Starting phenix.real_space_refine on Fri Jul 3 10:15:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yge_39245/07_2026/8yge_39245.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yge_39245/07_2026/8yge_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 { model { file = "/net/cci-nas-00/data/ceres_data/8yge_39245/07_2026/8yge_39245.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yge_39245/07_2026/8yge_39245.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yge_39245/07_2026/8yge_39245.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yge_39245/07_2026/8yge_39245.map" } 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-dev-6108/lib/python3.11/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: 2.74, per 1000 atoms: 0.20 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: 0.88 Conformation dependent library (CDL) restraints added in 551.7 milliseconds 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: 1.36 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: 2.35 Time building geometry restraints manager: 1.24 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: 18617 2.14 - 4.28: 264 4.28 - 6.42: 29 6.42 - 8.57: 5 8.57 - 10.71: 5 Bond angle restraints: 18920 Sorted by residual: angle pdb=" O4' DA C 22 " pdb=" C4' DA C 22 " pdb=" C3' DA C 22 " ideal model delta sigma weight residual 106.00 103.02 2.98 6.00e-01 2.78e+00 2.46e+01 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=" N3 DT C 20 " pdb=" C4 DT C 20 " pdb=" O4 DT C 20 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+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=" O4' DC C 21 " pdb=" C4' DC C 21 " pdb=" C3' DC C 21 " ideal model delta sigma weight residual 106.00 103.43 2.57 6.00e-01 2.78e+00 1.84e+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: 1661 0.053 - 0.106: 338 0.106 - 0.159: 46 0.159 - 0.212: 4 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: 1.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.230 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.610 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: 0.010 Load rotamer database and sin/cos tables:5.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 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= 0.331 Angle : 0.612 10.707 18920 Z= 0.383 Chirality : 0.042 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 are 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/Z covalent geometry : bond 0.00575 / 0.33 (13873) covalent geometry : angle 0.61250 / 0.38 (18920) hydrogen bonds : bond 0.13780 / 9.40 ( 654) hydrogen bonds : angle 5.53699 / 4.03 ( 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 : 0.554 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: 0.5263 time to fit residues: 49.1875 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 : 0.364 ------------------------------------------------------------------------------- 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: 2.9990 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... A 620 HIS B 566 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.065492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.046259 restraints weight = 42648.667| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 3.46 r_work: 0.2645 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.0718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13873 Z= 0.128 Angle : 0.576 8.204 18920 Z= 0.313 Chirality : 0.042 0.237 2050 Planarity : 0.004 0.045 2272 Dihedral : 15.988 167.055 2191 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.73 % Favored : 96.20 % Rotamer: Outliers : 2.72 % Allowed : 14.54 % 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 are not related in a simple way. whole: 0.53 (0.22), residues: 1554 helix: 1.87 (0.21), residues: 680 sheet: -1.22 (0.34), residues: 232 loop : -0.64 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 929 TYR 0.027 0.001 TYR A1067 PHE 0.014 0.001 PHE A1002 TRP 0.008 0.001 TRP A1189 HIS 0.004 0.001 HIS B 650 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.13 (13873) covalent geometry : angle 0.57577 / 0.31 (18920) hydrogen bonds : bond 0.04477 / 3.03 ( 654) hydrogen bonds : angle 4.62936 / 3.36 ( 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 100 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 63 time to evaluate : 0.507 Fit side-chains REVERT: A 929 ARG cc_start: 0.8033 (tpt90) cc_final: 0.7782 (tpt90) REVERT: A 931 MET cc_start: 0.7476 (mmm) cc_final: 0.7224 (mmm) REVERT: B 595 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8256 (pm20) outliers start: 37 outliers final: 18 residues processed: 96 average time/residue: 0.4440 time to fit residues: 47.3338 Evaluate side-chains 72 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 53 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 467 MET 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 674 THR Chi-restraints excluded: chain B residue 467 MET 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 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 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 53 optimal weight: 0.9980 chunk 128 optimal weight: 0.8980 chunk 134 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 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: 7.