue 1116 LYS Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 890 ILE Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain B residue 1121 CYS Chi-restraints excluded: chain B residue 1123 THR Chi-restraints excluded: chain B residue 1194 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 67 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 98 optimal weight: 0.0170 chunk 126 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 84 optimal weight: 8.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.9424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 620 HIS 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 = 0.064382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.045205 restraints weight = 43167.321| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 3.52 r_work: 0.2609 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13873 Z= 0.119 Angle : 0.556 12.803 18920 Z= 0.290 Chirality : 0.040 0.178 2050 Planarity : 0.003 0.067 2272 Dihedral : 15.770 163.845 2177 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.67 % Favored : 96.27 % Rotamer: Outliers : 1.91 % Allowed : 19.31 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.23), residues: 1554 helix: 2.18 (0.21), residues: 684 sheet: -1.04 (0.35), residues: 234 loop : -0.49 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1189 HIS 0.003 0.000 HIS B 566 PHE 0.011 0.001 PHE A1002 TYR 0.011 0.001 TYR B 698 ARG 0.021 0.000 ARG B 929 Details of bonding type rmsd hydrogen bonds : bond 0.03901 ( 654) hydrogen bonds : angle 4.23661 ( 1799) covalent geometry : bond 0.00260 (13873) covalent geometry : angle 0.55642 (18920) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 53 time to evaluate : 1.507 Fit side-chains REVERT: A 991 LYS cc_start: 0.9370 (mmmm) cc_final: 0.9089 (mmmt) REVERT: A 1061 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8471 (mp0) REVERT: A 1116 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8336 (mtmp) REVERT: A 1148 MET cc_start: 0.9315 (mtm) cc_final: 0.9084 (mtp) outliers start: 26 outliers final: 15 residues processed: 79 average time/residue: 1.0891 time to fit residues: 96.6545 Evaluate side-chains 65 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 48 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 803 VAL Chi-restraints excluded: chain A residue 1061 GLU Chi-restraints excluded: chain A residue 1116 LYS Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 1054 LEU Chi-restraints excluded: chain B residue 1123 THR Chi-restraints excluded: chain B residue 1194 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 137 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 95 optimal weight: 7.9990 chunk 141 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 143 optimal weight: 0.0970 chunk 93 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.064060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.044917 restraints weight = 43140.000| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 3.45 r_work: 0.2601 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13873 Z= 0.138 Angle : 0.575 12.847 18920 Z= 0.300 Chirality : 0.040 0.165 2050 Planarity : 0.003 0.042 2272 Dihedral : 15.783 163.388 2177 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.60 % Favored : 96.33 % Rotamer: Outliers : 1.76 % Allowed : 19.75 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.23), residues: 1554 helix: 2.22 (0.21), residues: 684 sheet: -1.00 (0.35), residues: 234 loop : -0.49 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 820 HIS 0.003 0.000 HIS B 566 PHE 0.011 0.001 PHE A1002 TYR 0.012 0.001 TYR B 698 ARG 0.006 0.000 ARG B 929 Details of bonding type rmsd hydrogen bonds : bond 0.04002 ( 654) hydrogen bonds : angle 4.22183 ( 1799) covalent geometry : bond 0.00313 (13873) covalent geometry : angle 0.57484 (18920) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 50 time to evaluate : 1.374 Fit side-chains REVERT: A 991 LYS cc_start: 0.9383 (mmmm) cc_final: 0.9096 (mmmt) REVERT: A 1061 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8476 (mp0) REVERT: A 1116 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8298 (mtmp) REVERT: B 1121 CYS cc_start: 0.6896 (OUTLIER) cc_final: 0.6606 (p) outliers start: 24 outliers final: 19 residues processed: 74 average time/residue: 1.1008 time to fit residues: 91.5261 Evaluate side-chains 70 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 48 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 803 VAL Chi-restraints excluded: chain A residue 1061 GLU Chi-restraints excluded: chain A residue 1116 LYS Chi-restraints excluded: chain A residue 1194 HIS Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 1121 CYS Chi-restraints excluded: chain B residue 1123 THR Chi-restraints excluded: chain B residue 1194 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 57 optimal weight: 0.2980 chunk 3 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 83 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 chunk 114 optimal weight: 0.1980 chunk 147 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.064734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.045424 restraints weight = 43305.885| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 3.56 r_work: 0.2619 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13873 Z= 0.122 Angle : 0.575 12.636 18920 Z= 0.299 Chirality : 0.040 0.176 2050 Planarity : 0.003 0.042 2272 Dihedral : 15.731 163.262 2177 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.60 % Favored : 96.33 % Rotamer: Outliers : 1.76 % Allowed : 19.68 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.23), residues: 1554 helix: 2.25 (0.21), residues: 684 sheet: -0.81 (0.37), residues: 206 loop : -0.63 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1189 HIS 0.003 0.000 HIS B 566 PHE 0.011 0.001 PHE A1002 TYR 0.011 0.001 TYR B 698 ARG 0.007 0.000 ARG A 929 Details of bonding type rmsd hydrogen bonds : bond 0.03829 ( 654) hydrogen bonds : angle 4.17459 ( 1799) covalent geometry : bond 0.00270 (13873) covalent geometry : angle 0.57524 (18920) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 50 time to evaluate : 1.456 Fit side-chains REVERT: A 1061 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8464 (mp0) REVERT: A 1116 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8294 (mtmp) REVERT: B 1121 CYS cc_start: 0.6940 (OUTLIER) cc_final: 0.6674 (p) outliers start: 24 outliers final: 19 residues processed: 74 average time/residue: 1.1221 time to fit residues: 93.2157 Evaluate side-chains 69 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 47 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 803 VAL Chi-restraints excluded: chain A residue 986 ILE Chi-restraints excluded: chain A residue 1061 GLU Chi-restraints excluded: chain A residue 1116 LYS Chi-restraints excluded: chain A residue 1194 HIS Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 890 ILE Chi-restraints excluded: chain B residue 1121 CYS Chi-restraints excluded: chain B residue 1123 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 106 optimal weight: 0.8980 chunk 26 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 141 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 149 optimal weight: 0.9980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.063434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.044184 restraints weight = 43469.379| |-----------------------------------------------------------------------------| r_work (start): 0.2742 rms_B_bonded: 3.52 r_work: 0.2580 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13873 Z= 0.177 Angle : 0.605 13.797 18920 Z= 0.314 Chirality : 0.041 0.166 2050 Planarity : 0.003 0.043 2272 Dihedral : 15.837 163.003 2177 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.99 % Favored : 95.95 % Rotamer: Outliers : 1.84 % Allowed : 19.75 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.23), residues: 1554 helix: 2.06 (0.20), residues: 702 sheet: -0.94 (0.35), residues: 234 loop : -0.59 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 820 HIS 0.003 0.001 HIS B 566 PHE 0.012 0.001 PHE A1002 TYR 0.013 0.001 TYR B 698 ARG 0.007 0.000 ARG B 929 Details of bonding type rmsd hydrogen bonds : bond 0.04238 ( 654) hydrogen bonds : angle 4.24902 ( 1799) covalent geometry : bond 0.00409 (13873) covalent geometry : angle 0.60461 (18920) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7561.71 seconds wall clock time: 129 minutes 52.20 seconds (7792.20 seconds total)