Starting phenix.real_space_refine on Thu Jul 2 18:26:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8avy_15687/07_2026/8avy_15687.cif Found real_map, /net/cci-nas-00/data/ceres_data/8avy_15687/07_2026/8avy_15687.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8avy_15687/07_2026/8avy_15687.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8avy_15687/07_2026/8avy_15687.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8avy_15687/07_2026/8avy_15687.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8avy_15687/07_2026/8avy_15687.map" model { file = "/net/cci-nas-00/data/ceres_data/8avy_15687/07_2026/8avy_15687.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8avy_15687/07_2026/8avy_15687.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 31 5.16 5 C 6116 2.51 5 N 1552 2.21 5 O 1726 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9433 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1175, 9085 Classifications: {'peptide': 1175} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 29, 'TRANS': 1145} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 348 Unusual residues: {' MG': 2, 'ATP': 2, 'Y01': 8} Classifications: {'undetermined': 12, 'water': 4} Link IDs: {None: 15} Time building chain proxies: 1.91, per 1000 atoms: 0.20 Number of scatterers: 9433 At special positions: 0 Unit cell: (72.819, 87.048, 148.986, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 31 16.00 P 6 15.00 Mg 2 11.99 O 1726 8.00 N 1552 7.00 C 6116 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.65 Conformation dependent library (CDL) restraints added in 215.4 milliseconds 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2156 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 4 sheets defined 71.1% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 43 through 62 Processing helix chain 'A' and resid 62 through 73 Processing helix chain 'A' and resid 74 through 85 Processing helix chain 'A' and resid 91 through 154 removed outlier: 3.891A pdb=" N ARG A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TRP A 132 " --> pdb=" O GLN A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 162 Processing helix chain 'A' and resid 164 through 180 removed outlier: 3.882A pdb=" N THR A 172 " --> pdb=" O ASN A 168 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N VAL A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 207 removed outlier: 3.900A pdb=" N GLY A 187 " --> pdb=" O GLY A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 256 Proline residue: A 219 - end of helix Processing helix chain 'A' and resid 256 through 263 Processing helix chain 'A' and resid 265 through 319 removed outlier: 3.545A pdb=" N ASN A 276 " --> pdb=" O ARG A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 334 Processing helix chain 'A' and resid 335 through 367 removed outlier: 4.486A pdb=" N PHE A 339 " --> pdb=" O CYS A 335 " (cutoff:3.500A) Proline residue: A 346 - end of helix removed outlier: 3.662A pdb=" N TYR A 359 " --> pdb=" O ARG A 355 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N GLU A 360 " --> pdb=" O GLY A 356 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL A 361 " --> pdb=" O ALA A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 437 Processing helix chain 'A' and resid 458 through 465 Processing helix chain 'A' and resid 479 through 486 Processing helix chain 'A' and resid 492 through 503 Processing helix chain 'A' and resid 505 through 511 Processing helix chain 'A' and resid 514 through 518 Processing helix chain 'A' and resid 521 through 525 Processing helix chain 'A' and resid 528 through 543 removed outlier: 4.028A pdb=" N ARG A 543 " --> pdb=" O ARG A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 571 removed outlier: 3.541A pdb=" N VAL A 564 " --> pdb=" O GLU A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 576 removed outlier: 3.638A pdb=" N GLY A 575 " --> pdb=" O ALA A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 590 removed outlier: 4.047A pdb=" N VAL A 588 " --> pdb=" O ARG A 584 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG A 589 " --> pdb=" O LEU A 585 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ASN A 590 " --> pdb=" O SER A 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 584 through 590' Processing helix chain 'A' and resid 607 through 615 Processing helix chain 'A' and resid 616 through 623 Processing helix chain 'A' and resid 691 through 698 Processing helix chain 'A' and resid 699 through 702 removed outlier: 4.914A pdb=" N THR A 702 " --> pdb=" O LEU A 699 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 699 through 702' Processing helix chain 'A' and resid 703 through 737 removed outlier: 3.797A pdb=" N GLN A 721 " --> pdb=" O ASN A 717 " (cutoff:3.500A) Proline residue: A 722 - end of helix removed outlier: 4.237A pdb=" N SER A 725 " --> pdb=" O GLN A 721 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL A 726 " --> pdb=" O PRO A 722 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL A 734 " --> pdb=" O LYS A 730 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ASN A 737 " --> pdb=" O GLY A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 743 No H-bonds generated for 'chain 'A' and resid 741 through 743' Processing helix chain 'A' and resid 744 through 795 removed outlier: 3.675A pdb=" N PHE A 773 " --> pdb=" O GLN A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 801 removed outlier: 3.516A pdb=" N PHE A 800 " --> pdb=" O ASP A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 805 Processing helix chain 'A' and resid 806 through 823 removed outlier: 4.163A pdb=" N ALA A 818 " --> pdb=" O LEU A 814 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA A 819 " --> pdb=" O ALA A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 850 Processing helix chain 'A' and resid 852 through 899 removed outlier: 3.852A pdb=" N LEU A 856 " --> pdb=" O GLN A 852 " (cutoff:3.500A) Proline residue: A 862 - end of helix removed outlier: 3.625A pdb=" N ALA A 867 " --> pdb=" O ILE A 863 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS A 881 " --> pdb=" O GLY A 877 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU A 887 " --> pdb=" O