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1092 HIS ** B 930 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.064232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.044918 restraints weight = 43691.439| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 3.49 r_work: 0.2596 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 13873 Z= 0.177 Angle : 0.572 7.210 18920 Z= 0.311 Chirality : 0.042 0.276 2050 Planarity : 0.004 0.043 2272 Dihedral : 15.959 165.901 2185 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.05 % Favored : 95.88 % Rotamer: Outliers : 2.94 % Allowed : 14.61 % Favored : 82.45 % 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 are not related in a simple way. whole: 0.62 (0.22), residues: 1554 helix: 1.94 (0.21), residues: 680 sheet: -1.13 (0.35), residues: 232 loop : -0.61 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 985 TYR 0.014 0.001 TYR A1067 PHE 0.017 0.001 PHE A 629 TRP 0.011 0.001 TRP A 820 HIS 0.004 0.001 HIS B 620 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.18 (13873) covalent geometry : angle 0.57156 / 0.31 (18920) hydrogen bonds : bond 0.04601 / 3.13 ( 654) hydrogen bonds : angle 4.50614 / 3.29 ( 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 95 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 55 time to evaluate : 0.377 Fit side-chains REVERT: B 677 GLN cc_start: 0.9438 (OUTLIER) cc_final: 0.9234 (mm-40) outliers start: 40 outliers final: 17 residues processed: 89 average time/residue: 0.4392 time to fit residues: 43.5516 Evaluate side-chains 67 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 49 time to evaluate : 0.478 ------------------------------------------------------------------------------- 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 677 GLN Chi-restraints excluded: chain B residue 890 ILE 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: 6.9990 chunk 129 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 131 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 79 optimal weight: 9.9990 chunk 120 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 75 optimal weight: 0.8980 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 620 HIS B 930 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.062953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.043539 restraints weight = 43632.888| |-----------------------------------------------------------------------------| r_work (start): 0.2729 rms_B_bonded: 3.52 r_work: 0.2567 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 13873 Z= 0.234 Angle : 0.602 8.074 18920 Z= 0.325 Chirality : 0.044 0.310 2050 Planarity : 0.004 0.045 2272 Dihedral : 16.060 165.737 2181 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.38 % Favored : 95.50 % Rotamer: Outliers : 3.30 % Allowed : 15.49 % Favored : 81.20 % 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 are not related in a simple way. whole: 0.56 (0.22), residues: 1554 helix: 1.90 (0.21), residues: 680 sheet: -1.09 (0.35), residues: 234 loop : -0.68 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 929 TYR 0.016 0.001 TYR B 698 PHE 0.017 0.001 PHE A1002 TRP 0.014 0.001 TRP A 820 HIS 0.003 0.001 HIS A 883 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.23 (13873) covalent geometry : angle 0.60243 / 0.33 (18920) hydrogen bonds : bond 0.04817 / 3.28 ( 654) hydrogen bonds : angle 4.52664 / 3.30 ( 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 99 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 54 time to evaluate : 0.547 Fit side-chains revert: symmetry clash REVERT: B 677 GLN cc_start: 0.9440 (OUTLIER) cc_final: 0.9240 (mm-40) outliers start: 45 outliers final: 19 residues processed: 95 average time/residue: 0.3972 time to fit residues: 42.9403 Evaluate side-chains 69 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 49 time to evaluate : 0.409 ------------------------------------------------------------------------------- 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 803 VAL Chi-restraints excluded: chain A residue 1074 LEU 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 677 GLN Chi-restraints excluded: chain B residue 871 LEU 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 149 optimal weight: 5.9990 chunk 140 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 chunk 128 optimal weight: 4.9990 chunk 137 optimal weight: 0.9980 chunk 57 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 145 optimal weight: 6.