Starting phenix.real_space_refine on Thu Sep 18 03:15:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yge_39245/09_2025/8yge_39245.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yge_39245/09_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_39245/09_2025/8yge_39245.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yge_39245/09_2025/8yge_39245.map" model { file = "/net/cci-nas-00/data/ceres_data/8yge_39245/09_2025/8yge_39245.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yge_39245/09_2025/8yge_39245.cif" } resolution = 2.76 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= 0.038 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): 0.01s 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: 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: 3.12, per 1000 atoms: 0.23 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: 1.17 Conformation dependent library (CDL) restraints added in 576.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.79 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: 2.53 Time building geometry restraints manager: 1.56 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 1201) selection = (chain 'B' and resid 416 through 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: 1.770 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 14.430 Find NCS groups from input model: 0.240 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: 0.000 Load rotamer database and sin/cos tables:6.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.460 ------------------------------------------------------------------------------- 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 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: 0.62 (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 ARG 0.005 0.000 ARG B 929 TYR 0.011 0.001 TYR B 698 PHE 0.013 0.001 PHE A 959 TRP 0.013 0.001 TRP A 820 HIS 0.002 0.001 HIS B 566 Details of bonding type rmsd covalent geometry : bond 0.00556 (13873) covalent geometry : angle 0.58888 (18920) hydrogen bonds : bond 0.13780 ( 654) hydrogen bonds : angle 5.53699 ( 1799) *********************** 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 : 0.375 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: 0.5771 time to fit residues: 53.8584 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 : 0.538 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.1980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 6.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3302 r_free = 0.3302 target = 0.065818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.046591 restraints weight = 42635.727| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 3.48 r_work: 0.2653 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.0857 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= 0.118 Angle : 0.540 7.139 18920 Z= 0.288 Chirality : 0.039 0.168 2050 Planarity : 0.004 0.040 2272 Dihedral : 15.948 162.949 2191 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.67 % Favored : 96.27 % Rotamer: Outliers : 2.86 % Allowed : 14.39 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.69 (0.22), residues: 1554 helix: 2.05 (0.21), residues: 670 sheet: -1.20 (0.35), residues: 232 loop : -0.56 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 929 TYR 0.019 0.001 TYR A1067 PHE 0.014 0.001 PHE A 959 TRP 0.008 0.001 TRP A1189 HIS 0.005 0.000 HIS B 566 Details of bonding type rmsd covalent geometry : bond 0.00252 (13873) covalent geometry : angle 0.53974 (18920) hydrogen bonds : bond 0.04144 ( 654) hydrogen bonds : angle 4.52560 ( 1799) *********************** 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 103 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 64 time to evaluate : 0.479 Fit side-chains REVERT: A 543 ASP cc_start: 0.8983 (OUTLIER) cc_final: 0.8777 (p0) REVERT: A 916 TYR cc_start: 0.8808 (m-80) cc_final: 0.8603 (m-80) REVERT: A 929 ARG cc_start: 0.8068 (tpt90) cc_final: 0.7416 (tpt90) REVERT: A 931 MET cc_start: 0.7515 (mmm) cc_final: 0.7035 (mmm) REVERT: A 1115 GLN cc_start: 0.8672 (tm-30) cc_final: 0.8325 (tm-30) REVERT: B 677 GLN cc_start: 0.9426 (OUTLIER) cc_final: 0.9214 (mm-40) REVERT: B 882 LYS cc_start: 0.9191 (OUTLIER) cc_final: 0.8979 (mtmm) REVERT: B 988 GLU cc_start: 0.9377 (mm-30) cc_final: 0.9119 (mm-30) outliers start: 39 outliers final: 14 residues processed: 98 average time/residue: 0.5692 time to fit residues: 61.5135 Evaluate side-chains 68 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 51 time to evaluate : 0.526 ------------------------------------------------------------------------------- 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 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 677 GLN Chi-restraints excluded: chain B residue 882 LYS 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 53 optimal weight: 0.9990 chunk 128 optimal weight: 3.9990 chunk 134 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 83 optimal weight: 8.9990 chunk 31 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 chunk 149 