LYS A 883 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLY A 888 " --> pdb=" O LYS A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 899 through 906 Processing helix chain 'A' and resid 908 through 920 Processing helix chain 'A' and resid 920 through 962 removed outlier: 3.621A pdb=" N HIS A 932 " --> pdb=" O MET A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 989 removed outlier: 3.573A pdb=" N PHE A 979 " --> pdb=" O SER A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 990 through 1010 removed outlier: 3.866A pdb=" N LYS A 996 " --> pdb=" O PRO A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1071 through 1080 removed outlier: 3.810A pdb=" N VAL A1076 " --> pdb=" O LYS A1072 " (cutoff:3.500A) Processing helix chain 'A' and resid 1101 through 1107 Processing helix chain 'A' and resid 1122 through 1129 Processing helix chain 'A' and resid 1137 through 1148 Processing helix chain 'A' and resid 1150 through 1156 Processing helix chain 'A' and resid 1159 through 1163 Processing helix chain 'A' and resid 1166 through 1170 Processing helix chain 'A' and resid 1173 through 1187 Processing helix chain 'A' and resid 1203 through 1217 Processing helix chain 'A' and resid 1229 through 1233 removed outlier: 3.554A pdb=" N THR A1232 " --> pdb=" O ARG A1229 " (cutoff:3.500A) Processing helix chain 'A' and resid 1252 through 1259 Processing helix chain 'A' and resid 1261 through 1267 removed outlier: 3.565A pdb=" N VAL A1267 " --> pdb=" O TYR A1263 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 406 through 413 removed outlier: 6.859A pdb=" N LYS A 407 " --> pdb=" O HIS A 394 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N HIS A 394 " --> pdb=" O LYS A 407 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N LEU A 409 " --> pdb=" O ASN A 392 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N PHE A 390 " --> pdb=" O SER A 448 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N SER A 448 " --> pdb=" O PHE A 390 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N ASN A 392 " --> pdb=" O MET A 446 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N MET A 446 " --> pdb=" O ASN A 392 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 466 through 469 removed outlier: 6.691A pdb=" N GLY A 467 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N ASP A 551 " --> pdb=" O GLY A 467 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL A 469 " --> pdb=" O ASP A 551 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU A 548 " --> pdb=" O ILE A 579 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ILE A 581 " --> pdb=" O LEU A 548 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU A 550 " --> pdb=" O ILE A 581 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL A 419 " --> pdb=" O VAL A 580 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N THR A 418 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ALA A 595 " --> pdb=" O THR A 418 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N ALA A 420 " --> pdb=" O ALA A 595 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N PHE A 597 " --> pdb=" O ALA A 420 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL A 422 " --> pdb=" O PHE A 597 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLU A 604 " --> pdb=" O GLY A 596 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1053 through 1056 removed outlier: 5.626A pdb=" N PHE A1033 " --> pdb=" O PHE A1091 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N PHE A1091 " --> pdb=" O PHE A1033 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N GLY A1035 " --> pdb=" O SER A1089 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N SER A1089 " --> pdb=" O GLY A1035 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1109 through 1112 removed outlier: 6.233A pdb=" N GLY A1110 " --> pdb=" O LEU A1194 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N ASP A1196 " --> pdb=" O GLY A1110 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL A1112 " --> pdb=" O ASP A1196 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU A1193 " --> pdb=" O ILE A1224 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ILE A1226 " --> pdb=" O LEU A1193 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU A1195 " --> pdb=" O ILE A1226 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N THR A1061 " --> pdb=" O LEU A1238 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N VAL A1240 " --> pdb=" O THR A1061 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ALA A1063 " --> pdb=" O VAL A1240 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE A1242 " --> pdb=" O ALA A1063 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N VAL A1065 " --> pdb=" O ILE A1242 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLN A1243 " --> pdb=" O VAL A1247 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N VAL A1247 " --> pdb=" O GLN A1243 " (cutoff:3.500A) 614 hydrogen bonds defined for protein. 1791 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: 1.30 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1517 1.30 - 1.42: 2378 1.42 - 1.55: 5636 1.55 - 1.68: 31 1.68 - 1.81: 61 Bond restraints: 9623 Sorted by residual: bond pdb=" CA ALA A 56 " pdb=" CB ALA A 56 " ideal model delta sigma weight residual 1.528 1.440 0.089 1.56e-02 4.11e+03 3.25e+01 bond pdb=" C TRP A 132 " pdb=" O TRP A 132 " ideal model delta sigma weight residual 1.236 1.167 0.069 1.29e-02 6.01e+03 2.90e+01 bond pdb=" CA ALA A 125 " pdb=" CB ALA A 125 " ideal model delta sigma weight residual 1.528 1.449 0.079 1.59e-02 3.96e+03 2.47e+01 bond pdb=" CA SER A 130 " pdb=" CB SER A 130 " ideal model delta sigma weight residual 1.529 1.454 0.075 1.55e-02 4.16e+03 2.33e+01 bond pdb=" C PHE A 131 " pdb=" O PHE A 131 " ideal model delta sigma weight residual 1.237 1.180 0.057 1.19e-02 7.06e+03 2.27e+01 ... (remaining 9618 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 12738 2.14 - 4.29: 267 4.29 - 6.43: 56 6.43 - 8.58: 4 8.58 - 10.72: 7 Bond angle restraints: 13072 Sorted by residual: angle pdb=" N THR A 37 " pdb=" CA THR A 37 " pdb=" C THR A 37 " ideal model delta sigma weight residual 111.40 100.68 10.72 1.22e+00 6.72e-01 7.73e+01 angle pdb=" C