Starting phenix.real_space_refine on Wed Aug 5 11:59:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vmh_65188/08_2026/9vmh_65188.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vmh_65188/08_2026/9vmh_65188.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vmh_65188/08_2026/9vmh_65188.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vmh_65188/08_2026/9vmh_65188.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vmh_65188/08_2026/9vmh_65188.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vmh_65188/08_2026/9vmh_65188.map" } resolution = 2.96 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= 0.005 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 Zn 1 6.06 5 P 2 5.49 5 S 35 5.16 5 C 5852 2.51 5 N 1664 2.21 5 O 1798 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9352 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4263 Classifications: {'peptide': 577} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 546} Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "B" Number of atoms: 5031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 673, 5031 Classifications: {'peptide': 673} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 43, 'TRANS': 629} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'ADP': 1, 'BTN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'BTN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {' ZN': 1, 'BTN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'BTN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 1.92, per 1000 atoms: 0.21 Number of scatterers: 9352 At special positions: 0 Unit cell: (104.92, 147.92, 82.56, 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) Zn 1 29.99 S 35 16.00 P 2 15.00 O 1798 8.00 N 1664 7.00 C 5852 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 318.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" NE2 HIS B 732 " pdb="ZN ZN B1201 " - pdb=" NE2 HIS B 734 " 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2278 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 12 sheets defined 38.2% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 11 through 25 removed outlier: 3.541A pdb=" N ILE A 15 " --> pdb=" O GLY A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 44 Processing helix chain 'A' and resid 56 through 62 removed outlier: 3.822A pdb=" N TYR A 61 " --> pdb=" O PRO A 57 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU A 62 " --> pdb=" O VAL A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 74 Processing helix chain 'A' and resid 89 through 96 removed outlier: 3.680A pdb=" N ALA A 93 " --> pdb=" O ASN A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 114 Processing helix chain 'A' and resid 115 through 118 Processing helix chain 'A' and resid 119 through 125 Processing helix chain 'A' and resid 140 through 149 Processing helix chain 'A' and resid 176 through 193 Processing helix chain 'A' and resid 248 through 267 removed outlier: 3.580A pdb=" N ARG A 252 " --> pdb=" O ASP A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 305 removed outlier: 4.103A pdb=" N THR A 300 " --> pdb=" O GLU A 296 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE A 303 " --> pdb=" O VAL A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 317 Processing helix chain 'A' and resid 398 through 413 Processing helix chain 'A' and resid 421 through 430 Processing helix chain 'A' and resid 431 through 437 Processing helix chain 'B' and resid 458 through 473 removed outlier: 3.748A pdb=" N LYS B 462 " --> pdb=" O ASP B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 489 Processing helix chain 'B' and resid 501 through 521 removed outlier: 3.613A pdb=" N ARG B 505 " --> pdb=" O GLY B 501 " (cutoff:3.500A) Proline residue: B 511 - end of helix Processing helix chain 'B' and resid 544 through 550 removed outlier: 3.716A pdb=" N LEU B 548 " --> pdb=" O ARG B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 559 Processing helix chain 'B' and resid 571 through 579 Processing helix chain 'B' and resid 583 through 595 Processing helix chain 'B' and resid 616 through 631 Processing helix chain 'B' and resid 647 through 658 removed outlier: 3.946A pdb=" N GLY B 658 " --> pdb=" O VAL B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 681 through 696 Processing helix chain 'B' and resid 710 through 725 removed outlier: 3.616A pdb=" N ARG B 716 " --> pdb=" O PRO B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 749 removed outlier: 3.615A pdb=" N TYR B 744 " --> pdb=" O GLN B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 763 Processing helix chain 'B' and resid 770 through 778 Processing helix chain 'B' and resid 788 through 795 removed outlier: 3.988A pdb=" N LEU B 795 " --> pdb=" O ALA B 791 " (cutoff:3.500A) Processing helix chain 'B' and resid 795 through 806 removed outlier: 3.811A pdb=" N TRP B 799 " --> pdb=" O LEU B 795 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR B 806 " --> pdb=" O LEU B 802 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 810 Processing helix chain 'B' and resid 826 through 837 removed outlier: 3.657A pdb=" N LEU B 830 " --> pdb=" O PRO B 826 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N SER B 831 " --> pdb=" O GLY B 827 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ASN B 832 " --> pdb=" O GLY B 