Starting phenix.real_space_refine on Sun Jul 27 20:41:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8avy_15687/07_2025/8avy_15687.cif Found real_map, /net/cci-nas-00/data/ceres_data/8avy_15687/07_2025/8avy_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8avy_15687/07_2025/8avy_15687.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8avy_15687/07_2025/8avy_15687.map" model { file = "/net/cci-nas-00/data/ceres_data/8avy_15687/07_2025/8avy_15687.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8avy_15687/07_2025/8avy_15687.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 5.99, per 1000 atoms: 0.64 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: 2.27 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.09 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: 3.50 Time building geometry restraints manager: 2.73 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: 5843 24.46 - 48.91: 234 48.91 - 73.37: 40 73.37 - 97.82: 20 97.82 - 122.28: 5 Dihedral angle restraints: 6142 sinusoidal: 2777 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 6139 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: 1.390 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: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 25.440 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 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:11.340 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 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 : 14.562 122.279 3986 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.020 0.002 TRP A 228 HIS 0.007 0.001 HIS A 60 PHE 0.027 0.002 PHE A 131 TYR 0.018 0.002 TYR A 49 ARG 0.003 0.000 ARG A 400 Details of bonding type rmsd hydrogen bonds : bond 0.13999 ( 614) hydrogen bonds : angle 4.94265 ( 1791) covalent geometry : bond 0.00527 ( 9623) covalent geometry : angle 0.77736 (13072) *********************** 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 : 0.888 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: 1.2573 time to fit residues: 225.3991 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 : 1.056 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.5980 chunk 88 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 35 optimal weight: 8.9990 chunk 55 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 717 ASN A1099 GLN A1244 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.179308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.130050 restraints weight = 9523.722| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.76 r_work: 0.3102 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1261 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= 0.155 Angle : 0.595 10.801 13072 Z= 0.293 Chirality : 0.042 0.202 1513 Planarity : 0.004 0.035 1610 Dihedral : 11.977 88.122 1904 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.05 % Allowed : 12.50 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.24), residues: 1171 helix: 1.55 (0.18), residues: 797 sheet: 0.85 (0.63), residues: 60 loop : -0.40 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 228 HIS 0.003 0.001 HIS A 141 PHE 0.022 0.002 PHE A 508 TYR 0.034 0.002 TYR A 306 ARG 0.003 0.000 ARG A1221 Details of bonding type rmsd hydrogen bonds : bond 0.05093 ( 614) hydrogen bonds : angle 4.06094 ( 1791) covalent geometry : bond 0.00344 ( 9623) covalent geometry : angle 0.59482 (13072) *********************** 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 152 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 123 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.7768 (mtm-85) cc_final: 0.7496 (mtt90) REVERT: A 168 ASN cc_start: 0.6961 (t0) cc_final: 0.6176 (m-40) REVERT: A 293 ILE cc_start: 0.8164 (OUTLIER) cc_final: 0.7869 (tt) REVERT: A 377 SER cc_start: 0.8842 (OUTLIER) cc_final: 0.8619 (p) REVERT: A 424 ASN cc_start: 0.8229 (m110) cc_final: 0.7648 (m-40) REVERT: A 497 GLU cc_start: 0.6577 (mt-10) cc_final: 0.6038 (tt0) REVERT: A 915 MET cc_start: 0.8779 (mtm) cc_final: 0.8474 (mtp) REVERT: A 1102 VAL cc_start: 0.8290 (OUTLIER) cc_final: 0.7976 (p) REVERT: A 1223 VAL cc_start: 0.8172 (p) cc_final: 0.7916 (t) REVERT: A 1237 ASP cc_start: 0.8034 (m-30) cc_final: 0.7730 (m-30) REVERT: A 1243 GLN cc_start: 0.7182 (tt0) cc_final: 0.6417 (tp40) outliers start: 29 outliers final: 14 residues processed: 138 average time/residue: 1.0908 time to fit residues: 162.5990 Evaluate side-chains 132 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.995 ------------------------------------------------------------------------------- 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 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 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 28 optimal weight: 20.0000 chunk 27 optimal weight: 0.9990 chunk 55 optimal weight: 8.9990 chunk 70 optimal weight: 0.4980 chunk 15 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 29 optimal weight: 10.0000 chunk 59 optimal weight: 0.8980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 GLN A1003 HIS A1244 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.179903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.127250 restraints weight = 9623.276| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.76 r_work: 0.3053 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1547 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= 0.131 Angle : 0.533 9.444 13072 Z= 0.266 Chirality : 0.040 0.208 1513 Planarity : 0.003 0.035 1610 Dihedral : 10.731 89.266 1902 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.94 % Allowed : 13.24 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.24), residues: 1171 helix: 1.72 (0.18), residues: 798 sheet: 0.85 (0.65), residues: 58 loop : -0.35 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 228 HIS 0.003 0.001 HIS A 141 PHE 0.017 0.001 PHE A 508 TYR 0.031 0.001 TYR A 306 ARG 0.002 0.000 ARG A 144 Details of bonding type rmsd hydrogen bonds : bond 0.04629 ( 614) hydrogen bonds : angle 3.89906 ( 1791) covalent geometry : bond 0.00277 ( 9623) covalent geometry : angle 0.53268 (13072) *********************** 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 146 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.7726 (mtm-85) cc_final: 0.7446 (mtt90) REVERT: A 168 ASN cc_start: 0.6940 (t0) cc_final: 0.6123 (m-40) REVERT: A 293 ILE cc_start: 0.8105 (OUTLIER) cc_final: 0.7820 (tt) REVERT: A 377 SER cc_start: 0.8826 (OUTLIER) cc_final: 0.8618 (p) REVERT: A 424 ASN cc_start: 0.8226 (m110) cc_final: 0.7647 (m-40) REVERT: A 455 ARG cc_start: 0.7520 (mtt180) cc_final: 0.7197 (mtp180) REVERT: A 497 GLU cc_start: 0.6544 (mt-10) cc_final: 0.5989 (tt0) REVERT: A 508 PHE cc_start: 0.7616 (OUTLIER) cc_final: 0.7246 (p90) REVERT: A 802 ASP cc_start: 0.8014 (OUTLIER) cc_final: 0.7488 (t70) REVERT: A 838 ASN cc_start: 0.7565 (t0) cc_final: 0.7356 (t0) REVERT: A 848 ILE cc_start: 0.7929 (OUTLIER) cc_final: 0.7636 (mp) REVERT: A 915 MET cc_start: 0.8738 (mtm) cc_final: 0.8432 (mtp) REVERT: A 1026 MET cc_start: 0.8272 (ttm) cc_final: 0.7962 (ptp) REVERT: A 1055 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7168 (pp20) REVERT: A 1102 VAL cc_start: 0.8323 (OUTLIER) cc_final: 0.8017 (p) REVERT: A 1237 ASP cc_start: 0.7961 (m-30) cc_final: 0.7705 (m-30) REVERT: A 1243 GLN cc_start: 0.7116 (tt0) cc_final: 0.6373 (tp40) outliers start: 28 outliers final: 12 residues processed: 134 average time/residue: 1.0760 time to fit residues: 156.2821 Evaluate side-chains 130 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.923 ------------------------------------------------------------------------------- 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 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 53 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN A1030 ASN A1244 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.179633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.126697 restraints weight = 9581.576| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.77 r_work: 0.3050 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9623 Z= 0.130 Angle : 0.514 8.375 13072 Z= 0.260 Chirality : 0.040 0.202 1513 Planarity : 