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 996 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.062066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.042654 restraints weight = 43735.699| |-----------------------------------------------------------------------------| r_work (start): 0.2698 rms_B_bonded: 3.52 r_work: 0.2533 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 13873 Z= 0.280 Angle : 0.628 8.407 18920 Z= 0.338 Chirality : 0.045 0.334 2050 Planarity : 0.004 0.046 2272 Dihedral : 16.150 167.235 2178 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.38 % Favored : 95.50 % Rotamer: Outliers : 3.74 % Allowed : 16.67 % Favored : 79.59 % 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 are not related in a simple way. whole: 0.49 (0.22), residues: 1554 helix: 1.80 (0.21), residues: 674 sheet: -0.92 (0.36), residues: 224 loop : -0.75 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 929 TYR 0.016 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 A 883 Details of bonding type rmsd/Z covalent geometry : bond 0.00638 / 0.28 (13873) covalent geometry : angle 0.62785 / 0.34 (18920) hydrogen bonds : bond 0.05128 / 3.49 ( 654) hydrogen bonds : angle 4.59598 / 3.35 ( 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 103 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 52 time to evaluate : 0.499 Fit side-chains REVERT: A 1061 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8376 (mp0) REVERT: A 1116 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.8139 (mttp) outliers start: 51 outliers final: 25 residues processed: 99 average time/residue: 0.4631 time to fit residues: 51.4385 Evaluate side-chains 72 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 45 time to evaluate : 0.395 ------------------------------------------------------------------------------- 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 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 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 972 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 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 871 LEU Chi-restraints excluded: chain B residue 890 ILE Chi-restraints excluded: chain B residue 949 SER Chi-restraints excluded: chain B residue 971 THR Chi-restraints excluded: chain B residue 1054 LEU 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: 0.4980 chunk 78 optimal weight: 5.9990 chunk 80 optimal weight: 7.9990 chunk 128 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 118 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 584 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.063627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.044293 restraints weight = 42954.527| |-----------------------------------------------------------------------------| r_work (start): 0.2747 rms_B_bonded: 3.49 r_work: 0.2584 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13873 Z= 0.126 Angle : 0.562 9.480 18920 Z= 0.304 Chirality : 0.042 0.266 2050 Planarity : 0.003 0.042 2272 Dihedral : 16.008 165.487 2178 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.73 % Favored : 96.20 % Rotamer: Outliers : 2.50 % Allowed : 18.43 % Favored : 79.07 % 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 are not related in a simple way. whole: 0.70 (0.22), residues: 1554 helix: 2.07 (0.21), residues: 668 sheet: -1.07 (0.35), residues: 234 loop : -0.59 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 929 TYR 0.013 0.001 TYR B 698 PHE 0.012 0.001 PHE A1002 TRP 0.008 0.001 TRP B1189 HIS 0.002 0.000 HIS B 557 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.13 (13873) covalent geometry : angle 0.56216 / 0.30 (18920) hydrogen bonds : bond 0.04348 / 2.96 ( 654) hydrogen bonds : angle 4.36690 / 3.18 ( 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 88 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 54 time to evaluate : 0.524 Fit side-chains revert: symmetry clash REVERT: A 1061 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8441 (mp0) REVERT: B 1050 GLU cc_start: 0.8707 (tp30) cc_final: 0.8389 (tp30) outliers start: 34 outliers final: 18 residues processed: 87 average time/residue: 0.4639 time to fit residues: 45.1410 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 : 0.518 ------------------------------------------------------------------------------- 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 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 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 1194 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 48 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 46 optimal weight: 0.1980 chunk 82 optimal weight: 9.9990 chunk 111 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 42 optimal weight: 0.4980 chunk 67 optimal weight: 0.9980 chunk 51 optimal weight: 10.0000 chunk 50 optimal weight: 8.