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 861 removed outlier: 3.966A pdb=" N GLU B 847 " --> pdb=" O GLY B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 888 through 893 removed outlier: 3.744A pdb=" N SER B 892 " --> pdb=" O ASP B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 900 through 909 Processing helix chain 'B' and resid 921 through 929 Processing helix chain 'B' and resid 940 through 948 Processing helix chain 'B' and resid 951 through 963 Processing helix chain 'B' and resid 963 through 978 Processing helix chain 'B' and resid 984 through 990 Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 50 removed outlier: 8.658A pdb=" N TYR A 49 " --> pdb=" O THR A 28 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ALA A 30 " --> pdb=" O TYR A 49 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N VAL A 31 " --> pdb=" O VAL A 7 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LYS A 4 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N TYR A 80 " --> pdb=" O LYS A 4 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU A 6 " --> pdb=" O TYR A 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 168 through 171 Processing sheet with id=AA3, first strand: chain 'A' and resid 236 through 241 removed outlier: 7.713A pdb=" N VAL A 231 " --> pdb=" O VAL A 238 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLU A 240 " --> pdb=" O CYS A 229 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N CYS A 229 " --> pdb=" O GLU A 240 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N GLN A 212 " --> pdb=" O LEU A 224 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLU A 226 " --> pdb=" O GLU A 210 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLU A 210 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLU A 288 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU A 277 " --> pdb=" O PHE A 286 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N PHE A 286 " --> pdb=" O LEU A 277 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 336 through 343 removed outlier: 3.903A pdb=" N VAL A 390 " --> pdb=" O ILE A 342 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 360 through 362 Processing sheet with id=AA6, first strand: chain 'A' and resid 1011 through 1015 removed outlier: 5.532A pdb=" N LEU A1012 " --> pdb=" O ILE A1029 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ILE A1029 " --> pdb=" O LEU A1012 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA A1014 " --> pdb=" O MET A1027 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1061 through 1062 removed outlier: 4.072A pdb=" N VAL A1124 " --> pdb=" O ILE A1062 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL A1125 " --> pdb=" O GLU A1107 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1094 through 1099 removed outlier: 6.529A pdb=" N MET A1094 " --> pdb=" O GLU A1090 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N GLU A1090 " --> pdb=" O MET A1094 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ALA A1096 " --> pdb=" O THR A1088 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N THR A1088 " --> pdb=" O ALA A1096 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ILE A1098 " --> pdb=" O ILE A1086 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 525 through 528 removed outlier: 6.924A pdb=" N VAL B 526 " --> pdb=" O SER B 564 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N GLU B 566 " --> pdb=" O VAL B 526 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ASP B 528 " --> pdb=" O GLU B 566 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N TRP B 568 " --> pdb=" O ASP B 528 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL B 565 " --> pdb=" O GLN B 601 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N LEU B 603 " --> pdb=" O VAL B 565 " (cutoff:3.500A) removed outlier: 9.357A pdb=" N CYS B 567 " --> pdb=" O LEU B 603 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU B 600 " --> pdb=" O ILE B 634 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ARG B 636 " --> pdb=" O LEU B 600 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N MET B 602 " --> pdb=" O ARG B 636 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N PHE B 635 " --> pdb=" O GLU B 663 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ALA B 665 " --> pdb=" O PHE B 635 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE B 637 " --> pdb=" O ALA B 665 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N CYS B 667 " --> pdb=" O ILE B 637 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ALA B 662 " --> pdb=" O VAL B 699 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ALA B 701 " --> pdb=" O ALA B 662 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL B 664 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N LYS B 703 " --> pdb=" O VAL B 664 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N MET B 666 " --> pdb=" O LYS B 703 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP B 756 " --> pdb=" O LEU B 731 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N THR B 733 " --> pdb=" O ASP B 756 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLY B 525 " --> pdb=" O VAL B 755 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N GLY B 757 " --> pdb=" O GLY B 525 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N THR B 527 " --> pdb=" O GLY B 757 