PHE A 131 " pdb=" CA PHE A 131 " pdb=" CB PHE A 131 " ideal model delta sigma weight residual 110.85 121.06 -10.21 1.70e+00 3.46e-01 3.61e+01 angle pdb=" C THR A 54 " pdb=" CA THR A 54 " pdb=" CB THR A 54 " ideal model delta sigma weight residual 110.85 120.04 -9.19 1.70e+00 3.46e-01 2.92e+01 angle pdb=" C PHE A 197 " pdb=" CA PHE A 197 " pdb=" CB PHE A 197 " ideal model delta sigma weight residual 110.85 119.70 -8.85 1.70e+00 3.46e-01 2.71e+01 angle pdb=" C THR A 37 " pdb=" CA THR A 37 " pdb=" CB THR A 37 " ideal model delta sigma weight residual 110.79 119.50 -8.71 1.68e+00 3.54e-01 2.69e+01 ... (remaining 13067 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.46: 5408 24.46 - 48.91: 173 48.91 - 73.37: 25 73.37 - 97.82: 7 97.82 - 122.28: 3 Dihedral angle restraints: 5616 sinusoidal: 2251 harmonic: 3365 Sorted by residual: dihedral pdb=" C THR A 54 " pdb=" N THR A 54 " pdb=" CA THR A 54 " pdb=" CB THR A 54 " ideal model delta harmonic sigma weight residual -122.00 -135.00 13.00 0 2.50e+00 1.60e-01 2.70e+01 dihedral pdb=" C PHE A 190 " pdb=" N PHE A 190 " pdb=" CA PHE A 190 " pdb=" CB PHE A 190 " ideal model delta harmonic sigma weight residual -122.60 -134.15 11.55 0 2.50e+00 1.60e-01 2.13e+01 dihedral pdb=" C PHE A 197 " pdb=" N PHE A 197 " pdb=" CA PHE A 197 " pdb=" CB PHE A 197 " ideal model delta harmonic sigma weight residual -122.60 -133.22 10.62 0 2.50e+00 1.60e-01 1.80e+01 ... (remaining 5613 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1394 0.082 - 0.163: 102 0.163 - 0.245: 8 0.245 - 0.327: 4 0.327 - 0.409: 5 Chirality restraints: 1513 Sorted by residual: chirality pdb=" CA THR A 54 " pdb=" N THR A 54 " pdb=" C THR A 54 " pdb=" CB THR A 54 " both_signs ideal model delta sigma weight residual False 2.53 2.12 0.41 2.00e-01 2.50e+01 4.18e+00 chirality pdb=" CB VAL A 124 " pdb=" CA VAL A 124 " pdb=" CG1 VAL A 124 " pdb=" CG2 VAL A 124 " both_signs ideal model delta sigma weight residual False -2.63 -2.23 -0.40 2.00e-01 2.50e+01 4.05e+00 chirality pdb=" CBB Y01 A2009 " pdb=" CAC Y01 A2009 " pdb=" CAO Y01 A2009 " pdb=" CBE Y01 A2009 " both_signs ideal model delta sigma weight residual False 2.58 2.20 0.38 2.00e-01 2.50e+01 3.53e+00 ... (remaining 1510 not shown) Planarity restraints: 1610 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 34 " -0.028 2.00e-02 2.50e+03 5.48e-02 3.00e+01 pdb=" C SER A 34 " 0.095 2.00e-02 2.50e+03 pdb=" O SER A 34 " -0.035 2.00e-02 2.50e+03 pdb=" N VAL A 35 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ATP A2001 " 0.046 2.00e-02 2.50e+03 2.08e-02 1.19e+01 pdb=" C2 ATP A2001 " -0.006 2.00e-02 2.50e+03 pdb=" C4 ATP A2001 " -0.016 2.00e-02 2.50e+03 pdb=" C5 ATP A2001 " -0.011 2.00e-02 2.50e+03 pdb=" C6 ATP A2001 " -0.003 2.00e-02 2.50e+03 pdb=" C8 ATP A2001 " 0.008 2.00e-02 2.50e+03 pdb=" N1 ATP A2001 " 0.014 2.00e-02 2.50e+03 pdb=" N3 ATP A2001 " -0.010 2.00e-02 2.50e+03 pdb=" N6 ATP A2001 " 0.025 2.00e-02 2.50e+03 pdb=" N7 ATP A2001 " -0.015 2.00e-02 2.50e+03 pdb=" N9 ATP A2001 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 37 " -0.016 2.00e-02 2.50e+03 3.34e-02 1.11e+01 pdb=" C THR A 37 " 0.058 2.00e-02 2.50e+03 pdb=" O THR A 37 " -0.022 2.00e-02 2.50e+03 pdb=" N MET A 38 " -0.019 2.00e-02 2.50e+03 ... (remaining 1607 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 69 2.59 - 3.17: 8034 3.17 - 3.74: 15125 3.74 - 4.32: 21496 4.32 - 4.90: 34891 Nonbonded interactions: 79615 Sorted by model distance: nonbonded pdb=" O3G ATP A2003 " pdb="MG MG A2004 " model vdw 2.008 2.170 nonbonded pdb="MG MG A2004 " pdb=" O HOH A2101 " model vdw 2.009 2.170 nonbonded pdb="MG MG A2002 " pdb=" O HOH A2102 " model vdw 2.059 2.170 nonbonded pdb=" OG SER A 430 " pdb="MG MG A2002 " model vdw 2.072 2.170 nonbonded pdb="MG MG A2002 " pdb=" O HOH A2103 " model vdw 2.077 2.170 ... (remaining 79610 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.370 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: 0.180 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.930 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:5.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 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 0.089 9623 Z= 0.350 Angle : 0.777 10.724 13072 Z= 0.496 Chirality : 0.052 0.409 1513 Planarity : 0.004 0.055 1610 Dihedral : 12.916 122.279 3460 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.74 % Allowed : 6.93 % Favored : 92.33 % Cbeta Deviations : 0.37 % 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: 1.35 (0.24), residues: 1171 helix: 1.46 (0.19), residues: 790 sheet: 0.76 (0.64), residues: 60 loop : -0.38 (0.33), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 400 TYR 0.018 0.002 TYR A 49 PHE 0.027 0.002 PHE A 131 TRP 0.020 0.002 TRP A 228 HIS 0.007 0.001 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.35 ( 9623) covalent geometry : angle 0.77736 / 0.50 (13072) hydrogen bonds : bond 0.13999 / 9.40 ( 614) hydrogen bonds : angle 4.94265 / 3.60 ( 1791) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 161 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 ASN cc_start: 0.7805 (m110) cc_final: 0.7501 (m-40) REVERT: A 848 ILE cc_start: 0.8270 (OUTLIER) cc_final: 0.7994 (mp) REVERT: A 1243 GLN cc_start: 0.7920 (tt0) cc_final: 0.7697 (tp40) outliers start: 7 outliers final: 4 residues processed: 167 average time/residue: 0.4653 time to fit residues: 83.4242 Evaluate side-chains 118 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 113 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1267 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 50.0000 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.2980 chunk 100 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 GLN A 717 ASN A1099 GLN A1244 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.178250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.128421 restraints weight = 9586.828| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.86 r_work: 0.2963 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9623 Z= 0.173 Angle : 0.578 10.868 13072 Z= 0.293 Chirality : 0.043 0.204 1513 Planarity : 0.004 0.036 1610 Dihedral : 9.856 119.377 1378 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.26 % Allowed : 12.39 % Favored : 84.35 % 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: 1.36 (0.24), residues: 1171 helix: 1.47 (0.18), residues: 798 sheet: 0.78 (0.63), residues: 60 loop : -0.42 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1221 TYR 0.033 0.002 TYR A 306 PHE 0.025 0.002 PHE A 508 TRP 0.018 0.002 TRP A 228 HIS 0.004 0.001 HIS A 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 ( 9623) covalent geometry : angle 0.57750 / 0.29 (13072) hydrogen bonds : bond 0.05177 / 3.41 ( 614) hydrogen bonds : angle 4.07828 / 3.03 ( 1791) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.7708 (mtm-85) cc_final: 0.7421 (mtt90) REVERT: A 168 ASN cc_start: 0.7018 (t0) cc_final: 0.6113 (m110) REVERT: A 293 ILE cc_start: 0.8115 (OUTLIER) cc_final: 0.7827 (tt) REVERT: A 424 ASN cc_start: 0.8229 (m110) cc_final: 0.7652 (m-40) REVERT: A 497 GLU cc_start: 0.6554 (mt-10) cc_final: 0.5993 (tt0) REVERT: A 802 ASP cc_start: 0.8059 (OUTLIER) cc_final: 0.7549 (t70) REVERT: A 915 MET cc_start: 0.8758 (mtm) cc_final: 0.8440 (mtp) REVERT: A 1102 VAL cc_start: 0.8318 (OUTLIER) cc_final: 0.8001 (p) REVERT: A 1159 ASP cc_start: 0.7323 (OUTLIER) cc_final: 0.6807 (t0) REVERT: A 1223 VAL cc_start: 0.8128 (OUTLIER) cc_final: 0.7879 (t) REVERT: A 1237 ASP cc_start: 0.7983 (m-30) cc_final: 0.7704 (m-30) REVERT: A 1243 GLN cc_start: 0.7149 (tt0) cc_final: 0.6382 (tp40) outliers start: 31 outliers final: 15 residues processed: 142 average time/residue: 0.3905 time to fit residues: 59.9783 Evaluate side-chains 133 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 802 ASP Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 948 SER Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain A residue 1102 VAL Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1159 ASP Chi-restraints excluded: chain A residue 1223 VAL Chi-restraints excluded: chain A residue 1232 THR Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1267 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 7 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 75 optimal weight: 10.0000 chunk 85 optimal weight: 0.6980 chunk 94 optimal weight: 3.9990 chunk 93 optimal weight: 0.0970 chunk 114 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 chunk 98 optimal weight: 0.5980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 437 GLN A1244 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.179321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.126623 restraints weight = 9561.050| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.75 r_work: 0.3067 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9623 Z= 0.131 Angle : 0.506 9.144 13072 Z= 0.259 Chirality : 0.040 0.204 1513 Planarity : 0.003 0.034 1610 Dihedral : 9.654 120.891 1376 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.84 % Allowed : 13.03 % Favored : 84.14 % 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: 1.61 (0.24), residues: 1171 helix: 1.68 (0.18), residues: 798 sheet: 0.80 (0.65), residues: 58 loop : -0.40 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 144 TYR 0.032 0.001 TYR A 306 PHE 0.017 0.001 PHE A 508 TRP 0.018 0.001 TRP A 228 HIS 0.003 0.001 HIS A 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 ( 9623) covalent geometry : angle 0.50645 / 0.26 (13072) hydrogen bonds : bond 0.04680 / 3.10 ( 614) hydrogen bonds : angle 3.89659 / 2.90 ( 1791) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.7683 (mtm-85) cc_final: 0.7396 (mtt90) REVERT: A 168 ASN cc_start: 0.6928 (t0) cc_final: 0.6137 (m-40) REVERT: A 293 ILE cc_start: 0.8156 (OUTLIER) cc_final: 0.7876 (tt) REVERT: A 377 SER cc_start: 0.8822 (OUTLIER) cc_final: 0.8608 (p) REVERT: A 424 ASN cc_start: 0.8216 (m110) cc_final: 0.7633 (m-40) REVERT: A 455 ARG cc_start: 0.7522 (mtt180) cc_final: 0.7191 (mtp180) REVERT: A 497 GLU cc_start: 0.6520 (mt-10) cc_final: 0.5974 (tt0) REVERT: A 508 PHE cc_start: 0.7674 (OUTLIER) cc_final: 0.7327 (p90) REVERT: A 802 ASP cc_start: 0.8030 (OUTLIER) cc_final: 0.7466 (t70) REVERT: A 848 ILE cc_start: 0.7934 (OUTLIER) cc_final: 0.7641 (mp) REVERT: A 915 MET cc_start: 0.8718 (mtm) cc_final: 0.8419 (mtp) REVERT: A 1026 MET cc_start: 0.8298 (ttm) cc_final: 0.7993 (ptp) REVERT: A 1055 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7053 (pp20) REVERT: A 1102 VAL cc_start: 0.8321 (OUTLIER) cc_final: 0.8021 (p) REVERT: A 1208 LYS cc_start: 0.6732 (ttpt) cc_final: 0.5912 (pttm) REVERT: A 1237 ASP cc_start: 0.7940 (m-30) cc_final: 0.7682 (m-30) REVERT: A 1243 GLN cc_start: 0.7135 (tt0) cc_final: 0.6367 (tp40) outliers start: 27 outliers final: 13 residues processed: 134 average time/residue: 0.3918 time to fit residues: 56.8469 Evaluate side-chains 130 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 802 ASP Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 925 ARG Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 953 PHE Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain A residue 1102 VAL Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1232 THR Chi-restraints excluded: chain A residue 1267 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 28 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 70 optimal weight: 0.0970 chunk 42 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 60 HIS A 145 GLN A 347 ASN A1244 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.176515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.123091 restraints weight = 9691.160| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.77 r_work: 0.2985 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9623 Z= 0.185 Angle : 0.549 8.418 13072 Z= 0.280 Chirality : 0.042 0.198 1513 Planarity : 0.004 0.033 1610 Dihedral : 9.620 118.262 1376 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.57 % Allowed : 13.24 % Favored : 83.19 % 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: 1.42 (0.24), residues: 1171 helix: 1.52 (0.18), residues: 798 sheet: 0.81 (0.66), residues: 58 loop : -0.44 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1121 TYR 0.031 0.002 TYR A 306 PHE 0.025 0.002 PHE A 508 TRP 0.017 0.002 TRP A 228 HIS 0.004 0.001 HIS A 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.18 ( 