Starting phenix.real_space_refine on Wed Feb 4 12:05:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n0u_48794/02_2026/9n0u_48794.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n0u_48794/02_2026/9n0u_48794.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9n0u_48794/02_2026/9n0u_48794.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n0u_48794/02_2026/9n0u_48794.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9n0u_48794/02_2026/9n0u_48794.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n0u_48794/02_2026/9n0u_48794.map" } resolution = 3.46 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= 0.001 sd= 0.022 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 75 5.16 5 C 6588 2.51 5 N 1747 2.21 5 O 1895 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10306 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1129, 8919 Classifications: {'peptide': 1129} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 58, 'TRANS': 1070} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 426 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 5, 'TRANS': 50} Chain: "C" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 320 Classifications: {'peptide': 40} Link IDs: {'TRANS': 39} Chain: "D" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 320 Classifications: {'peptide': 40} Link IDs: {'TRANS': 39} Chain: "E" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 320 Classifications: {'peptide': 40} Link IDs: {'TRANS': 39} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7697 SG CYS A 993 41.668 23.334 99.360 1.00104.72 S ATOM 8754 SG CYS A1210 43.619 21.664 99.960 1.00112.64 S ATOM 8776 SG CYS A1213 43.272 22.382 97.077 1.00113.00 S Time building chain proxies: 2.10, per 1000 atoms: 0.20 Number of scatterers: 10306 At special positions: 0 Unit cell: (89.64, 99.6, 120.184, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 75 16.00 O 1895 8.00 N 1747 7.00 C 6588 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.56 Conformation dependent library (CDL) restraints added in 401.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A1210 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 993 " pdb="ZN ZN A1801 " - pdb=" SG CYS A1213 " 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2486 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 6 sheets defined 60.5% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 33 through 40 removed outlier: 3.525A pdb=" N SER A 37 " --> pdb=" O GLY A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.583A pdb=" N GLN A 54 " --> pdb=" O ARG A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 64 through 70 Processing helix chain 'A' and resid 81 through 99 Processing helix chain 'A' and resid 104 through 118 removed outlier: 4.157A pdb=" N SER A 110 " --> pdb=" O LYS A 106 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASN A 118 " --> pdb=" O TYR A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 139 removed outlier: 3.722A pdb=" N GLN A 124 " --> pdb=" O ARG A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 201 removed outlier: 3.639A pdb=" N VAL A 197 " --> pdb=" O LEU A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 221 Processing helix chain 'A' and resid 225 through 235 Processing helix chain 'A' and resid 235 through 248 Processing helix chain 'A' and resid 261 through 266 Processing helix chain 'A' and resid 266 through 280 Processing helix chain 'A' and resid 280 through 289 removed outlier: 3.744A pdb=" N LEU A 285 " --> pdb=" O PRO A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 312 Processing helix chain 'A' and resid 318 through 346 removed outlier: 3.610A pdb=" N ILE A 332 " --> pdb=" O THR A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 368 removed outlier: 3.536A pdb=" N LYS A 362 " --> pdb=" O ASP A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 375 removed outlier: 3.580A pdb=" N PHE A 374 " --> pdb=" O SER A 371 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP A 375 " --> pdb=" O PRO A 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 371 through 375' Processing helix chain 'A' and resid 410 through 417 removed outlier: 3.750A pdb=" N ASP A 413 " --> pdb=" O SER A 410 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL A 415 " --> pdb=" O ARG A 412 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE A 416 " --> pdb=" O ASP A 413 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU A 417 " --> pdb=" O TRP A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 428 Processing helix chain 'A' and resid 442 through 449 removed outlier: 3.516A pdb=" N ASP A 449 " --> pdb=" O ASN A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 465 Proline residue: A 461 - end of helix Processing helix chain 'A' and resid 468 through 471 Processing helix chain 'A' and resid 494 through 512 removed outlier: 3.739A pdb=" N ARG A 498 " --> pdb=" O THR A 494 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE A 499 " --> pdb=" O LEU A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 521 Processing helix chain 'A' and resid 524 through 540 removed outlier: 3.616A pdb=" N HIS A 537 " --> pdb=" O ASN A 533 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N THR A 540 " --> pdb=" O SER A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 558 removed outlier: 4.109A pdb=" N PHE A 558 " --> pdb=" O TRP A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 574 removed outlier: 3.637A pdb=" N GLN A 563 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA A 564 " --> pdb=" O PRO A 560 " (cutoff:3.500A) Proline residue: A 565 - end of helix Processing helix chain 'A' and resid 581 through 586 removed outlier: 4.027A pdb=" N THR A 585 " --> pdb=" O ARG A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 645 removed outlier: 3.756A pdb=" N TRP A 638 " --> pdb=" O LEU A 634 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU A 639 " --> pdb=" O THR A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 688 removed outlier: 3.525A pdb=" N LEU A 674 " --> pdb=" O ASN A 670 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG A 687 " --> pdb=" O TYR A 683 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU A 688 " --> pdb=" O LYS A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 698 removed outlier: 4.015A pdb=" N CYS A 698 " --> pdb=" O VAL A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 727 Processing helix chain 'A' and resid 738 through 756 removed outlier: 3.656A pdb=" N