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 = 0.3236 r_free = 0.3236 target = 0.062530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.043113 restraints weight = 44033.767| |-----------------------------------------------------------------------------| r_work (start): 0.2720 rms_B_bonded: 3.52 r_work: 0.2557 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 13873 Z= 0.259 Angle : 0.605 6.869 18920 Z= 0.324 Chirality : 0.043 0.165 2050 Planarity : 0.004 0.044 2272 Dihedral : 16.115 162.651 2181 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.31 % Favored : 95.56 % Rotamer: Outliers : 3.30 % Allowed : 14.76 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.55 (0.23), residues: 1554 helix: 1.83 (0.21), residues: 682 sheet: -1.20 (0.35), residues: 232 loop : -0.58 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 929 TYR 0.016 0.001 TYR B 698 PHE 0.022 0.001 PHE A 629 TRP 0.015 0.001 TRP A 820 HIS 0.005 0.001 HIS A1092 Details of bonding type rmsd covalent geometry : bond 0.00600 (13873) covalent geometry : angle 0.60463 (18920) hydrogen bonds : bond 0.05058 ( 654) hydrogen bonds : angle 4.55884 ( 1799) *********************** 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 97 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 52 time to evaluate : 0.516 Fit side-chains REVERT: A 1061 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8382 (mp0) REVERT: B 983 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8780 (mm) outliers start: 45 outliers final: 15 residues processed: 93 average time/residue: 0.5427 time to fit residues: 56.2997 Evaluate side-chains 66 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 49 time to evaluate : 0.495 ------------------------------------------------------------------------------- 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 668 VAL Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 674 THR 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 971 THR Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 1054 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 18 optimal weight: 10.0000 chunk 129 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 7 optimal weight: 20.0000 chunk 79 optimal weight: 10.0000 chunk 120 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 75 optimal weight: 0.6980 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.3264 r_free = 0.3264 target = 0.063806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.044455 restraints weight = 43285.418| |-----------------------------------------------------------------------------| r_work (start): 0.2749 rms_B_bonded: 3.49 r_work: 0.2585 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13873 Z= 0.150 Angle : 0.549 7.436 18920 Z= 0.293 Chirality : 0.040 0.262 2050 Planarity : 0.003 0.042 2272 Dihedral : 15.927 161.894 2178 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.80 % Favored : 96.14 % Rotamer: Outliers : 2.35 % Allowed : 16.52 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.73 (0.22), residues: 1554 helix: 2.06 (0.21), residues: 670 sheet: -1.14 (0.35), residues: 232 loop : -0.52 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 929 TYR 0.013 0.001 TYR B 698 PHE 0.013 0.001 PHE A1002 TRP 0.009 0.001 TRP A 820 HIS 0.003 0.001 HIS B 566 Details of bonding type rmsd covalent geometry : bond 0.00341 (13873) covalent geometry : angle 0.54861 (18920) hydrogen bonds : bond 0.04308 ( 654) hydrogen bonds : angle 4.36586 ( 1799) *********************** 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 85 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 53 time to evaluate : 0.561 Fit side-chains REVERT: A 1061 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8475 (mp0) REVERT: B 983 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8854 (mm) outliers start: 32 outliers final: 16 residues processed: 84 average time/residue: 0.5009 time to fit residues: 47.5979 Evaluate side-chains 66 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 48 time to evaluate : 0.572 ------------------------------------------------------------------------------- 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 803 VAL Chi-restraints excluded: chain A residue 1061 GLU Chi-restraints excluded: chain A residue 1074 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 1194 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 149 optimal weight: 6.9990 chunk 140 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 89 optimal weight: 8.9990 chunk 128 optimal weight: 5.9990 chunk 137 optimal weight: 5.9990 chunk 57 optimal weight: 8.9990 chunk 60 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 145 optimal weight: 7.