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.063636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.044328 restraints weight = 43142.550| |-----------------------------------------------------------------------------| r_work (start): 0.2747 rms_B_bonded: 3.47 r_work: 0.2586 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13873 Z= 0.143 Angle : 0.566 9.845 18920 Z= 0.304 Chirality : 0.041 0.266 2050 Planarity : 0.003 0.055 2272 Dihedral : 15.885 165.606 2177 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.73 % Favored : 96.20 % Rotamer: Outliers : 2.20 % Allowed : 19.02 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.22), residues: 1554 helix: 2.11 (0.21), residues: 668 sheet: -1.03 (0.35), residues: 234 loop : -0.55 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG B 929 TYR 0.013 0.001 TYR B 698 PHE 0.013 0.001 PHE A 959 TRP 0.009 0.001 TRP A 820 HIS 0.002 0.000 HIS A 883 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (13873) covalent geometry : angle 0.56564 / 0.30 (18920) hydrogen bonds : bond 0.04312 / 2.93 ( 654) hydrogen bonds : angle 4.31240 / 3.14 ( 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 82 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 52 time to evaluate : 0.475 Fit side-chains REVERT: A 886 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8917 (tm) REVERT: A 1061 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8461 (mp0) outliers start: 30 outliers final: 20 residues processed: 81 average time/residue: 0.4756 time to fit residues: 43.1777 Evaluate side-chains 71 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 49 time to evaluate : 0.497 ------------------------------------------------------------------------------- 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 641 LEU 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 886 LEU 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 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 871 LEU Chi-restraints excluded: chain B residue 882 LYS Chi-restraints excluded: chain B residue 890 ILE 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: 9.9990 chunk 34 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 152 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 150 optimal weight: 0.8980 chunk 11 optimal weight: 6.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.063257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.043980 restraints weight = 42806.197| |-----------------------------------------------------------------------------| r_work (start): 0.2736 rms_B_bonded: 3.45 r_work: 0.2573 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13873 Z= 0.182 Angle : 0.590 12.226 18920 Z= 0.317 Chirality : 0.043 0.287 2050 Planarity : 0.004 0.063 2272 Dihedral : 15.877 166.128 2177 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.12 % Favored : 95.82 % Rotamer: Outliers : 2.42 % Allowed : 19.16 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.22), residues: 1554 helix: 1.96 (0.21), residues: 682 sheet: -1.03 (0.35), residues: 234 loop : -0.59 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 929 TYR 0.014 0.001 TYR B 698 PHE 0.030 0.001 PHE A 959 TRP 0.011 0.001 TRP A 820 HIS 0.002 0.001 HIS A 789 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 (13873) covalent geometry : angle 0.58964 / 0.32 (18920) hydrogen bonds : bond 0.04461 / 3.04 ( 654) hydrogen bonds : angle 4.34936 / 3.17 ( 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 84 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 51 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1061 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8476 (mp0) REVERT: B 1121 CYS cc_start: 0.6863 (OUTLIER) cc_final: 0.6619 (p) outliers start: 33 outliers final: 22 residues processed: 83 average time/residue: 0.4309 time to fit residues: 40.3509 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 : 0.463 ------------------------------------------------------------------------------- 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 641 LEU 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 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 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 871 LEU Chi-restraints excluded: chain B residue 882 LYS 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 1194 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 127 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 142 optimal weight: 5.9990 chunk 110 optimal weight: 7.9990 chunk 42 optimal weight: 0.9990 chunk 128 optimal weight: 0.9980 chunk 74 optimal weight: 0.0870 chunk 62 optimal weight: 0.8980 chunk 123 optimal weight: 0.4980 chunk 19 optimal weight: 6.