LYS A 742 " --> pdb=" O ASN A 738 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA A 756 " --> pdb=" O SER A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 779 removed outlier: 3.811A pdb=" N CYS A 769 " --> pdb=" O ALA A 765 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLU A 778 " --> pdb=" O GLU A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 794 removed outlier: 3.517A pdb=" N CYS A 794 " --> pdb=" O LEU A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 835 removed outlier: 3.699A pdb=" N ILE A 832 " --> pdb=" O LEU A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 847 removed outlier: 3.868A pdb=" N VAL A 842 " --> pdb=" O THR A 838 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS A 847 " --> pdb=" O ASN A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 862 removed outlier: 3.621A pdb=" N LEU A 859 " --> pdb=" O ASP A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 890 removed outlier: 3.715A pdb=" N ALA A 887 " --> pdb=" O GLU A 883 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR A 888 " --> pdb=" O GLU A 884 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER A 890 " --> pdb=" O ILE A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 901 removed outlier: 3.904A pdb=" N PHE A 898 " --> pdb=" O ARG A 894 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLN A 901 " --> pdb=" O THR A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 915 removed outlier: 3.670A pdb=" N MET A 906 " --> pdb=" O PRO A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 931 Processing helix chain 'A' and resid 932 through 946 removed outlier: 3.866A pdb=" N TYR A 936 " --> pdb=" O SER A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 950 through 957 Processing helix chain 'A' and resid 958 through 979 removed outlier: 4.433A pdb=" N VAL A 962 " --> pdb=" O HIS A 958 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ALA A 963 " --> pdb=" O ILE A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 991 removed outlier: 3.731A pdb=" N GLU A 991 " --> pdb=" O PRO A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1007 removed outlier: 3.710A pdb=" N ALA A 997 " --> pdb=" O CYS A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1021 Processing helix chain 'A' and resid 1031 through 1037 removed outlier: 4.010A pdb=" N ASP A1037 " --> pdb=" O GLU A1033 " (cutoff:3.500A) Processing helix chain 'A' and resid 1048 through 1053 removed outlier: 3.504A pdb=" N LEU A1052 " --> pdb=" O SER A1049 " (cutoff:3.500A) Processing helix chain 'A' and resid 1151 through 1156 removed outlier: 3.568A pdb=" N THR A1156 " --> pdb=" O ASN A1152 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1196 Processing helix chain 'B' and resid 128 through 167 removed outlier: 3.613A pdb=" N THR B 151 " --> pdb=" O THR B 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 165 removed outlier: 3.892A pdb=" N ASN C 137 " --> pdb=" O ILE C 133 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ILE C 140 " --> pdb=" O GLU C 136 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP C 142 " --> pdb=" O ILE C 138 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LYS C 158 " --> pdb=" O LEU C 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 160 Processing helix chain 'D' and resid 160 through 166 removed outlier: 4.381A pdb=" N ALA D 164 " --> pdb=" O ASP D 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 166 removed outlier: 3.735A pdb=" N LEU E 134 " --> pdb=" O SER E 130 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LEU E 141 " --> pdb=" O ASN E 137 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ASP E 142 " --> pdb=" O ILE E 138 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG E 143 " --> pdb=" O LYS E 139 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 58 through 60 removed outlier: 4.448A pdb=" N LEU A 173 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N PHE A 158 " --> pdb=" O GLY A 147 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N GLY A 147 " --> pdb=" O PHE A 158 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 351 through 353 Processing sheet with id=AA3, first strand: chain 'A' and resid 489 through 492 Processing sheet with id=AA4, first strand: chain 'A' and resid 650 through 655 Processing sheet with id=AA5, first strand: chain 'A' and resid 704 through 707 removed outlier: 3.552A pdb=" N LYS A 710 " --> pdb=" O TYR A 707 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1022 through 1025 removed outlier: 3.560A pdb=" N HIS A1025 " --> pdb=" O LEU A1205 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LEU A1205 " --> pdb=" O HIS A1025 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE A1040 " --> pdb=" O SER A1161 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER A1161 " --> pdb=" O ILE A1040 " (cutoff:3.500A) 550 hydrogen bonds defined for protein. 1614 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: 1.38 Time building geometry restraints manager: 0.76 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: 3275 1.34 - 1.46: 2222 1.46 - 1.58: 4903 1.58 - 1.70: 0 1.70 - 1.82: 123 Bond restraints: 10523 Sorted by residual: bond pdb=" C MET B 174 " pdb=" N LEU B 175 " ideal model delta sigma weight residual 1.331 1.299 0.032 1.59e-02 3.96e+03 4.04e+00 bond pdb=" CA THR A 660 " pdb=" CB THR A 660 " ideal model delta sigma weight residual 1.531 1.561 -0.030 1.52e-02 4.33e+03 3.88e+00 bond pdb=" C SER A 237 " pdb=" N PRO A 238 " ideal model delta sigma weight residual 1.335 1.359 -0.024 1.28e-02 6.10e+03 3.49e+00 bond pdb=" N GLN A 160 " pdb=" CA GLN A 160 " ideal model delta sigma weight residual 1.457 1.481 -0.023 1.29e-02 6.01e+03 3.31e+00 bond pdb=" C LEU A 586 " pdb=" N PRO A 587 " ideal model delta sigma weight residual 1.335 1.356 -0.022 1.19e-02 7.06e+03 3.29e+00 ... (remaining 10518 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 13676 2.10 - 4.20: 486 4.20 - 6.30: 78 6.30 - 8.40: 21 8.40 - 10.50: 4 Bond angle restraints: 14265 Sorted by residual: angle pdb=" N ILE A 882 " pdb=" CA ILE A 882 " pdb=" C ILE A 882 " ideal model delta sigma weight residual 111.77 105.66 6.11 1.04e+00 9.25e-01 3.45e+01 angle pdb=" C LEU A 459 " pdb=" N GLU A 460 " pdb=" CA GLU A 460 " ideal model delta sigma weight residual 120.09 126.08 -5.99 1.25e+00 6.40e-01 2.30e+01 angle pdb=" CA ARG A 22 " pdb=" CB ARG A 22 " pdb=" CG ARG A 22 " ideal model delta sigma weight residual 114.10 123.30 -9.20 2.00e+00 2.50e-01 