Starting phenix.real_space_refine on Sat Jul 4 02:53:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m5v_23683/07_2026/7m5v_23683_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m5v_23683/07_2026/7m5v_23683.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 { model { file = "/net/cci-nas-00/data/ceres_data/7m5v_23683/07_2026/7m5v_23683_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m5v_23683/07_2026/7m5v_23683_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7m5v_23683/07_2026/7m5v_23683.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m5v_23683/07_2026/7m5v_23683.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.024 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: 7 Type Number sf(0) Gaussians P 6 5.49 5 Mg 1 5.21 5 S 51 5.16 5 C 5427 2.51 5 N 1349 2.21 5 O 1476 1.98 5 H 7985 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16295 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 15855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1046, 15855 Classifications: {'peptide': 1046} Link IDs: {'PCIS': 3, 'PTRANS': 71, 'TRANS': 971} Chain breaks: 6 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 313 Unresolved non-hydrogen dihedrals: 218 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'ARG:plan': 10, 'TRP:plan': 5, 'TYR:plan': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 5, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 149 Chain: "A" Number of atoms: 440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 440 Unusual residues: {' MG': 1, '1DO': 4, 'ANP': 1, 'D10': 9, 'D12': 2, 'EUJ': 1, 'LMT': 1, 'NAG': 1, 'Y01': 4} Classifications: {'undetermined': 24, 'water': 6} Link IDs: {None: 29} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.57, per 1000 atoms: 0.16 Number of scatterers: 16295 At special positions: 0 Unit cell: (78.85, 84.66, 136.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 51 16.00 P 6 15.00 Mg 1 11.99 O 1476 8.00 N 1349 7.00 C 5427 6.00 H 7985 1.00 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 Links applied NAG-ASN " NAG A1218 " - " ASN A1033 " Time building additional restraints: 1.15 Conformation dependent library (CDL) restraints added in 338.2 milliseconds 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1956 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 8 sheets defined 49.5% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 46 through 58 Processing helix chain 'A' and resid 59 through 65 removed outlier: 3.951A pdb=" N LEU A 63 " --> pdb=" O GLY A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 76 removed outlier: 3.784A pdb=" N GLY A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 188 No H-bonds generated for 'chain 'A' and resid 186 through 188' Processing helix chain 'A' and resid 193 through 200 Processing helix chain 'A' and resid 205 through 217 Processing helix chain 'A' and resid 227 through 237 removed outlier: 3.531A pdb=" N LEU A 237 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 254 removed outlier: 3.548A pdb=" N ASP A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 287 removed outlier: 3.702A pdb=" N LEU A 285 " --> pdb=" O GLN A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 312 No H-bonds generated for 'chain 'A' and resid 310 through 312' Processing helix chain 'A' and resid 369 through 371 No H-bonds generated for 'chain 'A' and resid 369 through 371' Processing helix chain 'A' and resid 398 through 401 removed outlier: 4.176A pdb=" N CYS A 401 " --> pdb=" O THR A 398 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 398 through 401' Processing helix chain 'A' and resid 402 through 413 Processing helix chain 'A' and resid 424 through 450 removed outlier: 3.540A pdb=" N PHE A 428 " --> pdb=" O HIS A 424 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR A 442 " --> pdb=" O LEU A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 469 removed outlier: 3.615A pdb=" N VAL A 469 " --> pdb=" O VAL A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 492 Processing helix chain 'A' and resid 497 through 507 removed outlier: 4.449A pdb=" N ASN A 502 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU A 507 " --> pdb=" O GLY A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 546 