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 998 through 1003 removed outlier: 7.034A pdb=" N VAL B1006 " --> pdb=" O LEU B1002 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N LEU B1012 " --> pdb=" O ILE B1029 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ILE B1029 " --> pdb=" O LEU B1012 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA B1014 " --> pdb=" O MET B1027 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 1062 through 1063 removed outlier: 6.879A pdb=" N ILE B1062 " --> pdb=" O LEU B1123 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N LEU B1123 " --> pdb=" O VAL B1109 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N VAL B1109 " --> pdb=" O LEU B1123 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL B1125 " --> pdb=" O GLU B1107 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 1095 through 1099 removed outlier: 6.895A pdb=" N ALA B1096 " --> pdb=" O THR B1088 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N THR B1088 " --> pdb=" O ALA B1096 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ILE B1098 " --> pdb=" O ILE B1086 " (cutoff:3.500A) 383 hydrogen bonds defined for protein. 1077 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.73 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3234 1.34 - 1.46: 1897 1.46 - 1.58: 4336 1.58 - 1.70: 3 1.70 - 1.82: 56 Bond restraints: 9526 Sorted by residual: bond pdb=" N ALA B 706 " pdb=" CA ALA B 706 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.36e-02 5.41e+03 4.95e+00 bond pdb=" N MET B 705 " pdb=" CA MET B 705 " ideal model delta sigma weight residual 1.458 1.486 -0.029 1.30e-02 5.92e+03 4.81e+00 bond pdb=" N ASP B 704 " pdb=" CA ASP B 704 " ideal model delta sigma weight residual 1.463 1.490 -0.027 1.37e-02 5.33e+03 3.93e+00 bond pdb=" C SER A1016 " pdb=" N GLU A1017 " ideal model delta sigma weight residual 1.331 1.287 0.044 2.83e-02 1.25e+03 2.41e+00 bond pdb=" C ASP B 704 " pdb=" O ASP B 704 " ideal model delta sigma weight residual 1.232 1.250 -0.019 1.32e-02 5.74e+03 1.99e+00 ... (remaining 9521 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 12799 2.02 - 4.05: 141 4.05 - 6.07: 34 6.07 - 8.09: 2 8.09 - 10.11: 1 Bond angle restraints: 12977 Sorted by residual: angle pdb=" C MET B 705 " pdb=" N ALA B 706 " pdb=" CA ALA B 706 " ideal model delta sigma weight residual 122.42 116.94 5.48 1.77e+00 3.19e-01 9.60e+00 angle pdb=" C ASP A 279 " pdb=" N GLU A 280 " pdb=" CA GLU A 280 " ideal model delta sigma weight residual 121.54 127.28 -5.74 1.91e+00 2.74e-01 9.02e+00 angle pdb=" CA GLU A 280 " pdb=" CB GLU A 280 " pdb=" CG GLU A 280 " ideal model delta sigma weight residual 114.10 120.02 -5.92 2.00e+00 2.50e-01 8.77e+00 angle pdb=" CA ASP B 704 " pdb=" CB ASP B 704 " pdb=" CG ASP B 704 " ideal model delta sigma weight residual 112.60 115.53 -2.93 1.00e+00 1.00e+00 8.60e+00 angle pdb=" CA LEU A 451 " pdb=" CB LEU A 451 " pdb=" CG LEU A 451 " ideal model delta sigma weight residual 116.30 126.41 -10.11 3.50e+00 8.16e-02 8.35e+00 ... (remaining 12972 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.78: 5541 20.78 - 41.57: 206 41.57 - 62.35: 19 62.35 - 83.14: 6 83.14 - 103.92: 2 Dihedral angle restraints: 5774 sinusoidal: 2218 harmonic: 3556 Sorted by residual: dihedral pdb=" C2' ADP A1201 " pdb=" C1' ADP A1201 " pdb=" N9 ADP A1201 " pdb=" C4 ADP A1201 " ideal model delta sinusoidal sigma weight residual 91.55 -12.37 103.92 1 2.00e+01 2.50e-03 2.98e+01 dihedral pdb=" CA VAL B 866 " pdb=" C VAL B 866 " pdb=" N THR B 867 " pdb=" CA THR B 867 " ideal model delta harmonic sigma weight residual -180.00 -163.04 -16.96 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA ASP A1041 " pdb=" C ASP A1041 " pdb=" N ARG A1042 " pdb=" CA ARG A1042 " ideal model delta harmonic sigma weight residual 180.00 163.95 16.05 0 5.00e+00 4.00e-02 1.03e+01 ... (remaining 5771 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 897 0.029 - 0.058: 354 0.058 - 0.086: 117 0.086 - 0.115: 109 0.115 - 0.144: 23 Chirality restraints: 1500 Sorted by residual: chirality pdb=" CA TRP B 748 " pdb=" N TRP B 748 " pdb=" C TRP B 748 " pdb=" CB TRP B 748 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.17e-01 chirality pdb=" CA VAL B1124 " pdb=" N VAL B1124 " pdb=" C VAL B1124 " pdb=" CB VAL B1124 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.63e-01 chirality pdb=" CA SER B 965 " pdb=" N SER B 965 " pdb=" C SER B 965 " pdb=" CB SER B 965 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.55e-01 ... (remaining 1497 not shown) Planarity restraints: 1724 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A1035 " -0.023 5.00e-02 4.00e+02 3.53e-02 1.99e+00 pdb=" N PRO A1036 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO A1036 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A1036 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 748 " 0.013 2.00e-02 2.50e+03 8.73e-03 1.90e+00 pdb=" CG TRP B 748 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP B 748 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP B 748 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 748 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 748 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 748 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 748 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 748 