2.11e+01 angle pdb=" C SER A1169 " pdb=" N LYS A1170 " pdb=" CA LYS A1170 " ideal model delta sigma weight residual 121.54 129.67 -8.13 1.91e+00 2.74e-01 1.81e+01 angle pdb=" C ILE B 131 " pdb=" N ARG B 132 " pdb=" CA ARG B 132 " ideal model delta sigma weight residual 121.66 114.51 7.15 1.76e+00 3.23e-01 1.65e+01 ... (remaining 14260 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.03: 5782 15.03 - 30.07: 500 30.07 - 45.10: 102 45.10 - 60.14: 14 60.14 - 75.17: 3 Dihedral angle restraints: 6401 sinusoidal: 2569 harmonic: 3832 Sorted by residual: dihedral pdb=" CA LYS A1216 " pdb=" C LYS A1216 " pdb=" N ILE A1217 " pdb=" CA ILE A1217 " ideal model delta harmonic sigma weight residual 180.00 153.95 26.05 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" CA HIS A 958 " pdb=" C HIS A 958 " pdb=" N ILE A 959 " pdb=" CA ILE A 959 " ideal model delta harmonic sigma weight residual -180.00 -158.57 -21.43 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA MET A 918 " pdb=" C MET A 918 " pdb=" N PRO A 919 " pdb=" CA PRO A 919 " ideal model delta harmonic sigma weight residual 180.00 159.10 20.90 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 6398 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1185 0.052 - 0.103: 349 0.103 - 0.155: 92 0.155 - 0.206: 17 0.206 - 0.258: 8 Chirality restraints: 1651 Sorted by residual: chirality pdb=" CB ILE A 594 " pdb=" CA ILE A 594 " pdb=" CG1 ILE A 594 " pdb=" CG2 ILE A 594 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CB ILE A1217 " pdb=" CA ILE A1217 " pdb=" CG1 ILE A1217 " pdb=" CG2 ILE A1217 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CB ILE A 236 " pdb=" CA ILE A 236 " pdb=" CG1 ILE A 236 " pdb=" CG2 ILE A 236 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 1648 not shown) Planarity restraints: 1792 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 638 " 0.031 2.00e-02 2.50e+03 2.93e-02 2.14e+01 pdb=" CG TRP A 638 " -0.080 2.00e-02 2.50e+03 pdb=" CD1 TRP A 638 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP A 638 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 638 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 638 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 638 " 0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 638 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 638 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 638 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A1202 " -0.060 5.00e-02 4.00e+02 9.22e-02 1.36e+01 pdb=" N PRO A1203 " 0.159 5.00e-02 4.00e+02 pdb=" CA PRO A1203 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO A1203 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 918 " 0.050 5.00e-02 4.00e+02 7.57e-02 9.16e+00 pdb=" N PRO A 919 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO A 919 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 919 " 0.044 5.00e-02 4.00e+02 ... (remaining 1789 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 47 2.59 - 3.17: 8106 3.17 - 3.75: 15665 3.75 - 4.32: 21413 4.32 - 4.90: 35513 Nonbonded interactions: 80744 Sorted by model distance: nonbonded pdb=" OE2 GLU A1020 " pdb="ZN ZN A1801 " model vdw 2.018 2.230 nonbonded pdb=" OH TYR A 418 " pdb=" O ILE A 594 " model vdw 2.262 3.040 nonbonded pdb=" O LEU A 285 " pdb=" OG SER A 289 " model vdw 2.268 3.040 nonbonded pdb=" O ARG A 113 " pdb=" OG1 THR A 117 " model vdw 2.281 3.040 nonbonded pdb=" O LEU A 586 " pdb=" OG1 THR A 590 " model vdw 2.291 3.040 ... (remaining 80739 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 'C' selection = chain 'D' selection = chain 'E' } 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: 3.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.120 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 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 0.071 10527 Z= 0.246 Angle : 0.936 10.497 14265 Z= 0.521 Chirality : 0.055 0.258 1651 Planarity : 0.010 0.092 1792 Dihedral : 11.750 75.171 3915 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.20), residues: 1293 helix: -0.89 (0.17), residues: 691 sheet: -0.03 (0.63), residues: 67 loop : -2.01 (0.22), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 376 TYR 0.043 0.003 TYR A 131 PHE 0.039 0.003 PHE A 944 TRP 0.080 0.004 TRP A 638 HIS 0.015 0.002 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00499 (10523) covalent geometry : angle 0.93553 (14265) hydrogen bonds : bond 0.16642 ( 550) hydrogen bonds : angle 6.76611 ( 1614) metal coordination : bond 0.00267 ( 3) Misc. bond : bond 0.00391 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 ARG cc_start: 0.7121 (mtm-85) cc_final: 0.6745 (mtm-85) REVERT: A 196 SER cc_start: 0.8195 (p) cc_final: 0.7902 (t) REVERT: A 261 THR cc_start: 0.8050 (p) cc_final: 0.7706 (p) REVERT: A 283 LEU cc_start: 0.7814 (tp) cc_final: 0.7448 (tt) REVERT: A 301 MET cc_start: 0.6734 (mmm) cc_final: 0.6531 (mmm) REVERT: A 350 PRO cc_start: 0.7252 (Cg_exo) cc_final: 0.7046 (Cg_endo) REVERT: A 377 ARG cc_start: 0.7470 (mtp180) cc_final: 0.7260 (ptp90) REVERT: A 394 MET cc_start: 0.6776 (mtt) cc_final: 0.6551 (mtt) REVERT: A 407 ILE cc_start: 0.8347 (mt) cc_final: 0.8143 (mt) REVERT: A 408 ILE cc_start: 0.7818 (mt) cc_final: 0.7362 (tt) REVERT: A 479 LYS cc_start: 0.7640 (mtmt) cc_final: 0.7389 (mtmt) REVERT: A 484 LYS cc_start: 0.8016 (mttm) cc_final: 0.7738 (mttp) REVERT: A 492 LYS cc_start: 0.7792 (ttpt) cc_final: 0.7460 (mtpt) REVERT: A 541 LYS cc_start: 0.7977 (mtpp) cc_final: 0.7622 (mtpp) REVERT: A 553 SER cc_start: 0.7358 (m) cc_final: 0.6954 (t) REVERT: A 665 LYS cc_start: 0.8006 (tttp) cc_final: 0.7756 (ttpp) REVERT: A 710 LYS cc_start: 0.8306 (ttmt) cc_final: 0.7946 (ttmm) REVERT: A 800 ILE cc_start: 0.8057 (pt) cc_final: 0.7804 (pt) REVERT: A 862 ASP cc_start: 0.6389 (t0) cc_final: 0.6098 (t0) REVERT: A 918 MET cc_start: 0.5679 (tpp) cc_final: 0.5301 (tpp) REVERT: A 971 GLU cc_start: 0.7648 (tm-30) cc_final: 0.7214 (tm-30) REVERT: A 1015 MET cc_start: 0.7866 (mtt) cc_final: 0.7629 (mtm) REVERT: A 1018 VAL cc_start: 0.7932 (t) cc_final: 0.7706 (m) REVERT: A 1051 HIS cc_start: 0.8260 (m90) cc_final: 0.7644 (m-70) REVERT: A 1204 TYR cc_start: 0.7018 (p90) cc_final: 0.6731 (p90) REVERT: C 145 MET cc_start: 0.7085 (mmm) cc_final: 0.6585 (mmm) REVERT: C 155 MET cc_start: 0.6963 (tpp) cc_final: 0.6754 (tpp) REVERT: D 145 MET cc_start: 0.7866 (mtm) cc_final: 0.7034 (mtm) REVERT: D 155 MET cc_start: 0.6749 (tpp) cc_final: 0.6270 (tpp) REVERT: E 145 MET cc_start: 0.6599 (mmm) cc_final: 0.6066 (mmm) REVERT: E 148 MET cc_start: 0.5404 (mtm) cc_final: 0.5029 (mtm) outliers start: 0 outliers final: 0 residues processed: 259 average time/residue: 0.1047 time to fit residues: 37.1505 Evaluate side-chains 211 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.0970 chunk 66 optimal weight: 1.