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.064604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.045467 restraints weight = 43289.864| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 3.52 r_work: 0.2618 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 13873 Z= 0.115 Angle : 0.564 11.144 18920 Z= 0.304 Chirality : 0.041 0.247 2050 Planarity : 0.003 0.041 2272 Dihedral : 15.737 165.464 2177 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.73 % Favored : 96.20 % 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 are not related in a simple way. whole: 0.82 (0.22), residues: 1554 helix: 2.16 (0.21), residues: 670 sheet: -1.05 (0.35), residues: 234 loop : -0.52 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 929 TYR 0.012 0.001 TYR B 698 PHE 0.023 0.001 PHE A 959 TRP 0.009 0.001 TRP A1189 HIS 0.003 0.000 HIS B 620 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 (13873) covalent geometry : angle 0.56409 / 0.30 (18920) hydrogen bonds : bond 0.03997 / 2.72 ( 654) hydrogen bonds : angle 4.23880 / 3.08 ( 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 : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1061 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8494 (mp0) outliers start: 30 outliers final: 17 residues processed: 82 average time/residue: 0.5129 time to fit residues: 47.0038 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 : 0.536 ------------------------------------------------------------------------------- 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 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 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 882 LYS 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: 1.9990 chunk 61 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 chunk 145 optimal weight: 7.9990 chunk 26 optimal weight: 7.9990 chunk 135 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.063131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.043835 restraints weight = 43350.657| |-----------------------------------------------------------------------------| r_work (start): 0.2731 rms_B_bonded: 3.50 r_work: 0.2569 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 13873 Z= 0.210 Angle : 0.615 11.563 18920 Z= 0.327 Chirality : 0.043 0.294 2050 Planarity : 0.004 0.044 2272 Dihedral : 15.793 166.304 2177 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.18 % Favored : 95.69 % Rotamer: Outliers : 1.54 % Allowed : 19.97 % Favored : 78.49 % 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 are not related in a simple way. whole: 0.72 (0.23), residues: 1554 helix: 2.00 (0.21), residues: 682 sheet: -1.01 (0.35), residues: 234 loop : -0.57 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 736 TYR 0.014 0.001 TYR B 698 PHE 0.017 0.001 PHE A 959 TRP 0.014 0.001 TRP A 820 HIS 0.003 0.001 HIS A 789 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.21 (13873) covalent geometry : angle 0.61546 / 0.33 (18920) hydrogen bonds : bond 0.04519 / 3.08 ( 654) hydrogen bonds : angle 4.33580 / 3.15 ( 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 71 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 50 time to evaluate : 0.512 Fit side-chains revert: symmetry clash REVERT: A 1061 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8487 (mp0) outliers start: 21 outliers final: 17 residues processed: 71 average time/residue: 0.4954 time to fit residues: 39.2716 Evaluate side-chains 67 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 49 time to evaluate : 0.517 ------------------------------------------------------------------------------- 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 882 LYS Chi-restraints excluded: chain B residue 1113 LEU 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: 1.9990 chunk 60 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 78 optimal weight: 0.8980 chunk 154 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 148 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.063569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.044338 restraints weight = 43426.822| |-----------------------------------------------------------------------------| r_work (start): 0.2748 rms_B_bonded: 3.52 r_work: 0.2586 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13873 Z= 0.154 Angle : 0.595 13.749 18920 Z= 0.317 Chirality : 0.042 0.275 2050 Planarity : 0.004 0.071 2272 Dihedral : 15.789 165.755 2177 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.86 % Favored : 96.07 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.23), residues: 1554 helix: 2.11 (0.21), residues: 672 sheet: -0.98 (0.35), residues: 234 loop : -0.51 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B 929 TYR 0.013 0.001 TYR B 698 PHE 0.015 0.001 PHE A 959 TRP 0.009 0.001 TRP A 820 HIS 0.002 0.001 HIS A 883 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (13873) covalent geometry : angle 0.59483 / 0.32 (18920) hydrogen bonds : bond 0.04280 / 2.91 ( 654) hydrogen bonds : angle 4.28684 / 3.11 ( 1799) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3256.31 seconds wall clock time: 56 minutes 30.04 seconds (3390.04 seconds total)