0.003 0.032 1610 Dihedral : 10.087 88.830 1902 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.47 % Allowed : 13.24 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.24), residues: 1171 helix: 1.77 (0.18), residues: 799 sheet: 0.77 (0.63), residues: 60 loop : -0.38 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 228 HIS 0.003 0.001 HIS A 141 PHE 0.017 0.001 PHE A 508 TYR 0.031 0.001 TYR A 306 ARG 0.002 0.000 ARG A 144 Details of bonding type rmsd hydrogen bonds : bond 0.04490 ( 614) hydrogen bonds : angle 3.80951 ( 1791) covalent geometry : bond 0.00280 ( 9623) covalent geometry : angle 0.51387 (13072) *********************** 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 147 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 114 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.7734 (mtm-85) cc_final: 0.7450 (mtt90) REVERT: A 168 ASN cc_start: 0.7004 (t0) cc_final: 0.6190 (m-40) REVERT: A 293 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7891 (tt) REVERT: A 377 SER cc_start: 0.8824 (OUTLIER) cc_final: 0.8618 (p) REVERT: A 404 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.8187 (mt0) REVERT: A 414 LYS cc_start: 0.7075 (mtpt) cc_final: 0.6216 (mmpt) REVERT: A 424 ASN cc_start: 0.8238 (m110) cc_final: 0.7648 (m-40) REVERT: A 455 ARG cc_start: 0.7426 (mtt180) cc_final: 0.7102 (mtp180) REVERT: A 497 GLU cc_start: 0.6551 (mt-10) cc_final: 0.5987 (tt0) REVERT: A 508 PHE cc_start: 0.7657 (OUTLIER) cc_final: 0.7275 (p90) REVERT: A 802 ASP cc_start: 0.7966 (OUTLIER) cc_final: 0.7430 (t70) REVERT: A 848 ILE cc_start: 0.7872 (OUTLIER) cc_final: 0.7601 (mp) REVERT: A 1026 MET cc_start: 0.8277 (ttm) cc_final: 0.7976 (ptp) REVERT: A 1055 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7176 (pp20) REVERT: A 1102 VAL cc_start: 0.8329 (OUTLIER) cc_final: 0.8037 (p) REVERT: A 1208 LYS cc_start: 0.6749 (ttpt) cc_final: 0.5922 (pttm) REVERT: A 1237 ASP cc_start: 0.7990 (m-30) cc_final: 0.7717 (m-30) REVERT: A 1243 GLN cc_start: 0.7155 (tt0) cc_final: 0.6345 (tp40) outliers start: 33 outliers final: 16 residues processed: 135 average time/residue: 1.1279 time to fit residues: 164.4994 Evaluate side-chains 133 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 1.054 ------------------------------------------------------------------------------- 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 884 LYS 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 1242 ILE 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 45 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 3 optimal weight: 0.1980 chunk 22 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 113 optimal weight: 4.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1244 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.178953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.126095 restraints weight = 9601.661| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.77 r_work: 0.3064 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9623 Z= 0.137 Angle : 0.511 8.351 13072 Z= 0.259 Chirality : 0.040 0.198 1513 Planarity : 0.003 0.034 1610 Dihedral : 9.912 88.242 1902 Min Nonbonded Distance : 1.933 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.24), residues: 1171 helix: 1.77 (0.18), residues: 799 sheet: 0.67 (0.63), residues: 60 loop : -0.39 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 228 HIS 0.003 0.001 HIS A 141 PHE 0.018 0.001 PHE A 508 TYR 0.031 0.001 TYR A 306 ARG 0.002 0.000 ARG A 144 Details of bonding type rmsd hydrogen bonds : bond 0.04509 ( 614) hydrogen bonds : angle 3.78779 ( 1791) covalent geometry : bond 0.00305 ( 9623) covalent geometry : angle 0.51110 (13072) *********************** 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 148 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 115 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.7718 (mtm-85) cc_final: 0.7450 (mtt90) REVERT: A 168 ASN cc_start: 0.6995 (t0) cc_final: 0.6173 (m-40) REVERT: A 293 ILE cc_start: 0.8130 (OUTLIER) cc_final: 0.7858 (tt) REVERT: A 377 SER cc_start: 0.8810 (OUTLIER) cc_final: 0.8601 (p) REVERT: A 404 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.8159 (mt0) REVERT: A 414 LYS cc_start: 0.7080 (mtpt) cc_final: 0.6505 (mmpt) REVERT: A 424 ASN cc_start: 0.8149 (m110) cc_final: 0.7547 (m-40) REVERT: A 455 ARG cc_start: 0.7406 (mtt180) cc_final: 0.7076 (mtp180) REVERT: A 497 GLU cc_start: 0.6520 (mt-10) cc_final: 0.5970 (tt0) REVERT: A 508 PHE cc_start: 0.7629 (OUTLIER) cc_final: 0.7170 (p90) REVERT: A 802 ASP cc_start: 0.7965 (OUTLIER) cc_final: 0.7391 (t70) REVERT: A 848 ILE cc_start: 0.7842 (OUTLIER) cc_final: 0.7574 (mp) REVERT: A 1026 MET cc_start: 0.8282 (ttm) cc_final: 0.7984 (ptp) REVERT: A 1055 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7122 (pp20) REVERT: A 1102 VAL cc_start: 0.8298 (OUTLIER) cc_final: 0.8038 (p) REVERT: A 1159 ASP cc_start: 0.7280 (OUTLIER) cc_final: 0.6771 (t0) REVERT: A 1208 LYS cc_start: 0.6714 (ttpt) cc_final: 0.6374 (mtpp) REVERT: A 1237 ASP cc_start: 0.7963 (m-30) cc_final: 0.7668 (m-30) REVERT: A 1243 GLN cc_start: 0.7057 (tt0) cc_final: 0.6322 (tp40) outliers start: 33 outliers final: 14 residues processed: 136 average time/residue: 1.1349 time to fit residues: 166.4815 Evaluate side-chains 134 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 0.928 ------------------------------------------------------------------------------- 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 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 1159 ASP Chi-restraints excluded: chain A residue 1232 THR 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 56 optimal weight: 8.9990 chunk 11 optimal weight: 0.5980 chunk 7 optimal weight: 5.9990 chunk 98 optimal weight: 0.8980 chunk 58 optimal weight: 9.9990 chunk 100 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 4 optimal weight: 20.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1244 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.177709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.124519 restraints weight = 9564.052| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 1.76 r_work: 0.3006 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1926 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= 0.159 Angle : 0.534 9.066 13072 Z= 0.270 Chirality : 0.041 0.196 1513 Planarity : 0.003 0.032 1610 Dihedral : 9.900 89.965 1902 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.47 % Allowed : 13.97 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.24), residues: 1171 helix: 1.72 (0.18), residues: 797 sheet: 0.68 (0.66), residues: 60 loop : -0.45 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 228 HIS 0.004 0.001 HIS A 141 PHE 0.021 0.001 PHE A 508 TYR 0.030 0.001 TYR A 306 ARG 0.002 0.000 ARG A 355 Details of bonding type rmsd hydrogen bonds : bond 0.04705 ( 614) hydrogen bonds : angle 3.82113 ( 1791) covalent geometry : bond 0.00366 ( 9623) covalent geometry : angle 0.53361 (13072) *********************** 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 149 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 116 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.7729 (mtm-85) cc_final: 0.7433 (mtt90) REVERT: A 168 ASN cc_start: 0.7058 (t0) cc_final: 0.6220 (m-40) REVERT: A 293 ILE cc_start: 0.8186 (OUTLIER) cc_final: 0.7921 (tt) REVERT: A 377 SER cc_start: 0.8807 (OUTLIER) cc_final: 0.8579 (p) REVERT: A 404 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.8149 (mt0) REVERT: A 414 LYS cc_start: 0.7104 (mtpt) cc_final: 0.6498 (mmpt) REVERT: A 424 ASN cc_start: 0.8120 (m110) cc_final: 0.7504 (m-40) REVERT: A 455 ARG cc_start: 0.7471 (mtt180) cc_final: 0.7138 (mtp180) REVERT: A 497 GLU cc_start: 0.6579 (mt-10) cc_final: 0.6057 (tt0) REVERT: A 802 ASP cc_start: 0.8019 (OUTLIER) cc_final: 0.7412 (t70) REVERT: A 844 ILE cc_start: 0.7516 (mp) cc_final: 0.7178 (mp) REVERT: A 848 ILE cc_start: 0.7859 (OUTLIER) cc_final: 0.7589 (mp) REVERT: A 915 MET cc_start: 0.8735 (mtm) cc_final: 0.8458 (mtp) REVERT: A 925 ARG cc_start: 0.7538 (OUTLIER) cc_final: 0.7205 (mtm-85) REVERT: A 1026 MET cc_start: 0.8281 (ttm) cc_final: 0.7994 (ptp) REVERT: A 1055 