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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 = 0.3224 r_free = 0.3224 target = 0.062068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.042657 restraints weight = 43583.687| |-----------------------------------------------------------------------------| r_work (start): 0.2701 rms_B_bonded: 3.51 r_work: 0.2535 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 13873 Z= 0.250 Angle : 0.594 7.523 18920 Z= 0.318 Chirality : 0.042 0.211 2050 Planarity : 0.004 0.044 2272 Dihedral : 16.108 162.741 2178 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.38 % Favored : 95.50 % Rotamer: Outliers : 2.79 % Allowed : 17.40 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 (0.22), residues: 1554 helix: 1.83 (0.21), residues: 686 sheet: -1.07 (0.35), residues: 234 loop : -0.70 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 929 TYR 0.015 0.001 TYR B 698 PHE 0.016 0.001 PHE A1002 TRP 0.015 0.001 TRP A 820 HIS 0.004 0.001 HIS B 566 Details of bonding type rmsd covalent geometry : bond 0.00579 (13873) covalent geometry : angle 0.59360 (18920) hydrogen bonds : bond 0.04933 ( 654) hydrogen bonds : angle 4.51696 ( 1799) *********************** 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 89 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 51 time to evaluate : 0.563 Fit side-chains revert: symmetry clash REVERT: A 1061 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8376 (mp0) REVERT: A 1148 MET cc_start: 0.9257 (mtm) cc_final: 0.9056 (mtp) outliers start: 38 outliers final: 21 residues processed: 86 average time/residue: 0.5169 time to fit residues: 50.0749 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 : 0.652 ------------------------------------------------------------------------------- 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 963 ILE Chi-restraints excluded: chain A residue 1061 GLU Chi-restraints excluded: chain A residue 1074 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 871 LEU 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 74 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 chunk 128 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 930 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.064095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.044886 restraints weight = 43287.697| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 3.47 r_work: 0.2601 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.1877 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= 0.124 Angle : 0.531 8.595 18920 Z= 0.283 Chirality : 0.039 0.190 2050 Planarity : 0.003 0.042 2272 Dihedral : 15.845 161.916 2178 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.22 % Favored : 96.72 % Rotamer: Outliers : 2.42 % Allowed : 18.65 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.83 (0.23), residues: 1554 helix: 2.17 (0.21), residues: 668 sheet: -1.03 (0.35), residues: 234 loop : -0.52 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 929 TYR 0.012 0.001 TYR B 698 PHE 0.012 0.001 PHE A1002 TRP 0.008 0.001 TRP A1189 HIS 0.003 0.000 HIS B 566 Details of bonding type rmsd covalent geometry : bond 0.00273 (13873) covalent geometry : angle 0.53105 (18920) hydrogen bonds : bond 0.04038 ( 654) hydrogen bonds : angle 4.28021 ( 1799) *********************** 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 89 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 56 time to evaluate : 0.534 Fit side-chains REVERT: A 1061 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8492 (mp0) REVERT: B 576 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8870 (pt) REVERT: B 1050 GLU cc_start: 0.8754 (tp30) cc_final: 0.8530 (tp30) outliers start: 33 outliers final: 14 residues processed: 89 average time/residue: 0.5965 time to fit residues: 58.7413 Evaluate side-chains 66 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 50 time to evaluate : 0.555 ------------------------------------------------------------------------------- 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 641 LEU 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 1061 GLU Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 576 LEU 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 1054 LEU Chi-restraints excluded: chain B residue 1123 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 48 optimal weight: 4.9990 chunk 128 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 82 optimal weight: 7.9990 chunk 111 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 51 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 = 0.062698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.043409 restraints weight = 43814.119| |-----------------------------------------------------------------------------| r_work (start): 0.2719 rms_B_bonded: 3.50 r_work: 0.2556 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 13873 Z= 0.203 Angle : 0.584 9.809 18920 Z= 0.311 Chirality : 0.041 0.209 2050 Planarity : 0.003 0.043 2272 Dihedral : 15.977 162.874 2177 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.31 % Favored : 95.56 % Rotamer: Outliers : 2.64 % Allowed : 18.72 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.71 (0.23), residues: 1554 helix: 1.93 (0.20), residues: 702 sheet: -1.02 (0.35), residues: 234 loop : -0.59 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 929 TYR 0.014 0.001 TYR B 698 PHE 0.020 0.001 PHE A 