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 748 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 745 " 0.007 2.00e-02 2.50e+03 1.33e-02 1.77e+00 pdb=" C VAL B 745 " -0.023 2.00e-02 2.50e+03 pdb=" O VAL B 745 " 0.009 2.00e-02 2.50e+03 pdb=" N ALA B 746 " 0.008 2.00e-02 2.50e+03 ... (remaining 1721 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 82 2.68 - 3.24: 9259 3.24 - 3.79: 14036 3.79 - 4.35: 17823 4.35 - 4.90: 29909 Nonbonded interactions: 71109 Sorted by model distance: nonbonded pdb=" CH2 TRP B 568 " pdb=" CB PRO B 584 " model vdw 2.130 3.740 nonbonded pdb=" CE LYS B1093 " pdb=" C11 BTN B1202 " model vdw 2.149 2.936 nonbonded pdb=" O2' ADP A1201 " pdb=" O3' ADP A1201 " model vdw 2.474 2.432 nonbonded pdb=" O THR A 441 " pdb=" OG SER A 442 " model vdw 2.598 3.040 nonbonded pdb=" N VAL B 866 " pdb=" O VAL B 866 " model vdw 2.606 2.496 ... (remaining 71104 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=1.00 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: 2.940 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: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 10.930 Find NCS groups from input model: 0.060 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:6.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 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 : 0.005 0.264 9530 Z= 0.331 Angle : 0.586 10.115 12977 Z= 0.294 Chirality : 0.043 0.144 1500 Planarity : 0.004 0.035 1724 Dihedral : 10.961 103.921 3496 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 0.42 % Allowed : 7.19 % Favored : 92.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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: -0.11 (0.25), residues: 1244 helix: 1.55 (0.27), residues: 434 sheet: -0.26 (0.36), residues: 205 loop : -1.25 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1024 TYR 0.014 0.001 TYR B 573 PHE 0.010 0.001 PHE A 103 TRP 0.024 0.001 TRP B 748 HIS 0.004 0.001 HIS B 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 ( 9526) covalent geometry : angle 0.58595 / 0.29 (12977) hydrogen bonds : bond 0.14822 / 9.73 ( 383) hydrogen bonds : angle 5.82360 / 4.35 ( 1077) metal coordination : bond 0.00128 / 0.06 ( 2) Misc. bond : bond 0.19872 / 9.59 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.5267 (ppp) cc_final: 0.4767 (ppp) REVERT: A 255 MET cc_start: 0.8692 (mmm) cc_final: 0.8317 (mmm) REVERT: A 1061 HIS cc_start: 0.9198 (m-70) cc_final: 0.8873 (m-70) REVERT: B 586 GLU cc_start: 0.9163 (mt-10) cc_final: 0.8958 (mp0) REVERT: B 1004 ARG cc_start: 0.9000 (ttp80) cc_final: 0.8401 (tmt170) REVERT: B 1123 LEU cc_start: 0.9786 (tm) cc_final: 0.9453 (mt) outliers start: 4 outliers final: 3 residues processed: 60 average time/residue: 0.7201 time to fit residues: 45.8696 Evaluate side-chains 43 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 705 MET Chi-restraints excluded: chain B residue 1106 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 9.9990 chunk 113 optimal weight: 7.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 323 GLN A 339 GLN B 601 GLN B 835 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.085511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.054058 restraints weight = 32434.816| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 4.33 r_work: 0.2808 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.0875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9530 Z= 0.208 Angle : 0.639 12.096 12977 Z= 0.320 Chirality : 0.045 0.187 1500 Planarity : 0.005 0.058 1724 Dihedral : 5.805 98.940 1426 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 2.33 % Allowed : 9.20 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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: -0.31 (0.24), residues: 1244 helix: 1.28 (0.26), residues: 452 sheet: -0.35 (0.36), residues: 211 loop : -1.37 (0.25), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 495 TYR 0.015 0.001 TYR B 573 PHE 0.010 0.001 PHE A 103 TRP 0.028 0.002 TRP B 748 HIS 0.006 0.001 HIS B 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.21 ( 9526) covalent geometry : angle 0.63887 / 0.32 (12977) hydrogen bonds : bond 0.04627 / 3.14 ( 383) hydrogen bonds : angle 4.73582 / 3.51 ( 1077) metal coordination : bond 0.00208 / 0.10 ( 2) Misc. bond : bond 0.00189 / 0.10 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 42 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: A 133 MET cc_start: 0.5005 (ppp) cc_final: 0.4565 (ppp) REVERT: A 323 GLN cc_start: 0.9516 (OUTLIER) cc_final: 0.9277 (pm20) REVERT: A 1061 HIS cc_start: 0.9269 (m-70) cc_final: 0.8976 (m-70) REVERT: B 568 TRP cc_start: 0.9579 (OUTLIER) cc_final: 0.9086 (t60) REVERT: B 748 TRP cc_start: 0.9435 (OUTLIER) cc_final: 0.8937 (p90) REVERT: B 1004 ARG cc_start: 0.9039 (ttp80) cc_final: 0.8456 (tmt170) REVERT: B 1123 LEU cc_start: 0.9832 (tm) cc_final: 0.9623 (pp) outliers start: 22 outliers final: 8 residues processed: 57 average time/residue: 0.5855 time to fit residues: 35.9351 Evaluate side-chains 47 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain B residue 568 TRP Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 705 MET Chi-restraints excluded: chain B residue 748 TRP Chi-restraints excluded: chain B residue 907 LEU Chi-restraints excluded: chain B residue 1048 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 