9623) covalent geometry : angle 0.54860 / 0.28 (13072) hydrogen bonds : bond 0.05043 / 3.36 ( 614) hydrogen bonds : angle 3.93414 / 2.91 ( 1791) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 117 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.7655 (mtm-85) cc_final: 0.7363 (mtt90) REVERT: A 168 ASN cc_start: 0.7042 (t0) cc_final: 0.6193 (m-40) REVERT: A 293 ILE cc_start: 0.8155 (OUTLIER) cc_final: 0.7882 (tt) REVERT: A 404 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.8184 (mt0) REVERT: A 424 ASN cc_start: 0.8123 (m110) cc_final: 0.7518 (m-40) REVERT: A 455 ARG cc_start: 0.7568 (mtt180) cc_final: 0.7230 (mtp180) REVERT: A 497 GLU cc_start: 0.6514 (mt-10) cc_final: 0.5984 (tt0) REVERT: A 802 ASP cc_start: 0.8060 (OUTLIER) cc_final: 0.7482 (t70) REVERT: A 848 ILE cc_start: 0.7861 (OUTLIER) cc_final: 0.7592 (mp) REVERT: A 915 MET cc_start: 0.8726 (mtm) cc_final: 0.8365 (mtp) REVERT: A 925 ARG cc_start: 0.7470 (OUTLIER) cc_final: 0.7196 (mtm-85) REVERT: A 1026 MET cc_start: 0.8320 (ttm) cc_final: 0.7994 (ptp) REVERT: A 1055 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7029 (pp20) REVERT: A 1102 VAL cc_start: 0.8307 (OUTLIER) cc_final: 0.8040 (p) REVERT: A 1208 LYS cc_start: 0.6728 (ttpt) cc_final: 0.6392 (mtpp) REVERT: A 1237 ASP cc_start: 0.7948 (m-30) cc_final: 0.7582 (m-30) REVERT: A 1243 GLN cc_start: 0.7049 (tt0) cc_final: 0.6287 (tp40) outliers start: 34 outliers final: 16 residues processed: 139 average time/residue: 0.4469 time to fit residues: 66.8442 Evaluate side-chains 137 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 404 GLN Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 802 ASP Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 925 ARG Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 948 SER Chi-restraints excluded: chain A residue 953 PHE Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain A residue 1102 VAL Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1232 THR Chi-restraints excluded: chain A residue 1267 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 22 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 chunk 112 optimal weight: 8.9990 chunk 7 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 106 optimal weight: 0.4980 chunk 42 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 608 HIS A1244 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.177339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.124269 restraints weight = 9748.494| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.76 r_work: 0.3003 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9623 Z= 0.152 Angle : 0.518 8.097 13072 Z= 0.265 Chirality : 0.040 0.195 1513 Planarity : 0.003 0.035 1610 Dihedral : 9.456 117.736 1376 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.47 % Allowed : 13.45 % Favored : 83.09 % 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: 1.46 (0.24), residues: 1171 helix: 1.59 (0.18), residues: 799 sheet: 0.69 (0.66), residues: 60 loop : -0.52 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 144 TYR 0.032 0.001 TYR A 306 PHE 0.019 0.001 PHE A 508 TRP 0.018 0.001 TRP A 228 HIS 0.004 0.001 HIS A 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 9623) covalent geometry : angle 0.51828 / 0.26 (13072) hydrogen bonds : bond 0.04720 / 3.15 ( 614) hydrogen bonds : angle 3.85496 / 2.86 ( 1791) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 116 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.7721 (mtm-85) cc_final: 0.7415 (mtt90) REVERT: A 168 ASN cc_start: 0.7070 (t0) cc_final: 0.6223 (m-40) REVERT: A 293 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7912 (tt) REVERT: A 377 SER cc_start: 0.8820 (OUTLIER) cc_final: 0.8575 (p) REVERT: A 404 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.8174 (mt0) REVERT: A 414 LYS cc_start: 0.7116 (mtpt) cc_final: 0.6518 (mmpt) REVERT: A 424 ASN cc_start: 0.8106 (m110) cc_final: 0.7480 (m-40) REVERT: A 455 ARG cc_start: 0.7539 (mtt180) cc_final: 0.7202 (mtp180) REVERT: A 497 GLU cc_start: 0.6567 (mt-10) cc_final: 0.6034 (tt0) REVERT: A 508 PHE cc_start: 0.7761 (OUTLIER) cc_final: 0.7344 (p90) REVERT: A 802 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7401 (t70) REVERT: A 848 ILE cc_start: 0.7897 (OUTLIER) cc_final: 0.7635 (mp) REVERT: A 925 ARG cc_start: 0.7540 (OUTLIER) cc_final: 0.7261 (mtm-85) REVERT: A 965 MET cc_start: 0.7423 (mtp) cc_final: 0.6737 (mtp) REVERT: A 1026 MET cc_start: 0.8295 (ttm) cc_final: 0.8003 (ptp) REVERT: A 1055 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7185 (pp20) REVERT: A 1102 VAL cc_start: 0.8337 (OUTLIER) cc_final: 0.8085 (p) REVERT: A 1208 LYS cc_start: 0.6721 (ttpt) cc_final: 0.6343 (mtpp) REVERT: A 1237 ASP cc_start: 0.7974 (m-30) cc_final: 0.7655 (m-30) REVERT: A 1243 GLN cc_start: 0.7144 (tt0) cc_final: 0.6353 (tp40) outliers start: 33 outliers final: 16 residues processed: 141 average time/residue: 0.4432 time to fit residues: 67.5653 Evaluate side-chains 138 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 404 GLN Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 802 ASP Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 925 ARG Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 953 PHE Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain A residue 1102 VAL Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1232 THR Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1267 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 15 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 96 optimal weight: 8.9990 chunk 11 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1030 ASN A1244 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.174623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.119944 restraints weight = 9712.332| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.81 r_work: 0.3050 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9623 Z= 0.124 Angle : 0.498 8.787 13072 Z= 0.253 Chirality : 0.039 0.192 1513 Planarity : 0.003 0.033 1610 Dihedral : 9.283 117.713 1376 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.36 % Allowed : 13.66 % Favored : 82.98 % 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: 1.65 (0.24), residues: 1171 helix: 1.74 (0.18), residues: 798 sheet: 0.74 (0.67), residues: 60 loop : -0.47 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 144 TYR 0.029 0.001 TYR A 306 PHE 0.016 0.001 PHE A 508 TRP 0.016 0.001 TRP A 228 HIS 0.003 0.001 HIS A 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 9623) covalent geometry : angle 0.49755 / 0.25 (13072) hydrogen bonds : bond 0.04416 / 2.95 ( 614) hydrogen bonds : angle 3.77714 / 2.79 ( 1791) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 115 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.7643 (mtm-85) cc_final: 0.7337 (mtt90) REVERT: A 168 ASN cc_start: 0.6910 (t0) cc_final: 0.6070 (m-40) REVERT: A 293 ILE cc_start: 0.8101 (OUTLIER) cc_final: 0.7829 (tt) REVERT: A 377 SER cc_start: 0.8823 (OUTLIER) cc_final: 0.8603 (p) REVERT: A 404 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.8131 (mt0) REVERT: A 414 LYS cc_start: 0.7046 (mtpt) cc_final: 0.6428 (mmpt) REVERT: A 424 ASN cc_start: 0.8058 (m110) cc_final: 0.7414 (m-40) REVERT: A 455 ARG cc_start: 0.7450 (mtt180) cc_final: 0.7120 (mtp180) REVERT: A 497 GLU cc_start: 0.6487 (mt-10) cc_final: 0.5959 (tt0) REVERT: A 508 PHE cc_start: 0.7585 (OUTLIER) cc_final: 0.7283 (p90) REVERT: A 802 ASP cc_start: 0.7987 (OUTLIER) cc_final: 0.7385 (t70) REVERT: A 848 ILE cc_start: 0.7763 (OUTLIER) cc_final: 0.7530 (mp) REVERT: A 915 MET cc_start: 0.8634 (mtm) cc_final: 0.8376 (mtp) REVERT: A 925 ARG cc_start: 0.7492 (OUTLIER) cc_final: 0.7203 (mtm-85) REVERT: A 1026 MET cc_start: 0.8322 (ttm) cc_final: 0.8041 (ptp) REVERT: A 1055 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7105 (pp20) REVERT: A 1102 VAL cc_start: 0.8268 (OUTLIER) cc_final: 0.8024 (p) REVERT: A 1208 LYS cc_start: 0.6608 (ttpt) cc_final: 0.6232 (mtpp) REVERT: A 1237 ASP cc_start: 0.7942 (m-30) cc_final: 0.7625 (m-30) REVERT: A 1243 GLN cc_start: 0.7004 (tt0) cc_final: 0.6278 (tp40) outliers start: 32 outliers final: 16 residues processed: 137 average time/residue: 0.4560 time to fit residues: 67.1280 Evaluate side-chains 134 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 306 TYR Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 404 GLN Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 802 ASP Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 925 ARG Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 944 MET Chi-restraints excluded: chain A residue 953 PHE Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain A residue 1102 VAL Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1232 THR Chi-restraints excluded: chain A residue 1267 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 99 optimal weight: 0.7980 chunk 75 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 60 optimal weight: 0.4980 chunk 42 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 4 optimal weight: 8.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1244 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.174164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.119489 restraints weight = 9726.088| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.81 r_work: 0.3021 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9623 Z= 0.135 Angle : 0.502 9.420 13072 Z= 0.255 Chirality : 0.040 0.190 1513 Planarity : 0.003 0.036 1610 Dihedral : 9.220 117.847 1376 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.15 % Allowed : 14.50 % Favored : 82.35 % 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: 1.68 (0.24), residues: 1171 helix: 1.78 (0.18), residues: 798 sheet: 0.66 (0.67), residues: 60 loop : -0.46 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 908 TYR 0.030 0.001 TYR A 306 PHE 0.018 0.001 PHE A 508 TRP 0.016 0.001 TRP A 228 HIS 0.003 0.001 HIS A 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 9623) covalent geometry : angle 0.50214 / 0.26 (13072) hydrogen bonds : bond 0.04468 / 2.98 ( 614) hydrogen bonds : angle 3.76280 / 2.78 ( 1791) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 112 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.7602 (mtm-85) cc_final: 0.7290 (mtt90) REVERT: A 168 ASN cc_start: 0.6899 (t0) cc_final: 0.6047 (m-40) REVERT: A 180 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7619 (mt-10) REVERT: A 293 ILE cc_start: 0.8073 (OUTLIER) cc_final: 0.7805 (tt) REVERT: A 377 SER cc_start: 0.8815 (OUTLIER) cc_final: 0.8596 (p) REVERT: A 404 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.8111 (mt0) REVERT: A 414 LYS cc_start: 0.6967 (mtpt) cc_final: 0.6358 (mmpt) REVERT: A 424 ASN cc_start: 0.8046 (m110) cc_final: 0.7401 (m-40) REVERT: A 455 ARG cc_start: 0.7369 (mtt180) cc_final: 0.7019 (mtp180) REVERT: A 497 GLU cc_start: 0.6444 (mt-10) cc_final: 0.5922 (tt0) REVERT: A 508 PHE cc_start: 0.7596 (OUTLIER) cc_final: 0.7139 (p90) REVERT: A 511 LYS cc_start: 0.7773 (ttpt) cc_final: 0.6869 (mttt) REVERT: A 802 ASP cc_start: 0.7968 (OUTLIER) cc_final: 0.7352 (t70) REVERT: A 848 ILE cc_start: 0.7753 (OUTLIER) cc_final: 0.7516 (mp) REVERT: A 915 MET cc_start: 0.8615 (mtm) cc_final: 0.8338 (mtp) REVERT: A 925 ARG cc_start: 0.7470 (OUTLIER) cc_final: 0.7185 (mtm-85) REVERT: A 1026 MET cc_start: 0.8335 (ttm) cc_final: 0.8051 (ptp) REVERT: A 1055 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7114 (pp20) REVERT: A 1102 VAL cc_start: 0.8253 (OUTLIER) cc_final: 0.8001 (p) REVERT: A 1208 LYS cc_start: 0.6560 (ttpt) cc_final: 0.6194 (mtpp) REVERT: A 1237 ASP cc_start: 0.7929 (m-30) cc_final: 0.7605 (m-30) REVERT: A 1243 GLN cc_start: 0.6946 (tt0) cc_final: 0.6253 (tp40) outliers start: 30 outliers final: 17 residues processed: 133 average time/residue: 0.4585 time to fit residues: 65.8587 Evaluate side-chains 135 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 306 TYR Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 404 GLN Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 760 ILE Chi-restraints excluded: chain A residue 802 ASP Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 925 ARG Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 953 PHE Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain A residue 1102 VAL Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1232 THR Chi-restraints excluded: chain A residue 1267 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 104 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 55 optimal weight: 0.0010 chunk 57 optimal weight: 8.9990 chunk 11 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 overall best weight: 1.