Processing helix chain 'A' and resid 549 through 558 Processing helix chain 'A' and resid 571 through 582 Processing helix chain 'A' and resid 612 through 616 removed outlier: 4.164A pdb=" N GLU A 616 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 664 Processing helix chain 'A' and resid 672 through 682 Processing helix chain 'A' and resid 708 through 712 Processing helix chain 'A' and resid 732 through 742 Processing helix chain 'A' and resid 753 through 764 Processing helix chain 'A' and resid 827 through 837 Processing helix chain 'A' and resid 840 through 847 Processing helix chain 'A' and resid 855 through 869 Processing helix chain 'A' and resid 882 through 889 Processing helix chain 'A' and resid 914 through 955 removed outlier: 3.829A pdb=" N MET A 918 " --> pdb=" O GLU A 914 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE A 945 " --> pdb=" O SER A 941 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER A 947 " --> pdb=" O THR A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 968 removed outlier: 3.786A pdb=" N LEU A 964 " --> pdb=" O ASP A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 979 removed outlier: 3.642A pdb=" N VAL A 974 " --> pdb=" O ILE A 970 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N SER A 979 " --> pdb=" O ALA A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1025 Processing helix chain 'A' and resid 1046 through 1066 removed outlier: 3.505A pdb=" N SER A1066 " --> pdb=" O ALA A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1078 through 1097 Processing helix chain 'A' and resid 1102 through 1107 Processing helix chain 'A' and resid 1115 through 1150 Proline residue: A1143 - end of helix Processing helix chain 'A' and resid 1157 through 1169 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 40 Processing sheet with id=AA2, first strand: chain 'A' and resid 108 through 110 removed outlier: 4.949A pdb=" N ARG A 164 " --> pdb=" O TRP A 175 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 294 through 297 Processing sheet with id=AA4, first strand: chain 'A' and resid 317 through 319 removed outlier: 7.439A pdb=" N ASP A 330 " --> pdb=" O THR A 396 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 326 removed outlier: 6.547A pdb=" N MET A 339 " --> pdb=" O LEU A 381 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ALA A 383 " --> pdb=" O GLU A 337 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N GLU A 337 " --> pdb=" O ALA A 383 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 493 through 495 removed outlier: 5.978A pdb=" N GLY A 892 " --> pdb=" O PHE A 906 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N SER A 908 " --> pdb=" O GLY A 892 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N SER A 894 " --> pdb=" O SER A 908 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU A 509 " --> pdb=" O GLY A 874 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N CYS A 876 " --> pdb=" O LEU A 509 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N CYS A 511 " --> pdb=" O CYS A 876 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL A 510 " --> pdb=" O VAL A 747 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N VAL A 749 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N PHE A 512 " --> pdb=" O VAL A 749 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ALA A 746 " --> pdb=" O THR A 849 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N PHE A 851 " --> pdb=" O ALA A 746 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N MET A 748 " --> pdb=" O PHE A 851 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N THR A 849 " --> pdb=" O ARG A 821 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LEU A 823 " --> pdb=" O THR A 849 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N PHE A 851 " --> pdb=" O LEU A 823 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU A 825 " --> pdb=" O PHE A 851 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N SER A 826 " --> pdb=" O VAL A 776 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 524 through 530 removed outlier: 5.613A pdb=" N VAL A 525 " --> pdb=" O ARG A 725 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ARG A 725 " --> pdb=" O VAL A 525 