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7186 (pp20) REVERT: A 1102 VAL cc_start: 0.8333 (OUTLIER) cc_final: 0.8080 (p) REVERT: A 1159 ASP cc_start: 0.7341 (OUTLIER) cc_final: 0.6870 (t0) REVERT: A 1208 LYS cc_start: 0.6757 (ttpt) cc_final: 0.6378 (mtpp) REVERT: A 1237 ASP cc_start: 0.7958 (m-30) cc_final: 0.7637 (m-30) REVERT: A 1243 GLN cc_start: 0.7116 (tt0) cc_final: 0.6391 (tp40) outliers start: 33 outliers final: 19 residues processed: 138 average time/residue: 1.1361 time to fit residues: 169.8526 Evaluate side-chains 140 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 0.935 ------------------------------------------------------------------------------- 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 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 884 LYS 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 1159 ASP 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 92 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 95 optimal weight: 0.2980 chunk 115 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS A 145 GLN A 816 ASN A1244 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.171661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.116715 restraints weight = 9750.003| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 1.81 r_work: 0.2971 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9623 Z= 0.204 Angle : 0.579 10.922 13072 Z= 0.292 Chirality : 0.043 0.198 1513 Planarity : 0.004 0.035 1610 Dihedral : 10.016 86.708 1902 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.57 % Allowed : 13.97 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.24), residues: 1171 helix: 1.57 (0.18), residues: 796 sheet: 0.65 (0.67), residues: 60 loop : -0.49 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 228 HIS 0.004 0.001 HIS A 141 PHE 0.025 0.002 PHE A 508 TYR 0.033 0.002 TYR A 306 ARG 0.002 0.000 ARG A 613 Details of bonding type rmsd hydrogen bonds : bond 0.05080 ( 614) hydrogen bonds : angle 3.91402 ( 1791) covalent geometry : bond 0.00487 ( 9623) covalent geometry : angle 0.57936 (13072) *********************** 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 154 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 120 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.7633 (mtm-85) cc_final: 0.7329 (mtt90) REVERT: A 168 ASN cc_start: 0.7001 (t0) cc_final: 0.6099 (m-40) REVERT: A 293 ILE cc_start: 0.8148 (OUTLIER) cc_final: 0.7875 (tt) REVERT: A 404 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.8115 (mt0) REVERT: A 414 LYS cc_start: 0.6965 (mtpt) cc_final: 0.6374 (mmpt) REVERT: A 424 ASN cc_start: 0.8080 (m110) cc_final: 0.7421 (m-40) REVERT: A 455 ARG cc_start: 0.7419 (mtt180) cc_final: 0.7053 (mtp180) REVERT: A 497 GLU cc_start: 0.6476 (mt-10) cc_final: 0.5925 (tt0) REVERT: A 612 MET cc_start: 0.5038 (mmm) cc_final: 0.4546 (mmm) REVERT: A 802 ASP cc_start: 0.8009 (OUTLIER) cc_final: 0.7389 (t70) REVERT: A 820 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.6900 (mp10) REVERT: A 844 ILE cc_start: 0.7425 (mp) cc_final: 0.7084 (mp) REVERT: A 848 ILE cc_start: 0.7805 (OUTLIER) cc_final: 0.7549 (mp) REVERT: A 925 ARG cc_start: 0.7450 (OUTLIER) cc_final: 0.7192 (mtm-85) REVERT: A 1026 MET cc_start: 0.8327 (ttm) cc_final: 0.8022 (ptp) REVERT: A 1055 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7077 (pp20) REVERT: A 1102 VAL cc_start: 0.8279 (OUTLIER) cc_final: 0.8023 (p) REVERT: A 1159 ASP cc_start: 0.7274 (OUTLIER) cc_final: 0.6836 (t0) REVERT: A 1208 LYS cc_start: 0.6624 (ttpt) cc_final: 0.6228 (mtpp) REVERT: A 1237 ASP cc_start: 0.7970 (m-30) cc_final: 0.7621 (m-30) REVERT: A 1243 GLN cc_start: 0.6996 (tt0) cc_final: 0.6264 (tp40) outliers start: 34 outliers final: 18 residues processed: 143 average time/residue: 1.1167 time to fit residues: 172.3318 Evaluate side-chains 142 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 ILE 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 820 GLN 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 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 1159 ASP 