959 TRP 0.013 0.001 TRP A 820 HIS 0.003 0.001 HIS B 566 Details of bonding type rmsd covalent geometry : bond 0.00468 (13873) covalent geometry : angle 0.58449 (18920) hydrogen bonds : bond 0.04585 ( 654) hydrogen bonds : angle 4.36226 ( 1799) *********************** 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 88 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 52 time to evaluate : 0.437 Fit side-chains REVERT: A 1061 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8521 (mp0) REVERT: A 1116 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8350 (mtmp) REVERT: A 1148 MET cc_start: 0.9274 (mtm) cc_final: 0.9065 (mtp) REVERT: B 1050 GLU cc_start: 0.8790 (tp30) cc_final: 0.8570 (tp30) outliers start: 36 outliers final: 17 residues processed: 86 average time/residue: 0.4883 time to fit residues: 47.4770 Evaluate side-chains 69 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 50 time to evaluate : 0.527 ------------------------------------------------------------------------------- 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 668 VAL Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 674 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 19 optimal weight: 10.0000 chunk 34 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 152 optimal weight: 0.9990 chunk 109 optimal weight: 0.5980 chunk 98 optimal weight: 3.9990 chunk 37 optimal weight: 0.0470 chunk 150 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 overall best weight: 0.7082 ------------------------------------------------------------------------------- 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 = 0.3291 r_free = 0.3291 target = 0.065020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.045887 restraints weight = 42735.161| |-----------------------------------------------------------------------------| r_work (start): 0.2791 rms_B_bonded: 3.49 r_work: 0.2632 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 13873 Z= 0.113 Angle : 0.548 10.557 18920 Z= 0.290 Chirality : 0.039 0.190 2050 Planarity : 0.003 0.043 2272 Dihedral : 15.734 162.498 2177 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.02 % Favored : 96.91 % Rotamer: Outliers : 1.91 % Allowed : 19.46 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.94 (0.23), residues: 1554 helix: 2.19 (0.21), residues: 684 sheet: -1.03 (0.35), residues: 234 loop : -0.41 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 929 TYR 0.011 0.001 TYR B 698 PHE 0.013 0.001 PHE A 959 TRP 0.009 0.001 TRP A1189 HIS 0.003 0.000 HIS B 566 Details of bonding type rmsd covalent geometry : bond 0.00242 (13873) covalent geometry : angle 0.54794 (18920) hydrogen bonds : bond 0.03820 ( 654) hydrogen bonds : angle 4.19092 ( 1799) *********************** 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 : 0.458 Fit side-chains revert: symmetry clash REVERT: A 1061 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8469 (mp0) REVERT: B 1050 GLU cc_start: 0.8733 (tp30) cc_final: 0.8461 (tp30) outliers start: 26 outliers final: 17 residues processed: 79 average time/residue: 0.5599 time to fit residues: 49.3745 Evaluate side-chains 68 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 50 time to evaluate : 0.574 ------------------------------------------------------------------------------- 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 1061 GLU 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 625 VAL Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 871 LEU 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 127 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 142 optimal weight: 4.9990 chunk 110 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 74 optimal weight: 0.0870 chunk 62 optimal weight: 0.0040 chunk 123 optimal weight: 0.9980 chunk 19 optimal weight: 10.0000 overall best weight: 1.6174 ------------------------------------------------------------------------------- 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 = 0.064107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.044909 restraints weight = 43387.355| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 3.46 r_work: 0.2599 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13873 Z= 0.147 Angle : 0.568 10.504 18920 Z= 0.298 Chirality : 0.040 0.165 2050 Planarity : 0.003 0.043 2272 Dihedral : 15.802 163.584 2177 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.80 % Favored : 96.14 % Rotamer: Outliers : 2.20 % Allowed : 19.31 % 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 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: 0.99 (0.23), residues: 1554 helix: 2.25 (0.21), residues: 684 sheet: -0.98 (0.35), residues: 234 loop : -0.41 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 929 TYR 0.012 0.001 TYR B 698 PHE 0.012 0.001 PHE A1002 TRP 0.011 0.001 TRP A 820 HIS 0.003 0.000 HIS B 566 Details of bonding type rmsd covalent geometry : bond 0.00334 (13873) covalent geometry : angle 0.56766 (18920) hydrogen bonds : bond 0.04072 ( 654) hydrogen bonds : angle 4.21366 ( 1799) *********************** 