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 HIS A 128 HIS A 205 GLN A 352 HIS A 572 GLN A 599 ASN A 651 ASN C 137 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.177676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.142682 restraints weight = 14361.280| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 2.42 r_work: 0.3560 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10527 Z= 0.189 Angle : 0.654 13.685 14265 Z= 0.341 Chirality : 0.044 0.166 1651 Planarity : 0.006 0.059 1792 Dihedral : 5.115 22.366 1417 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.04 % Allowed : 6.67 % Favored : 92.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.22), residues: 1293 helix: 0.41 (0.19), residues: 716 sheet: -0.21 (0.58), residues: 76 loop : -1.62 (0.25), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 412 TYR 0.026 0.002 TYR A 109 PHE 0.026 0.002 PHE A 490 TRP 0.040 0.002 TRP A 638 HIS 0.009 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00426 (10523) covalent geometry : angle 0.65413 (14265) hydrogen bonds : bond 0.05802 ( 550) hydrogen bonds : angle 4.86897 ( 1614) metal coordination : bond 0.00504 ( 3) Misc. bond : bond 0.00009 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 222 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 TRP cc_start: 0.7591 (m100) cc_final: 0.7367 (m100) REVERT: A 142 ARG cc_start: 0.7078 (mtm-85) cc_final: 0.6777 (mtm-85) REVERT: A 156 LEU cc_start: 0.7807 (mt) cc_final: 0.7527 (mp) REVERT: A 196 SER cc_start: 0.8246 (p) cc_final: 0.7965 (t) REVERT: A 261 THR cc_start: 0.7950 (p) cc_final: 0.7699 (p) REVERT: A 290 VAL cc_start: 0.8261 (m) cc_final: 0.7777 (p) REVERT: A 377 ARG cc_start: 0.7293 (mtp180) cc_final: 0.7059 (ptp90) REVERT: A 407 ILE cc_start: 0.8422 (mt) cc_final: 0.8199 (mt) REVERT: A 408 ILE cc_start: 0.7903 (mt) cc_final: 0.7501 (tt) REVERT: A 462 PHE cc_start: 0.7527 (m-80) cc_final: 0.7317 (m-10) REVERT: A 484 LYS cc_start: 0.7985 (mttm) cc_final: 0.7775 (mttp) REVERT: A 508 LEU cc_start: 0.7913 (mt) cc_final: 0.7508 (mp) REVERT: A 538 THR cc_start: 0.7200 (m) cc_final: 0.6988 (p) REVERT: A 553 SER cc_start: 0.7428 (m) cc_final: 0.7066 (t) REVERT: A 639 GLU cc_start: 0.6680 (mt-10) cc_final: 0.6346 (mt-10) REVERT: A 671 ASN cc_start: 0.7924 (m-40) cc_final: 0.7663 (m-40) REVERT: A 701 SER cc_start: 0.7567 (t) cc_final: 0.7180 (p) REVERT: A 784 MET cc_start: 0.8032 (mmm) cc_final: 0.7755 (mmm) REVERT: A 787 GLU cc_start: 0.7066 (tt0) cc_final: 0.6857 (mt-10) REVERT: A 800 ILE cc_start: 0.8067 (pt) cc_final: 0.7827 (pt) REVERT: A 862 ASP cc_start: 0.6457 (t0) cc_final: 0.6162 (t0) REVERT: A 918 MET cc_start: 0.5465 (tpp) cc_final: 0.4759 (tpp) REVERT: A 971 GLU cc_start: 0.7676 (tm-30) cc_final: 0.7306 (tm-30) REVERT: A 1015 MET cc_start: 0.7850 (mtt) cc_final: 0.7603 (ttp) REVERT: A 1018 VAL cc_start: 0.7859 (t) cc_final: 0.7612 (m) REVERT: A 1051 HIS cc_start: 0.8301 (m90) cc_final: 0.7866 (m90) REVERT: A 1150 TYR cc_start: 0.8138 (t80) cc_final: 0.7110 (t80) REVERT: C 155 MET cc_start: 0.6848 (tpp) cc_final: 0.6615 (tpp) REVERT: D 145 MET cc_start: 0.7911 (mtm) cc_final: 0.7641 (mtm) REVERT: E 145 MET cc_start: 0.6650 (mmm) cc_final: 0.6215 (mmm) outliers start: 12 outliers final: 9 residues processed: 224 average time/residue: 0.1048 time to fit residues: 32.2669 Evaluate side-chains 221 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 212 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1194 ILE Chi-restraints excluded: chain C residue 152 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 4 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 115 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 HIS A 205 GLN A 352 HIS A 572 GLN A 829 GLN A1023 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.176538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.141786 restraints weight = 14446.855| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.34 r_work: 0.3572 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10527 Z= 0.176 Angle : 0.616 14.267 14265 Z= 0.316 Chirality : 0.043 0.149 1651 Planarity : 0.005 0.049 1792 Dihedral : 4.894 20.758 1417 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.21 % Allowed : 10.65 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.23), residues: 1293 helix: 0.90 (0.19), residues: 717 sheet: 0.11 (0.57), residues: 76 loop : -1.57 (0.25), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 677 TYR 0.022 0.002 TYR A 109 PHE 0.028 0.002 PHE A 490 TRP 0.030 0.002 TRP A 638 HIS 0.009 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00397 (10523) covalent geometry : angle 0.61562 (14265) hydrogen bonds : bond 0.05348 ( 550) hydrogen bonds : angle 4.56330 ( 1614) metal coordination : bond 0.00443 ( 3) Misc. bond : bond 0.00033 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 225 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 VAL cc_start: 0.8201 (t) cc_final: 0.7988 (m) REVERT: A 104 MET cc_start: 0.7014 (mmm) cc_final: 0.6690 (mmm) REVERT: A 142 ARG cc_start: 0.7403 (mtm-85) cc_final: 0.7028 (mtm-85) REVERT: A 156 LEU cc_start: 0.7913 (mt) cc_final: 0.7558 (mp) REVERT: A 173 LEU cc_start: 0.8456 (tp) cc_final: 0.8090 (tt) REVERT: A 196 SER cc_start: 0.8387 (p) cc_final: 0.8089 (t) REVERT: A 261 THR cc_start: 0.7952 (p) cc_final: 0.7678 (p) REVERT: A 290 VAL cc_start: 0.8291 (m) cc_final: 0.7780 (p) REVERT: A 358 ASP cc_start: 0.7986 (t0) cc_final: 0.7697 (t0) REVERT: A 371 SER cc_start: 0.8681 (t) cc_final: 0.8379 (t) REVERT: A 377 ARG cc_start: 0.7509 (mtp180) cc_final: 0.7265 (ttm110) REVERT: A 407 ILE cc_start: 0.8577 (mt) cc_final: 0.8365 (mt) REVERT: A 408 ILE cc_start: 0.8082 (mt) cc_final: 0.7751 (tt) REVERT: A 538 THR cc_start: 0.7346 (m) cc_final: 0.7094 (p) REVERT: A 553 SER cc_start: 0.7606 (m) cc_final: 0.7182 (t) REVERT: A 571 ASP cc_start: 0.7566 (m-30) cc_final: 0.7297 (m-30) REVERT: A 671 ASN cc_start: 0.8160 (m-40) cc_final: 0.7956 (t0) REVERT: A 840 SER cc_start: 0.7870 (m) cc_final: 0.7558 (p) REVERT: A 862 ASP cc_start: 0.6879 (t0) cc_final: 0.6642 (t0) REVERT: A 918 MET cc_start: 0.5550 (tpp) cc_final: 0.4845 (tpp) REVERT: A 971 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7597 (tm-30) REVERT: A 989 TYR cc_start: 0.7049 (m-80) cc_final: 0.6698 (m-10) REVERT: A 1015 MET cc_start: 0.8071 (mtt) cc_final: 0.7816 (ttp) REVERT: A 1018 VAL cc_start: 0.7874 (t) cc_final: 0.7578 (m) REVERT: A 1150 TYR cc_start: 0.8240 (t80) cc_final: 0.7304 (t80) REVERT: D 152 MET cc_start: 0.5434 (mpp) cc_final: 0.5084 (mpp) REVERT: E 145 MET cc_start: 0.6710 (mmm) cc_final: 0.6219 (mmm) outliers start: 14 outliers final: 10 residues processed: 230 average time/residue: 0.0974 time to fit residues: 31.0641 Evaluate side-chains 218 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 208 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 1014 THR Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1194 ILE Chi-restraints excluded: chain E residue 148 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 79 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 41 optimal weight: 0.0070 chunk 38 optimal weight: 9.9990 chunk 126 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 117 optimal weight: 30.0000 chunk 72 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 overall best weight: 1.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 GLN A 205 GLN A 352 HIS A 738 ASN A 908 GLN ** A1051 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.173919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.138592 restraints weight = 14534.737| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.33 r_work: 0.3528 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 10527 Z= 0.287 Angle : 0.750 15.592 14265 Z= 0.379 Chirality : 0.049 0.180 1651 Planarity : 0.006 0.053 1792 Dihedral : 5.215 21.823 1417 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.34 % Allowed : 12.03 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.22), residues: 1293 helix: 0.54 (0.19), residues: 729 sheet: 0.01 (0.57), residues: 76 loop : -1.88 (0.25), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 677 TYR 0.026 0.003 TYR A 109 PHE 0.027 0.003 PHE A 490 TRP 0.033 0.003 TRP A 638 HIS 0.010 0.002 HIS A1181 Details of bonding type rmsd covalent geometry : bond 0.00668 (10523) covalent geometry : angle 0.74963 (14265) hydrogen bonds : bond 0.06300 ( 550) hydrogen bonds : angle 4.82758 ( 1614) metal coordination : bond 0.00838 ( 3) Misc. bond : bond 0.00010 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 222 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.7159 (mmm) cc_final: 0.6887 (mmm) REVERT: A 196 SER cc_start: 0.8389 (p) cc_final: 0.8162 (t) REVERT: A 212 ILE cc_start: 0.7955 (mm) cc_final: 0.7562 (tt) REVERT: A 290 VAL cc_start: 0.8312 (m) cc_final: 0.7817 (p) REVERT: A 307 GLU cc_start: 0.7370 (mt-10) cc_final: 0.7099 (mt-10) REVERT: A 371 SER cc_start: 0.8692 (t) cc_final: 0.8368 (t) REVERT: A 408 ILE cc_start: 0.8061 (mt) cc_final: 0.7767 (tt) REVERT: A 491 SER cc_start: 0.8349 (m) cc_final: 0.7859 (t) REVERT: A 493 GLN cc_start: 0.8037 (pm20) cc_final: 0.7806 (pm20) REVERT: A 538 THR cc_start: 0.7389 (m) cc_final: 0.7106 (p) REVERT: A 553 SER cc_start: 0.7673 (m) cc_final: 0.7172 (t) REVERT: A 671 ASN cc_start: 0.8223 (m-40) cc_final: 0.7899 (m-40) REVERT: A 701 SER cc_start: 0.7793 (t) cc_final: 0.7539 (p) REVERT: A 840 SER cc_start: 0.8006 (m) cc_final: 0.7720 (p) REVERT: A 862 ASP cc_start: 0.7002 (t0) cc_final: 0.6770 (m-30) REVERT: A 918 MET cc_start: 0.5582 (tpp) cc_final: 0.4871 (tpp) REVERT: A 971 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7647 (tm-30) REVERT: A 1015 MET cc_start: 0.8156 (mtt) cc_final: 0.7900 (ttp) REVERT: A 1018 VAL cc_start: 0.7889 (t) cc_final: 0.7616 (m) REVERT: D 145 MET cc_start: 0.7827 (mtm) cc_final: 0.7594 (ttm) REVERT: D 152 MET cc_start: 0.5351 (mpp) cc_final: 0.5073 (mpp) REVERT: E 145 MET cc_start: 0.6697 (mmm) cc_final: 0.6189 (mmm) outliers start: 27 outliers final: 18 residues processed: 232 average time/residue: 0.0996 time to fit residues: 31.7574 Evaluate side-chains 232 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 214 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 1014 THR Chi-restraints excluded: chain A residue 1191 ASP Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1194 ILE Chi-restraints excluded: chain C residue 148 MET Chi-restraints excluded: chain E residue 148 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 83 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 115 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 79 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 96 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 123 optimal weight: 8.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 HIS A 572 GLN A 785 GLN A 908 GLN ** A1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1051 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.175925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.141521 restraints weight = 14409.804| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.30 r_work: 0.3573 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10527 Z= 0.151 Angle : 0.610 14.309 14265 Z= 0.308 Chirality : 0.042 0.170 1651 Planarity : 0.005 0.043 1792 Dihedral : 4.814 20.092 1417 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.47 % Allowed : 14.98 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.23), residues: 1293 helix: 1.01 (0.20), residues: 731 sheet: 0.21 (0.58), residues: 76 loop : -1.79 (0.25), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 150 TYR 0.024 0.002 TYR A 705 PHE 0.026 0.002 PHE A 490 TRP 0.021 0.002 TRP A 638 HIS 0.009 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00350 (10523) covalent geometry : angle 0.61007 (14265) hydrogen bonds : bond 0.04988 ( 550) hydrogen bonds : angle 4.47386 ( 1614) metal coordination : bond 0.00405 ( 3) Misc. bond : bond 0.00013 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 219 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 VAL cc_start: 0.8274 (t) cc_final: 0.8059 (p) REVERT: A 196 SER cc_start: 0.8378 (p) cc_final: 0.8092 (t) REVERT: A 290 VAL cc_start: 0.8322 (m) cc_final: 0.7836 (p) REVERT: A 307 GLU cc_start: 0.7262 (mt-10) cc_final: 0.7002 (mt-10) REVERT: A 371 SER cc_start: 0.8651 (t) cc_final: 0.8326 (t) REVERT: A 408 ILE cc_start: 0.7969 (mt) cc_final: 0.7672 (tt) REVERT: A 491 SER cc_start: 0.8316 (m) cc_final: 0.7790 (t) REVERT: A 538 THR cc_start: 0.7294 (m) cc_final: 0.7026 (p) REVERT: A 553 SER cc_start: 0.7625 (m) cc_final: 