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 56 optimal weight: 0.4980 chunk 19 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 chunk 106 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 63 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 chunk 6 optimal weight: 8.9990 chunk 101 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1003 HIS A1244 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.175018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.120198 restraints weight = 9863.614| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.82 r_work: 0.3045 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9623 Z= 0.116 Angle : 0.513 12.776 13072 Z= 0.257 Chirality : 0.039 0.197 1513 Planarity : 0.003 0.034 1610 Dihedral : 9.690 89.894 1902 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.52 % Allowed : 15.55 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.24), residues: 1171 helix: 1.84 (0.18), residues: 797 sheet: 0.62 (0.67), residues: 60 loop : -0.48 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 228 HIS 0.003 0.001 HIS A 141 PHE 0.014 0.001 PHE A 508 TYR 0.030 0.001 TYR A 306 ARG 0.001 0.000 ARG A1134 Details of bonding type rmsd hydrogen bonds : bond 0.04306 ( 614) hydrogen bonds : angle 3.75370 ( 1791) covalent geometry : bond 0.00241 ( 9623) covalent geometry : angle 0.51308 (13072) *********************** 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 137 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 113 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.7716 (mtm-85) cc_final: 0.7407 (mtt90) REVERT: A 168 ASN cc_start: 0.6873 (t0) cc_final: 0.6064 (m-40) REVERT: A 180 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7689 (mt-10) REVERT: A 293 ILE cc_start: 0.8136 (OUTLIER) cc_final: 0.7861 (tt) REVERT: A 377 SER cc_start: 0.8832 (OUTLIER) cc_final: 0.8608 (p) REVERT: A 414 LYS cc_start: 0.7033 (mtpt) cc_final: 0.6461 (mmpt) REVERT: A 424 ASN cc_start: 0.8089 (m110) cc_final: 0.7468 (m-40) REVERT: A 455 ARG cc_start: 0.7428 (mtt180) cc_final: 0.7092 (mtp180) REVERT: A 497 GLU cc_start: 0.6494 (mt-10) cc_final: 0.6002 (tt0) REVERT: A 508 PHE cc_start: 0.7522 (OUTLIER) cc_final: 0.7300 (p90) REVERT: A 612 MET cc_start: 0.4991 (mmm) cc_final: 0.4641 (mmm) REVERT: A 802 ASP cc_start: 0.7999 (OUTLIER) cc_final: 0.7419 (t70) REVERT: A 820 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7046 (mp10) REVERT: A 848 ILE cc_start: 0.7791 (OUTLIER) cc_final: 0.7544 (mp) REVERT: A 915 MET cc_start: 0.8638 (mtm) cc_final: 0.8381 (mtp) REVERT: A 1026 MET cc_start: 0.8326 (ttm) cc_final: 0.8008 (ptp) REVERT: A 1055 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7109 (pp20) REVERT: A 1102 VAL cc_start: 0.8294 (OUTLIER) cc_final: 0.8058 (p) REVERT: A 1208 LYS cc_start: 0.6622 (ttpt) cc_final: 0.6241 (mtpp) REVERT: A 1237 ASP cc_start: 0.7936 (m-30) cc_final: 0.7627 (m-30) REVERT: A 1243 GLN cc_start: 0.7065 (tt0) cc_final: 0.6341 (tp40) outliers start: 24 outliers final: 13 residues processed: 130 average time/residue: 1.1369 time to fit residues: 159.1089 Evaluate side-chains 130 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.917 ------------------------------------------------------------------------------- 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 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 696 ILE Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 802 ASP Chi-restraints excluded: chain A residue 820 GLN Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 882 ASP 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 90 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 46 optimal weight: 0.0980 chunk 105 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1244 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.176247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.121902 restraints weight = 9656.833| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.81 r_work: 0.3062 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2207 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= 0.121 Angle : 0.511 11.177 13072 Z= 