35 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 50 optimal weight: 20.0000 chunk 47 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 chunk 110 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 601 GLN B 691 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.085413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.054097 restraints weight = 32155.798| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 4.35 r_work: 0.2812 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9530 Z= 0.170 Angle : 0.611 13.373 12977 Z= 0.303 Chirality : 0.044 0.138 1500 Planarity : 0.004 0.043 1724 Dihedral : 5.750 93.942 1425 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 2.43 % Allowed : 10.47 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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: -0.30 (0.24), residues: 1244 helix: 1.27 (0.26), residues: 453 sheet: -0.21 (0.36), residues: 213 loop : -1.41 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 495 TYR 0.014 0.001 TYR B 573 PHE 0.010 0.001 PHE A 103 TRP 0.026 0.002 TRP B 748 HIS 0.005 0.001 HIS B 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 ( 9526) covalent geometry : angle 0.61073 / 0.30 (12977) hydrogen bonds : bond 0.04219 / 2.85 ( 383) hydrogen bonds : angle 4.56080 / 3.35 ( 1077) metal coordination : bond 0.00149 / 0.07 ( 2) Misc. bond : bond 0.00081 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 39 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 LYS cc_start: 0.8801 (mmmt) cc_final: 0.8522 (mppt) REVERT: A 133 MET cc_start: 0.5416 (OUTLIER) cc_final: 0.4901 (ppp) REVERT: A 156 PHE cc_start: 0.4846 (OUTLIER) cc_final: 0.4591 (t80) REVERT: A 296 GLU cc_start: 0.9089 (OUTLIER) cc_final: 0.8886 (pm20) REVERT: A 323 GLN cc_start: 0.9514 (OUTLIER) cc_final: 0.9247 (pm20) REVERT: A 1061 HIS cc_start: 0.9241 (m-70) cc_final: 0.8944 (m-70) REVERT: B 568 TRP cc_start: 0.9565 (OUTLIER) cc_final: 0.9047 (t60) REVERT: B 1004 ARG cc_start: 0.9031 (ttp80) cc_final: 0.8460 (tmt170) outliers start: 23 outliers final: 8 residues processed: 59 average time/residue: 0.5909 time to fit residues: 37.6505 Evaluate side-chains 49 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 36 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain A residue 447 ARG Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain B residue 568 TRP Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 705 MET Chi-restraints excluded: chain B residue 907 LEU Chi-restraints excluded: chain B residue 1048 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 22 optimal weight: 8.9990 chunk 28 optimal weight: 7.9990 chunk 101 optimal weight: 6.9990 chunk 58 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 3 optimal weight: 0.5980 chunk 9 optimal weight: 0.1980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 601 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.086785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.055561 restraints weight = 32468.751| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 4.41 r_work: 0.2852 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9530 Z= 0.107 Angle : 0.574 12.677 12977 Z= 0.281 Chirality : 0.043 0.132 1500 Planarity : 0.004 0.056 1724 Dihedral : 5.535 88.741 1425 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 2.96 % Allowed : 10.47 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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: -0.14 (0.25), residues: 1244 helix: 1.39 (0.26), residues: 454 sheet: 0.01 (0.36), residues: 211 loop : -1.37 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 495 TYR 0.012 0.001 TYR B 573 PHE 0.009 0.001 PHE A 103 TRP 0.020 0.001 TRP B 748 HIS 0.003 0.001 HIS B 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 ( 9526) covalent geometry : angle 0.57395 / 0.28 (12977) hydrogen bonds : bond 0.03211 / 2.17 ( 383) hydrogen bonds : angle 4.27207 / 3.13 ( 1077) metal coordination : bond 0.00126 / 0.06 ( 2) Misc. bond : bond 0.00030 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 39 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: A 117 LYS cc_start: 0.8749 (mmmt) cc_final: 0.8460 (mppt) REVERT: A 133 MET cc_start: 0.5499 (ppp) cc_final: 0.4042 (ppp) REVERT: A 151 MET cc_start: 0.4035 (mtt) cc_final: 0.3461 (tpp) REVERT: A 296 GLU cc_start: 0.9061 (OUTLIER) cc_final: 0.8828 (mp0) REVERT: A 323 GLN cc_start: 0.9486 (OUTLIER) cc_final: 0.9169 (pm20) REVERT: A 1061 HIS cc_start: 0.9220 (m-70) cc_final: 0.8912 (m-70) REVERT: B 568 TRP cc_start: 0.9514 (OUTLIER) cc_final: 0.9023 (t60) REVERT: B 819 ARG cc_start: 0.5443 (mmt180) cc_final: 0.5241 (mmt180) REVERT: B 922 LEU cc_start: 0.6958 (OUTLIER) cc_final: 0.6740 (tm) REVERT: B 1004 ARG cc_start: 0.8996 (ttp80) cc_final: 0.8450 (tmt170) outliers start: 28 outliers final: 8 residues processed: 61 average time/residue: 0.5551 time to fit residues: 36.6612 Evaluate side-chains 48 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 36 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 447 ARG Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain B residue 568 TRP Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 748 TRP Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 1048 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 83 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 0.1980 chunk 18 optimal weight: 40.0000 chunk 122 optimal weight: 0.0870 chunk 89 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 chunk 1 optimal weight: 0.5980 chunk 20 optimal weight: 10.0000 chunk 87 optimal weight: 2.