0.7118 (t) REVERT: A 571 ASP cc_start: 0.7669 (OUTLIER) cc_final: 0.7317 (t70) REVERT: A 701 SER cc_start: 0.7770 (t) cc_final: 0.7532 (p) REVERT: A 840 SER cc_start: 0.7939 (m) cc_final: 0.7672 (p) REVERT: A 918 MET cc_start: 0.5544 (tpp) cc_final: 0.4839 (tpp) REVERT: A 971 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7555 (tm-30) REVERT: A 1015 MET cc_start: 0.8038 (mtt) cc_final: 0.7748 (ttp) REVERT: A 1018 VAL cc_start: 0.7916 (t) cc_final: 0.7637 (m) REVERT: A 1204 TYR cc_start: 0.7291 (p90) cc_final: 0.7042 (p90) REVERT: D 145 MET cc_start: 0.7811 (mtm) cc_final: 0.7582 (ttm) REVERT: D 152 MET cc_start: 0.5308 (OUTLIER) cc_final: 0.4916 (mpp) REVERT: E 145 MET cc_start: 0.6644 (mmm) cc_final: 0.6133 (mmm) outliers start: 17 outliers final: 7 residues processed: 222 average time/residue: 0.1040 time to fit residues: 31.9123 Evaluate side-chains 223 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 214 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 1014 THR Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain E residue 148 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 0.9990 chunk 101 optimal weight: 9.9990 chunk 3 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 chunk 119 optimal weight: 9.9990 chunk 85 optimal weight: 0.8980 chunk 38 optimal weight: 8.9990 chunk 81 optimal weight: 0.8980 chunk 86 optimal weight: 8.9990 chunk 47 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 HIS A 785 GLN A 908 GLN ** A1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.174561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.139278 restraints weight = 14656.032| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.44 r_work: 0.3518 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10527 Z= 0.170 Angle : 0.619 14.031 14265 Z= 0.312 Chirality : 0.042 0.165 1651 Planarity : 0.005 0.041 1792 Dihedral : 4.731 20.485 1417 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.08 % Allowed : 15.76 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.23), residues: 1293 helix: 1.10 (0.20), residues: 731 sheet: 0.26 (0.59), residues: 76 loop : -1.73 (0.25), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 677 TYR 0.026 0.002 TYR A 705 PHE 0.031 0.002 PHE A 490 TRP 0.022 0.002 TRP A 638 HIS 0.009 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00392 (10523) covalent geometry : angle 0.61907 (14265) hydrogen bonds : bond 0.05015 ( 550) hydrogen bonds : angle 4.37935 ( 1614) metal coordination : bond 0.00527 ( 3) Misc. bond : bond 0.00158 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 220 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: A 49 VAL cc_start: 0.8211 (t) cc_final: 0.7973 (p) REVERT: A 54 GLN cc_start: 0.7576 (OUTLIER) cc_final: 0.7284 (mt0) REVERT: A 56 LYS cc_start: 0.8232 (mmtt) cc_final: 0.8010 (mtpp) REVERT: A 196 SER cc_start: 0.8225 (p) cc_final: 0.7991 (t) REVERT: A 290 VAL cc_start: 0.8233 (m) cc_final: 0.7760 (p) REVERT: A 358 ASP cc_start: 0.7944 (t0) cc_final: 0.7667 (t0) REVERT: A 371 SER cc_start: 0.8628 (t) cc_final: 0.8311 (t) REVERT: A 408 ILE cc_start: 0.7820 (mt) cc_final: 0.7584 (tt) REVERT: A 491 SER cc_start: 0.8192 (m) cc_final: 0.7658 (t) REVERT: A 538 THR cc_start: 0.7241 (m) cc_final: 0.6954 (p) REVERT: A 553 SER cc_start: 0.7593 (m) cc_final: 0.7055 (t) REVERT: A 701 SER cc_start: 0.7677 (t) cc_final: 0.7392 (p) REVERT: A 840 SER cc_start: 0.7866 (m) cc_final: 0.7583 (p) REVERT: A 918 MET cc_start: 0.5398 (tpp) cc_final: 0.4695 (tpp) REVERT: A 971 GLU cc_start: 0.7723 (tm-30) cc_final: 0.7365 (tm-30) REVERT: A 1015 MET cc_start: 0.7773 (mtt) cc_final: 0.7486 (ttp) REVERT: A 1018 VAL cc_start: 0.7884 (t) cc_final: 0.7637 (m) REVERT: A 1204 TYR cc_start: 0.7085 (p90) cc_final: 0.6766 (p90) REVERT: D 145 MET cc_start: 0.7820 (mtm) cc_final: 0.7600 (ttm) REVERT: D 152 MET cc_start: 0.5321 (OUTLIER) cc_final: 0.5004 (mpp) REVERT: D 155 MET cc_start: 0.7160 (tpp) cc_final: 0.6689 (tpp) REVERT: E 145 MET cc_start: 0.6612 (mmm) cc_final: 0.6090 (mmm) outliers start: 24 outliers final: 14 residues processed: 230 average time/residue: 0.1089 time to fit residues: 34.5836 Evaluate side-chains 228 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 212 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLN Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 1014 THR Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain E residue 148 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 109 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 33 optimal weight: 0.0070 chunk 38 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 HIS A 572 GLN A 908 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.175177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.140747 restraints weight = 14371.655| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 2.35 r_work: 0.3559 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3388 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10527 Z= 0.153 Angle : 0.602 13.474 14265 Z= 0.304 Chirality : 0.042 0.221 1651 Planarity : 0.005 0.039 1792 Dihedral : 4.639 19.623 1417 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.08 % Allowed : 16.62 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.23), residues: 1293 helix: 1.28 (0.20), residues: 721 sheet: 0.40 (0.61), residues: 76 loop : -1.59 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 677 TYR 0.027 0.002 TYR A 705 PHE 0.029 0.002 PHE A 490 TRP 0.020 0.001 TRP A 638 HIS 0.009 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00353 (10523) covalent geometry : angle 0.60164 (14265) hydrogen bonds : bond 0.04756 ( 550) hydrogen bonds : angle 4.27810 ( 1614) metal coordination : bond 0.00452 ( 3) Misc. bond : bond 0.00173 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 209 time to evaluate : 0.481 Fit side-chains revert: symmetry clash REVERT: A 49 VAL cc_start: 0.8289 (t) cc_final: 0.8075 (p) REVERT: A 54 GLN cc_start: 0.7676 (OUTLIER) cc_final: 0.7431 (mt0) REVERT: A 290 VAL cc_start: 0.8313 (m) cc_final: 0.7795 (p) REVERT: A 371 SER cc_start: 0.8610 (t) cc_final: 0.8290 (t) REVERT: A 408 ILE cc_start: 0.7923 (mt) cc_final: 0.7720 (tt) REVERT: A 491 SER cc_start: 0.8325 (m) cc_final: 0.7985 (p) REVERT: A 493 GLN cc_start: 0.7839 (pm20) cc_final: 0.7587 (pm20) REVERT: A 538 THR cc_start: 0.7274 (m) cc_final: 0.7002 (p) REVERT: A 553 SER cc_start: 0.7650 (m) cc_final: 0.7141 (t) REVERT: A 571 ASP cc_start: 0.7692 (OUTLIER) cc_final: 