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 82 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 52 time to evaluate : 0.561 Fit side-chains REVERT: A 1061 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8504 (mp0) REVERT: A 1115 GLN cc_start: 0.8675 (tm-30) cc_final: 0.8444 (pp30) REVERT: B 991 LYS cc_start: 0.9273 (mmmt) cc_final: 0.9072 (mmmt) REVERT: B 1050 GLU cc_start: 0.8732 (tp30) cc_final: 0.8482 (tp30) outliers start: 30 outliers final: 18 residues processed: 80 average time/residue: 0.5415 time to fit residues: 48.1691 Evaluate side-chains 70 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 51 time to evaluate : 0.515 ------------------------------------------------------------------------------- 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 674 THR Chi-restraints excluded: chain A residue 803 VAL Chi-restraints excluded: chain A residue 1061 GLU 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 625 VAL Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 871 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 28 optimal weight: 6.9990 chunk 41 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 135 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 = 0.3259 r_free = 0.3259 target = 0.063628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.044383 restraints weight = 43187.883| |-----------------------------------------------------------------------------| r_work (start): 0.2745 rms_B_bonded: 3.51 r_work: 0.2584 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13873 Z= 0.167 Angle : 0.589 12.188 18920 Z= 0.310 Chirality : 0.040 0.255 2050 Planarity : 0.003 0.044 2272 Dihedral : 15.858 162.506 2177 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.93 % Favored : 96.01 % Rotamer: Outliers : 1.69 % Allowed : 19.82 % 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 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: 0.85 (0.23), residues: 1554 helix: 2.07 (0.20), residues: 702 sheet: -0.97 (0.35), residues: 234 loop : -0.53 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 929 TYR 0.013 0.001 TYR B 698 PHE 0.012 0.001 PHE A1002 TRP 0.011 0.001 TRP A 820 HIS 0.003 0.001 HIS B 566 Details of bonding type rmsd covalent geometry : bond 0.00381 (13873) covalent geometry : angle 0.58928 (18920) hydrogen bonds : bond 0.04266 ( 654) hydrogen bonds : angle 4.24637 ( 1799) ********************** 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 75 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 52 time to evaluate : 0.535 Fit side-chains REVERT: A 1061 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8526 (mp0) REVERT: A 1115 GLN cc_start: 0.8679 (tm-30) cc_final: 0.8459 (pp30) REVERT: B 991 LYS cc_start: 0.9315 (mmmt) cc_final: 0.9098 (mmmt) REVERT: B 1050 GLU cc_start: 0.8755 (tp30) cc_final: 0.8503 (tp30) outliers start: 23 outliers final: 17 residues processed: 72 average time/residue: 0.5930 time to fit residues: 47.2774 Evaluate side-chains 69 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 51 time to evaluate : 0.530 ------------------------------------------------------------------------------- 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 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 625 VAL Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 871 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 72 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 132 optimal weight: 9.9990 chunk 78 optimal weight: 9.9990 chunk 154 optimal weight: 4.9990 chunk 46 optimal weight: 0.0470 chunk 121 optimal weight: 3.9990 chunk 148 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 overall best weight: 2.4086 ------------------------------------------------------------------------------- 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 = 0.3250 r_free = 0.3250 target = 0.063154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.043916 restraints weight = 43549.289| |-----------------------------------------------------------------------------| r_work (start): 0.2730 rms_B_bonded: 3.50 r_work: 0.2566 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 13873 Z= 0.191 Angle : 0.611 16.192 18920 Z= 0.319 Chirality : 0.041 0.264 2050 Planarity : 0.004 0.046 2272 Dihedral : 15.918 162.449 2177 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.05 % Favored : 95.88 % Rotamer: Outliers : 1.32 % Allowed : 20.34 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.82 (0.23), residues: 1554 helix: 2.03 (0.20), residues: 702 sheet: -0.95 (0.35), residues: 234 loop : -0.53 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 929 TYR 0.014 0.001 TYR B 698 PHE 0.012 0.001 PHE A1002 TRP 0.012 0.001 TRP A 820 HIS 0.003 0.001 HIS B 566 Details of bonding type rmsd covalent geometry : bond 0.00441 (13873) covalent geometry : angle 0.61133 (18920) hydrogen bonds : bond 0.04455 ( 654) hydrogen bonds : angle 4.30816 ( 1799) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3717.56 seconds wall clock time: 64 minutes 23.48 seconds (3863.48 seconds total)