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 339 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.087237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.056175 restraints weight = 32198.233| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 4.34 r_work: 0.2875 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9530 Z= 0.099 Angle : 0.582 13.781 12977 Z= 0.281 Chirality : 0.043 0.133 1500 Planarity : 0.004 0.041 1724 Dihedral : 5.454 95.318 1422 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 1.48 % Allowed : 12.37 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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: -0.10 (0.25), residues: 1244 helix: 1.42 (0.26), residues: 454 sheet: 0.21 (0.38), residues: 204 loop : -1.41 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 495 TYR 0.011 0.001 TYR B 573 PHE 0.025 0.001 PHE A 156 TRP 0.018 0.001 TRP B 748 HIS 0.002 0.000 HIS B 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 ( 9526) covalent geometry : angle 0.58177 / 0.28 (12977) hydrogen bonds : bond 0.02955 / 1.99 ( 383) hydrogen bonds : angle 4.16967 / 3.03 ( 1077) metal coordination : bond 0.00102 / 0.05 ( 2) Misc. bond : bond 0.00004 / 0.00 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 44 time to evaluate : 0.442 Fit side-chains revert: symmetry clash REVERT: A 133 MET cc_start: 0.5319 (ppp) cc_final: 0.4921 (ppp) REVERT: A 151 MET cc_start: 0.3775 (mtt) cc_final: 0.3402 (tpp) REVERT: A 168 MET cc_start: 0.6380 (pmm) cc_final: 0.6152 (pmm) REVERT: A 296 GLU cc_start: 0.9041 (OUTLIER) cc_final: 0.8818 (mp0) REVERT: A 1061 HIS cc_start: 0.9197 (m-70) cc_final: 0.8891 (m-70) REVERT: B 568 TRP cc_start: 0.9494 (OUTLIER) cc_final: 0.9052 (t60) REVERT: B 1004 ARG cc_start: 0.9000 (ttp80) cc_final: 0.8454 (tmt170) outliers start: 14 outliers final: 6 residues processed: 56 average time/residue: 0.5121 time to fit residues: 31.4505 Evaluate side-chains 47 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain B residue 568 TRP Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 666 MET Chi-restraints excluded: chain B residue 907 LEU Chi-restraints excluded: chain B residue 1048 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 13 optimal weight: 30.0000 chunk 90 optimal weight: 0.9980 chunk 96 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 39 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 92 optimal weight: 0.4980 chunk 2 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 323 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.087148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.056001 restraints weight = 32224.274| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 4.43 r_work: 0.2863 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9530 Z= 0.106 Angle : 0.581 14.450 12977 Z= 0.279 Chirality : 0.043 0.134 1500 Planarity : 0.004 0.041 1724 Dihedral : 5.362 93.254 1422 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 2.22 % Allowed : 12.47 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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: -0.04 (0.25), residues: 1244 helix: 1.48 (0.26), residues: 448 sheet: 0.19 (0.38), residues: 206 loop : -1.34 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 495 TYR 0.011 0.001 TYR B 573 PHE 0.015 0.001 PHE A 156 TRP 0.017 0.001 TRP B 748 HIS 0.003 0.001 HIS B 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 ( 9526) covalent geometry : angle 0.58060 / 0.28 (12977) hydrogen bonds : bond 0.03067 / 2.08 ( 383) hydrogen bonds : angle 4.12832 / 3.01 ( 1077) metal coordination : bond 0.00110 / 0.05 ( 2) Misc. bond : bond 0.00017 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 41 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: A 117 LYS cc_start: 0.8692 (mmmt) cc_final: 0.8360 (mppt) REVERT: A 133 MET cc_start: 0.5468 (OUTLIER) cc_final: 0.5075 (ppp) REVERT: A 151 MET cc_start: 0.3907 (mtt) cc_final: 0.3506 (tpp) REVERT: A 255 MET cc_start: 0.8568 (mmm) cc_final: 0.8340 (mmm) REVERT: A 296 GLU cc_start: 0.9052 (OUTLIER) cc_final: 0.8833 (pm20) REVERT: A 323 GLN cc_start: 0.9534 (OUTLIER) cc_final: 0.9246 (pm20) REVERT: A 1061 HIS cc_start: 0.9210 (m-70) cc_final: 0.8909 (m-70) REVERT: B 568 TRP cc_start: 0.9515 (OUTLIER) cc_final: 0.9045 (t60) REVERT: B 1004 ARG cc_start: 0.9021 (ttp80) cc_final: 0.8472 (tmt170) outliers start: 21 outliers final: 6 residues processed: 57 average time/residue: 0.4740 time to fit residues: 29.4840 Evaluate side-chains 49 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain B residue 568 TRP Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 907 LEU Chi-restraints excluded: chain B residue 1048 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 105 optimal weight: 0.9980 chunk 101 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 117 optimal weight: 0.0020 chunk 5 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 49 optimal weight: 0.8980 chunk 45 optimal weight: 9.9990 chunk 6 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 overall best weight: 1.