0.7349 (t70) REVERT: A 590 THR cc_start: 0.7933 (m) cc_final: 0.7594 (p) REVERT: A 639 GLU cc_start: 0.7094 (mt-10) cc_final: 0.6706 (mt-10) REVERT: A 657 ASP cc_start: 0.7300 (p0) cc_final: 0.7043 (p0) REVERT: A 701 SER cc_start: 0.7832 (t) cc_final: 0.7527 (p) REVERT: A 840 SER cc_start: 0.7958 (m) cc_final: 0.7697 (p) REVERT: A 918 MET cc_start: 0.5552 (tpp) cc_final: 0.4822 (tpp) REVERT: A 971 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7577 (tm-30) REVERT: A 1018 VAL cc_start: 0.7969 (t) cc_final: 0.7715 (m) REVERT: A 1051 HIS cc_start: 0.8284 (OUTLIER) cc_final: 0.7743 (m170) REVERT: A 1204 TYR cc_start: 0.7268 (p90) cc_final: 0.6973 (p90) REVERT: D 145 MET cc_start: 0.7818 (mtm) cc_final: 0.7609 (ttm) REVERT: D 152 MET cc_start: 0.5397 (OUTLIER) cc_final: 0.5018 (mpp) REVERT: D 155 MET cc_start: 0.7174 (tpp) cc_final: 0.6636 (tpp) REVERT: E 145 MET cc_start: 0.6629 (mmm) cc_final: 0.6091 (mmm) outliers start: 24 outliers final: 13 residues processed: 218 average time/residue: 0.1143 time to fit residues: 34.0904 Evaluate side-chains 226 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 209 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLN Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 1014 THR Chi-restraints excluded: chain A residue 1051 HIS Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain D residue 152 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 94 optimal weight: 5.9990 chunk 100 optimal weight: 0.6980 chunk 93 optimal weight: 0.4980 chunk 22 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 122 optimal weight: 8.9990 chunk 108 optimal weight: 0.9990 chunk 54 optimal weight: 0.1980 chunk 58 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.175300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.141119 restraints weight = 14551.028| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.30 r_work: 0.3574 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10527 Z= 0.144 Angle : 0.591 12.832 14265 Z= 0.298 Chirality : 0.041 0.236 1651 Planarity : 0.004 0.037 1792 Dihedral : 4.518 19.108 1417 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.99 % Allowed : 16.88 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.24), residues: 1293 helix: 1.40 (0.20), residues: 721 sheet: 0.37 (0.60), residues: 76 loop : -1.53 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 677 TYR 0.025 0.002 TYR A 705 PHE 0.032 0.002 PHE A 490 TRP 0.019 0.001 TRP A 638 HIS 0.009 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00329 (10523) covalent geometry : angle 0.59147 (14265) hydrogen bonds : bond 0.04551 ( 550) hydrogen bonds : angle 4.20852 ( 1614) metal coordination : bond 0.00359 ( 3) Misc. bond : bond 0.00039 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 212 time to evaluate : 0.404 Fit side-chains revert: symmetry clash REVERT: A 49 VAL cc_start: 0.8298 (t) cc_final: 0.8097 (p) REVERT: A 54 GLN cc_start: 0.7648 (OUTLIER) cc_final: 0.7427 (mt0) REVERT: A 290 VAL cc_start: 0.8310 (m) cc_final: 0.7795 (p) REVERT: A 371 SER cc_start: 0.8544 (t) cc_final: 0.8219 (t) REVERT: A 491 SER cc_start: 0.8282 (m) cc_final: 0.7961 (p) REVERT: A 493 GLN cc_start: 0.7846 (pm20) cc_final: 0.7591 (pm20) REVERT: A 553 SER cc_start: 0.7598 (m) cc_final: 0.7125 (t) REVERT: A 590 THR cc_start: 0.7873 (m) cc_final: 0.7596 (p) REVERT: A 605 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7728 (mmt90) REVERT: A 639 GLU cc_start: 0.7051 (mt-10) cc_final: 0.6614 (mt-10) REVERT: A 645 GLU cc_start: 0.7476 (mt-10) cc_final: 0.7256 (mt-10) REVERT: A 701 SER cc_start: 0.7806 (t) cc_final: 0.7472 (p) REVERT: A 840 SER cc_start: 0.7891 (m) cc_final: 0.7645 (p) REVERT: A 918 MET cc_start: 0.5510 (tpp) cc_final: 0.4803 (tpp) REVERT: A 971 GLU cc_start: 0.7910 (tm-30) cc_final: 0.7539 (tm-30) REVERT: A 1018 VAL cc_start: 0.7981 (t) cc_final: 0.7712 (m) REVERT: A 1051 HIS cc_start: 0.8244 (OUTLIER) cc_final: 0.7760 (m170) REVERT: A 1204 TYR cc_start: 0.7243 (p90) cc_final: 0.6960 (p90) REVERT: D 145 MET cc_start: 0.7861 (mtm) cc_final: 0.7639 (ttm) REVERT: D 152 MET cc_start: 0.5543 (OUTLIER) cc_final: 0.5149 (mpp) REVERT: D 155 MET cc_start: 0.6996 (tpp) cc_final: 0.6434 (tpp) REVERT: E 145 MET cc_start: 0.6581 (mmm) cc_final: 0.6049 (mmm) outliers start: 23 outliers final: 14 residues processed: 221 average time/residue: 0.1083 time to fit residues: 32.9903 Evaluate side-chains 226 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 208 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLN Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 605 ARG Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 1014 THR Chi-restraints excluded: chain A residue 1051 HIS Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain E residue 148 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 45 optimal weight: 0.9980 chunk 2 optimal weight: 0.2980 chunk 91 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 76 optimal weight: 0.0770 chunk 118 optimal weight: 9.9990 chunk 123 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 124 optimal weight: 7.9990 chunk 83 optimal weight: 0.6980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 HIS A 908 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.175542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.141216 restraints weight = 14452.577| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.29 r_work: 0.3570 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10527 Z= 0.144 Angle : 0.598 12.649 14265 Z= 0.302 Chirality : 0.042 0.250 1651 Planarity : 0.004 0.038 1792 Dihedral : 4.493 18.991 1417 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.08 % Allowed : 17.49 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.24), residues: 1293 helix: 1.45 (0.20), residues: 717 sheet: 0.36 (0.60), residues: 76 loop : -1.44 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 677 TYR 0.026 0.002 TYR A 705 PHE 0.030 0.002 PHE A 490 TRP 0.019 0.001 TRP A 638 HIS 0.008 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00329 (10523) covalent geometry : angle 0.59785 (14265) hydrogen bonds : bond 0.04548 ( 550) hydrogen bonds : angle 4.20270 ( 1614) metal coordination : bond 0.00354 ( 3) Misc. bond : bond 0.00131 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 206 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: A 54 GLN cc_start: 0.7624 (OUTLIER) cc_final: 0.7421 (mt0) REVERT: A 290 VAL cc_start: 0.8319 (m) cc_final: 0.7794 (p) REVERT: A 491 SER cc_start: 0.8281 (m) cc_final: 0.7946 (p) REVERT: A 553 SER cc_start: 0.7663 (m) cc_final: 0.7144 (t) REVERT: A 590 THR cc_start: 0.7864 (m) cc_final: 0.7604 (p) REVERT: A 605 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7758 (mmt90) REVERT: A 639 GLU cc_start: 0.7054 (mt-10) cc_final: 0.6623 (mt-10) REVERT: A 645 GLU cc_start: 0.7468 (mt-10) cc_final: 0.7238 (mt-10) REVERT: A 840 SER cc_start: 0.7899 (m) cc_final: 0.7656 (p) REVERT: A 918 MET cc_start: 0.5502 (tpp) cc_final: 0.4799 (tpp) REVERT: A 971 GLU cc_start: 0.7838 (tm-30) cc_final: 0.7475 (tm-30) REVERT: A 1018 VAL cc_start: 0.7970 (t) cc_final: 0.7709 (m) REVERT: A 1051 HIS cc_start: 0.8250 (OUTLIER) cc_final: 0.7759 (m170) REVERT: A 1204 TYR cc_start: 0.7252 (p90) cc_final: 0.6966 (p90) REVERT: D 145 MET cc_start: 0.7874 (mtm) cc_final: 0.7658 (ttm) REVERT: D 152 MET cc_start: 0.5443 (OUTLIER) cc_final: 0.5121 (mpp) REVERT: D 155 MET cc_start: 0.6970 (tpp) cc_final: 0.6432 (tpp) REVERT: E 145 MET cc_start: 0.6588 (mmm) cc_final: 0.6054 (mmm) outliers start: 24 outliers final: 17 residues processed: 216 average time/residue: 0.1041 time to fit residues: 31.0202 Evaluate side-chains 224 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 203 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLN Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 484 LYS Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 605 ARG Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 1014 THR Chi-restraints excluded: chain A residue 1051 HIS Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1224 LEU Chi-restraints excluded: chain D residue 152 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 64 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.4980 chunk 30 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 118 optimal weight: 7.9990 chunk 75 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 HIS A 908 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.175607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.141461 restraints weight = 14269.669| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.28 r_work: 0.3530 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10527 Z= 0.139 Angle : 0.592 12.441 14265 Z= 0.299 Chirality : 0.042 0.249 1651 Planarity : 0.004 0.038 1792 Dihedral : 4.427 18.855 1417 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.08 % Allowed : 17.75 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.24), residues: 1293 helix: 1.51 (0.20), residues: 717 sheet: 0.37 (0.60), residues: 76 loop : -1.42 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 412 TYR 0.027 0.002 TYR A 705 PHE 0.031 0.002 PHE A 490 TRP 0.018 0.001 TRP A 638 HIS 0.009 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00319 (10523) covalent geometry : angle 0.59209 (14265) hydrogen bonds : bond 0.04458 ( 550) hydrogen bonds : angle 4.17032 ( 1614) metal coordination : bond 0.00333 ( 3) Misc. bond : bond 0.00047 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 207 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: A 114 TYR cc_start: 0.7593 (t80) cc_final: 0.6921 (t80) REVERT: A 290 VAL cc_start: 0.8319 (m) cc_final: 0.7791 (p) REVERT: A 491 SER cc_start: 0.8254 (m) cc_final: 0.7903 (p) REVERT: A 553 SER cc_start: 0.7632 (m) cc_final: 0.7132 (t) REVERT: A 590 THR cc_start: 0.7850 (m) cc_final: 0.7602 (p) REVERT: A 605 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7651 (mmm160) REVERT: A 639 GLU cc_start: 0.7064 (mt-10) cc_final: 0.6649 (mt-10) REVERT: A 645 GLU cc_start: 0.7434 (mt-10) cc_final: 0.7194 (mt-10) REVERT: A 840 SER cc_start: 0.7891 (m) cc_final: 0.7659 (p) REVERT: A 918 MET cc_start: 0.5472 (tpp) cc_final: 0.4774 (tpp) REVERT: A 971 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7525 (tm-30) REVERT: A 1018 VAL cc_start: 0.7982 (t) cc_final: 0.7724 (m) REVERT: A 1051 HIS cc_start: 0.8256 (OUTLIER) cc_final: 0.7755 (m170) REVERT: A 1204 TYR cc_start: 0.7265 (p90) cc_final: 0.6984 (p90) REVERT: D 145 MET cc_start: 0.7892 (mtm) cc_final: 0.7663 (ttm) REVERT: D 152 MET cc_start: 0.5385 (OUTLIER) cc_final: 0.5028 (mpp) REVERT: D 155 MET cc_start: 0.6939 (tpp) cc_final: 0.6424 (tpp) REVERT: E 145 MET cc_start: 0.6587 (mmm) cc_final: 0.6068 (mmm) outliers start: 24 outliers final: 16 residues processed: 218 average time/residue: 0.1000 time to fit residues: 30.2279 Evaluate side-chains 225 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 206 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 484 LYS Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 605 ARG Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 1014 THR Chi-restraints excluded: chain A residue 1051 HIS Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1224 LEU Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain E residue 148 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 5 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 79 optimal weight: 0.3980 chunk 57 optimal weight: 0.5980 chunk 37 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 77 optimal weight: 0.0670 chunk 64 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 106 optimal weight: 10.0000 chunk 121 optimal weight: 30.0000 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 GLN A 352 HIS A 572 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.174420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.140046 restraints weight = 14425.968| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.30 r_work: 0.3564 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10527 Z= 0.169 Angle : 0.622 12.335 14265 Z= 0.313 Chirality : 0.043 0.304 1651 Planarity : 0.005 0.039 1792 Dihedral : 4.525 19.303 1417 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.99 % Allowed : 17.66 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.24), residues: 1293 helix: 1.42 (0.20), residues: 718 sheet: 0.32 (0.59), residues: 76 loop : -1.43 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 677 TYR 0.028 0.002 TYR A 705 PHE 0.029 0.002 PHE A 490 TRP 0.022 0.002 TRP A 638 HIS 0.009 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00389 (10523) covalent geometry : angle 0.62207 (14265) hydrogen bonds : bond 0.04816 ( 550) hydrogen bonds : angle 4.21557 ( 1614) metal coordination : bond 0.00447 ( 3) Misc. bond : bond 0.00022 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2642.95 seconds wall clock time: 45 minutes 57.40 seconds (2757.40 seconds total)