0.256 Chirality : 0.040 0.195 1513 Planarity : 0.003 0.036 1610 Dihedral : 9.540 87.618 1901 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.73 % Allowed : 15.55 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.24), residues: 1171 helix: 1.92 (0.18), residues: 797 sheet: 0.59 (0.67), residues: 60 loop : -0.45 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 228 HIS 0.003 0.001 HIS A 141 PHE 0.017 0.001 PHE A 508 TYR 0.030 0.001 TYR A 306 ARG 0.002 0.000 ARG A 144 Details of bonding type rmsd hydrogen bonds : bond 0.04253 ( 614) hydrogen bonds : angle 3.71053 ( 1791) covalent geometry : bond 0.00256 ( 9623) covalent geometry : angle 0.51057 (13072) *********************** 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 137 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 111 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.7670 (mtm-85) cc_final: 0.7440 (mtt90) REVERT: A 168 ASN cc_start: 0.6863 (t0) cc_final: 0.6057 (m-40) REVERT: A 180 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7642 (mt-10) REVERT: A 293 ILE cc_start: 0.8106 (OUTLIER) cc_final: 0.7839 (tt) REVERT: A 377 SER cc_start: 0.8826 (OUTLIER) cc_final: 0.8614 (p) REVERT: A 404 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.8080 (mt0) REVERT: A 414 LYS cc_start: 0.6998 (mtpt) cc_final: 0.6443 (mmpt) REVERT: A 424 ASN cc_start: 0.8113 (m110) cc_final: 0.7467 (m-40) REVERT: A 455 ARG cc_start: 0.7402 (mtt180) cc_final: 0.7044 (mtp180) REVERT: A 497 GLU cc_start: 0.6477 (mt-10) cc_final: 0.5947 (tt0) REVERT: A 508 PHE cc_start: 0.7545 (OUTLIER) cc_final: 0.7176 (p90) REVERT: A 511 LYS cc_start: 0.7707 (ttpt) cc_final: 0.6842 (mttt) REVERT: A 612 MET cc_start: 0.5075 (mmm) cc_final: 0.4767 (mmm) REVERT: A 802 ASP cc_start: 0.7993 (OUTLIER) cc_final: 0.7379 (t70) REVERT: A 844 ILE cc_start: 0.7362 (OUTLIER) cc_final: 0.7079 (mp) REVERT: A 848 ILE cc_start: 0.7732 (OUTLIER) cc_final: 0.7486 (mp) REVERT: A 1026 MET cc_start: 0.8328 (ttm) cc_final: 0.8014 (ptp) REVERT: A 1055 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7100 (pp20) REVERT: A 1102 VAL cc_start: 0.8306 (OUTLIER) cc_final: 0.8054 (p) REVERT: A 1208 LYS cc_start: 0.6610 (ttpt) cc_final: 0.6229 (mtpp) REVERT: A 1237 ASP cc_start: 0.7925 (m-30) cc_final: 0.7616 (m-30) REVERT: A 1243 GLN cc_start: 0.7062 (tt0) cc_final: 0.6350 (tp40) outliers start: 26 outliers final: 13 residues processed: 129 average time/residue: 1.2322 time to fit residues: 171.0371 Evaluate side-chains 131 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 1.043 ------------------------------------------------------------------------------- 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 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 696 ILE Chi-restraints excluded: chain A residue 802 ASP Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 848 ILE 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 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 41 optimal weight: 5.9990 chunk 8 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 62 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 102 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 72 optimal weight: 0.4980 chunk 64 optimal weight: 0.5980 chunk 80 optimal weight: 0.9980 chunk 51 optimal weight: 0.0970 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1244 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.177924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.124031 restraints weight = 9845.073| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.83 r_work: 0.3091 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9623 Z= 0.108 Angle : 0.493 11.152 13072 Z= 0.248 Chirality : 0.039 0.192 1513 Planarity : 0.003 0.037 1610 Dihedral : 9.180 81.494 1901 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.52 % Allowed : 15.76 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.24), residues: 1171 helix: 2.05 (0.18), residues: 797 sheet: 0.48 (0.65), residues: 60 loop : -0.44 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 228 HIS 0.002 0.001 HIS A 60 PHE 0.012 0.001 