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.087069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.056049 restraints weight = 32088.741| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 4.31 r_work: 0.2868 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9530 Z= 0.109 Angle : 0.584 14.775 12977 Z= 0.282 Chirality : 0.043 0.134 1500 Planarity : 0.004 0.040 1724 Dihedral : 5.322 90.950 1422 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 1.90 % Allowed : 13.00 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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: -0.02 (0.25), residues: 1244 helix: 1.50 (0.26), residues: 448 sheet: 0.20 (0.38), residues: 206 loop : -1.33 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 495 TYR 0.011 0.001 TYR B 573 PHE 0.013 0.001 PHE A 156 TRP 0.025 0.001 TRP B 748 HIS 0.003 0.001 HIS B1061 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 ( 9526) covalent geometry : angle 0.58431 / 0.28 (12977) hydrogen bonds : bond 0.03052 / 2.06 ( 383) hydrogen bonds : angle 4.09806 / 2.98 ( 1077) metal coordination : bond 0.00092 / 0.04 ( 2) Misc. bond : bond 0.00016 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 39 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: A 117 LYS cc_start: 0.8652 (mmmt) cc_final: 0.8332 (mppt) REVERT: A 133 MET cc_start: 0.5530 (OUTLIER) cc_final: 0.4918 (ppp) REVERT: A 151 MET cc_start: 0.3636 (mtt) cc_final: 0.3004 (tpp) REVERT: A 296 GLU cc_start: 0.9051 (OUTLIER) cc_final: 0.8845 (pm20) REVERT: A 1061 HIS cc_start: 0.9169 (m-70) cc_final: 0.8849 (m-70) REVERT: B 568 TRP cc_start: 0.9509 (OUTLIER) cc_final: 0.8977 (t60) REVERT: B 1004 ARG cc_start: 0.8991 (ttp80) cc_final: 0.8474 (tmt170) outliers start: 18 outliers final: 8 residues processed: 54 average time/residue: 0.4658 time to fit residues: 27.3017 Evaluate side-chains 50 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain B residue 568 TRP Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 907 LEU Chi-restraints excluded: chain B residue 1048 VAL Chi-restraints excluded: chain B residue 1106 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 89 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 113 optimal weight: 6.9990 chunk 119 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 27 optimal weight: 10.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 601 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.085169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.053782 restraints weight = 32203.614| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 4.35 r_work: 0.2802 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9530 Z= 0.208 Angle : 0.665 15.161 12977 Z= 0.324 Chirality : 0.045 0.141 1500 Planarity : 0.004 0.058 1724 Dihedral : 5.499 85.984 1422 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 2.11 % Allowed : 13.42 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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: -0.28 (0.25), residues: 1244 helix: 1.31 (0.26), residues: 455 sheet: -0.07 (0.37), residues: 216 loop : -1.50 (0.25), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 495 TYR 0.016 0.001 TYR B 573 PHE 0.013 0.001 PHE A 156 TRP 0.023 0.002 TRP B 748 HIS 0.006 0.001 HIS B 732 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.21 ( 9526) covalent geometry : angle 0.66494 / 0.32 (12977) hydrogen bonds : bond 0.04425 / 2.99 ( 383) hydrogen bonds : angle 4.39749 / 3.20 ( 1077) metal coordination : bond 0.00175 / 0.09 ( 2) Misc. bond : bond 0.00028 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 38 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 LYS cc_start: 0.8761 (mmmt) cc_final: 0.8541 (mppt) REVERT: A 133 MET cc_start: 0.5670 (OUTLIER) cc_final: 0.5201 (ppp) REVERT: A 296 GLU cc_start: 0.9115 (OUTLIER) cc_final: 0.8913 (pm20) REVERT: A 1061 HIS cc_start: 0.9187 (m-70) cc_final: 0.8881 (m-70) REVERT: B 568 TRP cc_start: 0.9588 (OUTLIER) cc_final: 0.8965 (t60) REVERT: B 1004 ARG cc_start: 0.9042 (ttp80) cc_final: 0.8505 (tmt170) outliers start: 20 outliers final: 9 residues processed: 52 average time/residue: 0.4889 time to fit residues: 27.5375 Evaluate side-chains 49 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 37 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 447 ARG Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain B residue 568 TRP Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 907 LEU Chi-restraints excluded: chain B residue 1048 VAL Chi-restraints excluded: chain B residue 1106 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 59 optimal weight: 2.9990 chunk 120 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 70 optimal weight: 0.0970 chunk 48 optimal weight: 0.6980 chunk 112 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 overall best weight: 1.1580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.086715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.055587 restraints weight = 32055.443| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 4.36 r_work: 0.2855 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9530 Z= 0.112 Angle : 0.612 14.086 12977 Z= 0.294 Chirality : 0.043 0.135 1500 Planarity : 0.004 0.040 1724 Dihedral : 5.354 82.905 1422 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 1.59 % Allowed : 14.27 