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1244 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.173118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.118360 restraints weight = 9708.107| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.80 r_work: 0.3016 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9623 Z= 0.158 Angle : 0.522 9.868 13072 Z= 0.265 Chirality : 0.040 0.188 1513 Planarity : 0.003 0.035 1610 Dihedral : 9.240 118.038 1376 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.26 % Allowed : 15.13 % Favored : 81.62 % 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: 1.62 (0.24), residues: 1171 helix: 1.73 (0.18), residues: 798 sheet: 0.62 (0.67), residues: 60 loop : -0.46 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 908 TYR 0.031 0.001 TYR A 306 PHE 0.021 0.002 PHE A 934 TRP 0.015 0.001 TRP A 228 HIS 0.004 0.001 HIS A 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 ( 9623) covalent geometry : angle 0.52226 / 0.26 (13072) hydrogen bonds : bond 0.04650 / 3.11 ( 614) hydrogen bonds : angle 3.80437 / 2.81 ( 1791) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 113 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.7710 (mtm-85) cc_final: 0.7385 (mtt90) REVERT: A 168 ASN cc_start: 0.6986 (t0) cc_final: 0.6134 (m-40) REVERT: A 180 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7746 (mt-10) REVERT: A 293 ILE cc_start: 0.8176 (OUTLIER) cc_final: 0.7905 (tt) REVERT: A 377 SER cc_start: 0.8817 (OUTLIER) cc_final: 0.8575 (p) REVERT: A 404 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.8134 (mt0) REVERT: A 414 LYS cc_start: 0.7023 (mtpt) cc_final: 0.6453 (mmpt) REVERT: A 424 ASN cc_start: 0.8073 (m110) cc_final: 0.7425 (m-40) REVERT: A 455 ARG cc_start: 0.7458 (mtt180) cc_final: 0.7107 (mtp180) REVERT: A 497 GLU cc_start: 0.6570 (mt-10) cc_final: 0.6042 (tt0) REVERT: A 511 LYS cc_start: 0.7848 (ttpt) cc_final: 0.6948 (mttt) REVERT: A 802 ASP cc_start: 0.8031 (OUTLIER) cc_final: 0.7419 (t70) REVERT: A 848 ILE cc_start: 0.7778 (OUTLIER) cc_final: 0.7553 (mp) REVERT: A 915 MET cc_start: 0.8703 (mtm) cc_final: 0.8415 (mtp) REVERT: A 925 ARG cc_start: 0.7530 (OUTLIER) cc_final: 0.7249 (mtm-85) REVERT: A 1026 MET cc_start: 0.8340 (ttm) cc_final: 0.8059 (ptp) REVERT: A 1055 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7157 (pp20) REVERT: A 1102 VAL cc_start: 0.8329 (OUTLIER) cc_final: 0.8076 (p) REVERT: A 1208 LYS cc_start: 0.6672 (ttpt) cc_final: 0.6295 (mtpp) REVERT: A 1237 ASP cc_start: 0.7954 (m-30) cc_final: 0.7625 (m-30) REVERT: A 1243 GLN cc_start: 0.7024 (tt0) cc_final: 0.6345 (tp40) outliers start: 31 outliers final: 19 residues processed: 137 average time/residue: 0.4954 time to fit residues: 73.2093 Evaluate side-chains 138 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 306 TYR Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 404 GLN Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 802 ASP Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 882 ASP Chi-restraints excluded: chain A residue 925 ARG Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 953 PHE Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain A residue 1102 VAL Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1232 THR Chi-restraints excluded: chain A residue 1267 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 103 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 90 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 31 optimal weight: 0.4980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1244 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.174541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.120052 restraints weight = 9710.018| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.80 r_work: 0.3028 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9623 Z= 0.122 Angle : 0.497 10.139 13072 Z= 0.252 Chirality : 0.039 0.186 1513 Planarity : 0.003 0.036 1610 Dihedral : 9.105 118.069 1376 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.05 % Allowed : 15.55 % Favored : 81.41 % 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: 1.78 (0.24), residues: 1171 helix: 1.87 (0.18), residues: 797 sheet: 0.62 (0.67), residues: 60 loop : -0.46 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 144 TYR 0.030 0.001 TYR A 306 PHE 0.023 0.001 PHE A 934 TRP 0.017 0.001 TRP A 228 HIS 0.003 0.001 HIS A 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 9623) covalent geometry : angle 0.49705 / 0.25 (13072) hydrogen bonds : bond 0.04333 / 2.89 ( 614) hydrogen bonds : angle 3.72558 / 2.75 ( 1791) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.7649 (mtm-85) cc_final: 0.7401 (mtt90) REVERT: A 168 ASN cc_start: 0.6840 (t0) cc_final: 0.6017 (m-40) REVERT: A 180 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7666 (mt-10) REVERT: A 293 ILE cc_start: 0.8088 (OUTLIER) cc_final: 0.7819 (tt) REVERT: A 377 SER cc_start: 0.8833 (OUTLIER) cc_final: 0.8614 (p) REVERT: A 404 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.8100 (mt0) REVERT: A 414 LYS cc_start: 0.6981 (mtpt) cc_final: 0.6415 (mmpt) REVERT: A 424 ASN cc_start: 0.8058 (m110) cc_final: 0.7407 (m-40) REVERT: A 455 ARG cc_start: 0.7378 (mtt180) cc_final: 0.7016 (mtp180) REVERT: A 497 GLU cc_start: 0.6470 (mt-10) cc_final: 0.5953 (tt0) REVERT: A 508 PHE cc_start: 0.7570 (OUTLIER) cc_final: 0.7232 (p90) REVERT: A 511 LYS cc_start: 0.7723 (ttpt) cc_final: 0.6841 (mttt) REVERT: A 562 GLU cc_start: 0.6821 (tm-30) cc_final: 0.6372 (tt0) REVERT: A 802 ASP cc_start: 0.7976 (OUTLIER) cc_final: 0.7356 (t70) REVERT: A 848 ILE cc_start: 0.7725 (OUTLIER) cc_final: 0.7499 (mp) REVERT: A 915 MET cc_start: 0.8618 (mtm) cc_final: 0.8342 (mtp) REVERT: A 925 ARG cc_start: 0.7489 (OUTLIER) cc_final: 0.7210 (mtm-85) REVERT: A 1026 MET cc_start: 0.8330 (ttm) cc_final: 0.8050 (ptp) REVERT: A 1055 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7081 (pp20) REVERT: A 1102 VAL cc_start: 0.8270 (OUTLIER) cc_final: 0.8018 (p) REVERT: A 1115 GLU cc_start: 0.7051 (mp0) cc_final: 0.6725 (mt-10) REVERT: A 1208 LYS cc_start: 0.6597 (ttpt) cc_final: 0.5982 (mtpp) REVERT: A 1237 ASP cc_start: 0.7907 (m-30) cc_final: 0.7588 (m-30) REVERT: A 1243 GLN cc_start: 0.7029 (tt0) cc_final: 0.6336 (tp40) outliers start: 29 outliers final: 18 residues processed: 135 average time/residue: 0.4994 time to fit residues: 72.6289 Evaluate side-chains 138 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 306 TYR Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 404 GLN Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 802 ASP Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 882 ASP Chi-restraints excluded: chain A residue 925 ARG Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 953 PHE Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain A residue 1102 VAL Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1232 THR Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1267 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 25 optimal weight: 0.7980 chunk 114 optimal weight: 8.9990 chunk 107 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 87 optimal weight: 8.9990 chunk 92 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1244 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.174425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.119794 restraints weight = 9713.812| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.79 r_work: 0.3051 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9623 Z= 0.129 Angle : 0.508 10.181 13072 Z= 0.258 Chirality : 0.039 0.185 1513 Planarity : 0.003 0.039 1610 Dihedral : 9.041 118.188 1375 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.84 % Allowed : 15.65 % Favored : 81.51 % 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: 1.77 (0.24), residues: 1171 helix: 1.87 (0.18), residues: 797 sheet: 0.61 (0.67), residues: 60 loop : -0.47 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 908 TYR 0.029 0.001 TYR A 306 PHE 0.028 0.001 PHE A 934 TRP 0.017 0.001 TRP A 228 HIS 0.003 0.001 HIS A 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 9623) covalent geometry : angle 0.50832 / 0.26 (13072) hydrogen bonds : bond 0.04384 / 2.93 ( 614) hydrogen bonds : angle 3.72790 / 2.75 ( 1791) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 112 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.7737 (mtm-85) cc_final: 0.7481 (mtt90) REVERT: A 168 ASN cc_start: 0.6867 (t0) cc_final: 0.6056 (m-40) REVERT: A 180 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7715 (mt-10) REVERT: A 293 ILE cc_start: 0.8149 (OUTLIER) cc_final: 0.7885 (tt) REVERT: A 377 SER cc_start: 0.8846 (OUTLIER) cc_final: 0.8629 (p) REVERT: A 404 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.8124 (mt0) REVERT: A 414 LYS cc_start: 0.7038 (mtpt) cc_final: 0.6484 (mmpt) REVERT: A 424 ASN cc_start: 0.8094 (m110) cc_final: 0.7446 (m-40) REVERT: A 455 ARG cc_start: 0.7452 (mtt180) cc_final: 0.7186 (mtp180) REVERT: A 497 GLU cc_start: 0.6558 (mt-10) cc_final: 0.6037 (tt0) REVERT: A 511 LYS cc_start: 0.7812 (ttpt) cc_final: 0.6957 (mttt) REVERT: A 562 GLU cc_start: 0.6863 (tm-30) cc_final: 0.6404 (tt0) REVERT: A 802 ASP cc_start: 0.8044 (OUTLIER) cc_final: 0.7440 (t70) REVERT: A 844 ILE cc_start: 0.7480 (mp) cc_final: 0.7138 (mp) REVERT: A 848 ILE cc_start: 0.7800 (OUTLIER) cc_final: 0.7554 (mp) REVERT: A 915 MET cc_start: 0.8676 (mtm) cc_final: 0.8402 (mtp) REVERT: A 925 ARG cc_start: 0.7544 (OUTLIER) cc_final: 0.7267 (mtm-85) REVERT: A 1026 MET cc_start: 0.8330 (ttm) cc_final: 0.8023 (ptp) REVERT: A 1055 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7120 (pp20) REVERT: A 1102 VAL cc_start: 0.8341 (OUTLIER) cc_final: 0.8089 (p) REVERT: A 1115 GLU cc_start: 0.7161 (mp0) cc_final: 0.6864 (mt-10) REVERT: A 1208 LYS cc_start: 0.6504 (ttpt) cc_final: 0.6118 (mtpp) REVERT: A 1237 ASP cc_start: 0.7907 (m-30) cc_final: 0.7598 (m-30) REVERT: A 1243 GLN cc_start: 0.7081 (tt0) cc_final: 0.6390 (tp40) outliers start: 27 outliers final: 18 residues processed: 132 average time/residue: 0.4720 time to fit residues: 66.9811 Evaluate side-chains 135 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 306 TYR Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 404 GLN Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 802 ASP Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 882 ASP Chi-restraints excluded: chain A residue 925 ARG Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 953 PHE Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain A residue 1102 VAL Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1232 THR Chi-restraints excluded: chain A residue 1267 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 103 optimal weight: 3.9990 chunk 100 optimal weight: 0.2980 chunk 78 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 74 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 114 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1099 GLN A1244 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.176106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.121759 restraints weight = 9638.509| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.80 r_work: 0.3047 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9623 Z= 0.122 Angle : 0.499 10.179 13072 Z= 0.252 Chirality : 0.039 0.183 1513 Planarity : 0.003 0.037 1610 Dihedral : 8.952 118.272 1375 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.94 % Allowed : 15.76 % 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: 1.84 (0.24), residues: 1171 helix: 1.92 (0.18), residues: 797 sheet: 0.59 (0.67), residues: 60 loop : -0.45 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 144 TYR 0.027 0.001 TYR A 306 PHE 0.027 0.001 PHE A 934 TRP 0.017 0.001 TRP A 228 HIS 0.003 0.001 HIS A 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 9623) covalent geometry : angle 0.49914 / 0.25 (13072) hydrogen bonds : bond 0.04261 / 2.85 ( 614) hydrogen bonds : angle 3.69424 / 2.72 ( 1791) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2890.99 seconds wall clock time: 49 minutes 53.91 seconds (2993.91 seconds total)