PHE A 508 TYR 0.027 0.001 TYR A 306 ARG 0.002 0.000 ARG A 144 Details of bonding type rmsd hydrogen bonds : bond 0.03969 ( 614) hydrogen bonds : angle 3.62890 ( 1791) covalent geometry : bond 0.00216 ( 9623) covalent geometry : angle 0.49329 (13072) ********************** 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 136 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 1.054 Fit side-chains revert: symmetry clash REVERT: A 47 ARG cc_start: 0.7725 (mtm-85) cc_final: 0.7503 (mtt90) REVERT: A 168 ASN cc_start: 0.6849 (t0) cc_final: 0.6072 (m-40) REVERT: A 180 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7553 (mt-10) REVERT: A 293 ILE cc_start: 0.8070 (OUTLIER) cc_final: 0.7795 (tt) REVERT: A 377 SER cc_start: 0.8801 (OUTLIER) cc_final: 0.8592 (p) REVERT: A 404 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.8058 (mt0) REVERT: A 414 LYS cc_start: 0.7010 (mtpt) cc_final: 0.6456 (mmpt) REVERT: A 424 ASN cc_start: 0.8096 (m110) cc_final: 0.7456 (m-40) REVERT: A 455 ARG cc_start: 0.7336 (mtt180) cc_final: 0.7100 (mtp180) REVERT: A 497 GLU cc_start: 0.6526 (mt-10) cc_final: 0.6007 (tt0) REVERT: A 508 PHE cc_start: 0.7248 (OUTLIER) cc_final: 0.6995 (p90) REVERT: A 511 LYS cc_start: 0.7686 (ttpt) cc_final: 0.6797 (mttt) REVERT: A 562 GLU cc_start: 0.6825 (tm-30) cc_final: 0.6400 (tt0) REVERT: A 612 MET cc_start: 0.5137 (mmm) cc_final: 0.4853 (mmm) REVERT: A 802 ASP cc_start: 0.7990 (OUTLIER) cc_final: 0.7424 (t70) REVERT: A 844 ILE cc_start: 0.7422 (OUTLIER) cc_final: 0.7130 (mp) REVERT: A 848 ILE cc_start: 0.7723 (OUTLIER) cc_final: 0.7456 (mp) REVERT: A 915 MET cc_start: 0.8590 (mtm) cc_final: 0.8323 (mtp) REVERT: A 1026 MET cc_start: 0.8325 (ttm) cc_final: 0.8025 (ptp) REVERT: A 1055 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7081 (pp20) REVERT: A 1102 VAL cc_start: 0.8302 (t) cc_final: 0.8045 (p) REVERT: A 1208 LYS cc_start: 0.6553 (ttpt) cc_final: 0.6166 (mtpp) REVERT: A 1237 ASP cc_start: 0.7844 (m-30) cc_final: 0.7617 (m-30) REVERT: A 1243 GLN cc_start: 0.7101 (tt0) cc_final: 0.6377 (tp40) outliers start: 24 outliers final: 14 residues processed: 130 average time/residue: 1.5993 time to fit residues: 223.0072 Evaluate side-chains 128 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 1.038 ------------------------------------------------------------------------------- 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 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 696 ILE Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 802 ASP Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 882 ASP 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 1112 VAL Chi-restraints excluded: chain A residue 1187 VAL 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 56 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 17 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 95 optimal weight: 0.0050 chunk 75 optimal weight: 8.9990 chunk 96 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3932 r_free = 0.3932 target = 0.176836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.122571 restraints weight = 9738.196| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.82 r_work: 0.3063 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9623 Z= 0.118 Angle : 0.503 11.012 13072 Z= 0.252 Chirality : 0.039 0.192 1513 Planarity : 0.003 0.036 1610 Dihedral : 9.147 80.091 1901 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.42 % Allowed : 15.86 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.24), residues: 1171 helix: 2.08 (0.18), residues: 796 sheet: 0.43 (0.65), residues: 60 loop : -0.47 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 228 HIS 0.003 0.001 HIS A 141 PHE 0.016 0.001 PHE A 508 TYR 0.027 0.001 TYR A 306 ARG 0.002 0.000 ARG A 144 Details of bonding type rmsd hydrogen bonds : bond 0.04094 ( 614) hydrogen bonds : angle 3.64966 ( 1791) covalent geometry : bond 0.00250 ( 9623) covalent geometry : angle 0.50337 (13072) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7387.65 seconds wall clock time: 127 minutes 36.05 seconds (7656.05 seconds total)