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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: -0.11 (0.25), residues: 1244 helix: 1.42 (0.26), residues: 448 sheet: 0.17 (0.38), residues: 201 loop : -1.38 (0.26), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 495 TYR 0.012 0.001 TYR B 573 PHE 0.011 0.001 PHE A 156 TRP 0.024 0.001 TRP B 748 HIS 0.004 0.001 HIS B 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 ( 9526) covalent geometry : angle 0.61188 / 0.29 (12977) hydrogen bonds : bond 0.03101 / 2.10 ( 383) hydrogen bonds : angle 4.18361 / 3.04 ( 1077) metal coordination : bond 0.00139 / 0.07 ( 2) Misc. bond : bond 0.00007 / 0.00 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 41 time to evaluate : 0.256 Fit side-chains REVERT: A 117 LYS cc_start: 0.8700 (mmmt) cc_final: 0.8347 (mppt) REVERT: A 133 MET cc_start: 0.5947 (OUTLIER) cc_final: 0.5485 (ppp) REVERT: A 296 GLU cc_start: 0.9099 (OUTLIER) cc_final: 0.8864 (pm20) REVERT: A 1061 HIS cc_start: 0.9185 (m-70) cc_final: 0.8869 (m-70) REVERT: B 568 TRP cc_start: 0.9524 (OUTLIER) cc_final: 0.9015 (t60) REVERT: B 1004 ARG cc_start: 0.9021 (ttp80) cc_final: 0.8480 (tmt170) outliers start: 15 outliers final: 8 residues processed: 55 average time/residue: 0.4360 time to fit residues: 26.0781 Evaluate side-chains 50 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain B residue 568 TRP Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 907 LEU Chi-restraints excluded: chain B residue 1048 VAL Chi-restraints excluded: chain B residue 1106 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 120 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 95 optimal weight: 0.0040 chunk 8 optimal weight: 0.8980 chunk 88 optimal weight: 0.0470 chunk 116 optimal weight: 20.0000 chunk 13 optimal weight: 5.9990 chunk 106 optimal weight: 8.9990 chunk 77 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 overall best weight: 1.3892 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.086514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.055367 restraints weight = 32087.402| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 4.35 r_work: 0.2846 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9530 Z= 0.121 Angle : 0.633 14.457 12977 Z= 0.302 Chirality : 0.043 0.136 1500 Planarity : 0.004 0.081 1724 Dihedral : 5.291 79.467 1422 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 1.48 % Allowed : 14.59 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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: -0.11 (0.25), residues: 1244 helix: 1.40 (0.26), residues: 450 sheet: 0.21 (0.38), residues: 201 loop : -1.37 (0.26), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.000 ARG B 495 TYR 0.012 0.001 TYR B 573 PHE 0.012 0.001 PHE A 156 TRP 0.022 0.001 TRP B 748 HIS 0.003 0.001 HIS B 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 ( 9526) covalent geometry : angle 0.63299 / 0.30 (12977) hydrogen bonds : bond 0.03256 / 2.21 ( 383) hydrogen bonds : angle 4.15221 / 3.02 ( 1077) metal coordination : bond 0.00137 / 0.07 ( 2) Misc. bond : bond 0.00016 / 0.01 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 38 time to evaluate : 0.247 Fit side-chains REVERT: A 117 LYS cc_start: 0.8691 (mmmt) cc_final: 0.8339 (mppt) REVERT: A 133 MET cc_start: 0.5920 (OUTLIER) cc_final: 0.5209 (ppp) REVERT: A 296 GLU cc_start: 0.9093 (OUTLIER) cc_final: 0.8852 (pm20) REVERT: B 568 TRP cc_start: 0.9511 (OUTLIER) cc_final: 0.9031 (t60) REVERT: B 1004 ARG cc_start: 0.9018 (ttp80) cc_final: 0.8478 (tmt170) outliers start: 14 outliers final: 8 residues processed: 49 average time/residue: 0.4404 time to fit residues: 23.3843 Evaluate side-chains 48 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain B residue 568 TRP Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 907 LEU Chi-restraints excluded: chain B residue 1048 VAL Chi-restraints excluded: chain B residue 1106 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 61 optimal weight: 0.5980 chunk 104 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 102 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.086872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.055767 restraints weight = 31786.570| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 4.36 r_work: 0.2862 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9530 Z= 0.107 Angle : 0.613 14.049 12977 Z= 0.292 Chirality : 0.043 0.138 1500 Planarity : 0.004 0.040 1724 Dihedral : 5.207 75.898 1422 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 1.16 % Allowed : 14.80 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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: -0.06 (0.25), residues: 1244 helix: 1.44 (0.26), residues: 450 sheet: 0.26 (0.39), residues: 201 loop : -1.35 (0.26), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 495 TYR 0.011 0.001 TYR B 573 PHE 0.011 0.001 PHE A 156 TRP 0.022 0.001 TRP B 748 HIS 0.003 0.001 HIS B 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 9526) covalent geometry : angle 0.61272 / 0.29 (12977) hydrogen bonds : bond 0.02997 / 2.03 ( 383) hydrogen bonds : angle 4.08386 / 2.97 ( 1077) metal coordination : bond 0.00115 / 0.05 ( 2) Misc. bond : bond 0.00017 / 0.01 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2693.75 seconds wall clock time: 46 minutes 35.22 seconds (2795.22 seconds total)