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU A 690 " --> pdb=" O LEU A 719 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N LEU A 721 " --> pdb=" O VAL A 688 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL A 688 " --> pdb=" O LEU A 721 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N VAL A 723 " --> pdb=" O ARG A 686 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ARG A 686 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ARG A 636 " --> pdb=" O PHE A 630 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N PHE A 630 " --> pdb=" O ARG A 636 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ALA A 642 " --> pdb=" O VAL A 624 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N VAL A 624 " --> pdb=" O ALA A 642 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA A 601 " --> pdb=" O VAL A 624 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 562 through 563 433 hydrogen bonds defined for protein. 1215 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: 3.21 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 7959 1.03 - 1.23: 448 1.23 - 1.43: 2892 1.43 - 1.64: 5075 1.64 - 1.84: 79 Bond restraints: 16453 Sorted by residual: bond pdb=" O5' ANP A1223 " pdb=" PA ANP A1223 " ideal model delta sigma weight residual 1.655 1.836 -0.181 2.00e-02 2.50e+03 8.18e+01 bond pdb=" O3 EUJ A1224 " pdb=" P3 EUJ A1224 " ideal model delta sigma weight residual 1.727 1.634 0.093 2.00e-02 2.50e+03 2.15e+01 bond pdb=" CAI Y01 A1211 " pdb=" CAK Y01 A1211 " ideal model delta sigma weight residual 1.492 1.407 0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" CAI Y01 A1205 " pdb=" CAK Y01 A1205 " ideal model delta sigma weight residual 1.492 1.408 0.084 2.00e-02 2.50e+03 1.77e+01 bond pdb=" CAI Y01 A1210 " pdb=" CAK Y01 A1210 " ideal model delta sigma weight residual 1.492 1.408 0.084 2.00e-02 2.50e+03 1.77e+01 ... (remaining 16448 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.24: 29386 3.24 - 6.47: 220 6.47 - 9.71: 28 9.71 - 12.94: 12 12.94 - 16.18: 3 Bond angle restraints: 29649 Sorted by residual: angle pdb=" CA ASN A1033 " pdb=" CB ASN A1033 " pdb=" CG ASN A1033 " ideal model delta sigma weight residual 112.60 122.11 -9.51 1.00e+00 1.00e+00 9.04e+01 angle pdb=" N ASN A1033 " pdb=" CA ASN A1033 " pdb=" CB ASN A1033 " ideal model delta sigma weight residual 110.24 121.49 -11.25 1.45e+00 4.76e-01 6.02e+01 angle pdb=" O2A ANP A1223 " pdb=" PA ANP A1223 " pdb=" O5' ANP A1223 " ideal model delta sigma weight residual 108.82 92.64 16.18 3.00e+00 1.11e-01 2.91e+01 angle pdb=" O2B ANP A1223 " pdb=" PB ANP A1223 " pdb=" O3A ANP A1223 " ideal model delta sigma weight residual 105.57 90.45 15.12 3.00e+00 1.11e-01 2.54e+01 angle pdb=" C3 EUJ A1224 " pdb=" O3 EUJ A1224 " pdb=" P3 EUJ A1224 " ideal model delta sigma weight residual 118.28 131.95 -13.67 3.00e+00 1.11e-01 2.08e+01 ... (remaining 29644 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.41: 7876 34.41 - 68.83: 250 68.83 - 103.24: 25 103.24 - 137.66: 10 137.66 - 172.07: 2 Dihedral angle restraints: 8163 sinusoidal: 4729 harmonic: 3434 Sorted by residual: dihedral pdb=" N ASN A1033 " pdb=" C ASN A1033 " pdb=" CA ASN A1033 " pdb=" CB ASN A1033 " ideal model delta harmonic sigma weight residual 122.80 135.07 -12.27 0 2.50e+00 1.60e-01 2.41e+01 dihedral pdb=" C2C EUJ A1224 " pdb=" C1C EUJ A1224 " pdb=" O13 EUJ A1224 " pdb=" P1 EUJ A1224 " ideal model delta sinusoidal sigma weight residual 93.25 -78.82 172.07 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C1 EUJ A1224 " pdb=" O1 EUJ A1224 " pdb=" P1 EUJ A1224 " pdb=" O13 EUJ A1224 " ideal model delta sinusoidal sigma weight residual 298.68 132.25 166.43 1 3.00e+01 1.11e-03 2.10e+01 ... (remaining 8160 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.977: 1383 0.977 - 1.953: 0 1.953 - 2.930: 0 2.930 - 3.907: 0 3.907 - 4.883: 1 Chirality restraints: 1384 Sorted by residual: chirality pdb=" C4 EUJ A1224 " pdb=" C3 EUJ A1224 " pdb=" C5 EUJ A1224 " pdb=" O4 EUJ A1224 " both_signs ideal model delta sigma weight residual False 2.45 -2.43 4.88 2.00e-01 2.50e+01 5.96e+02 chirality pdb=" C3' ANP A1223 " pdb=" C2' ANP A1223 " pdb=" C4' ANP A1223 " pdb=" O3' ANP A1223 " both_signs ideal model delta sigma weight residual False -2.36 -2.74 0.38 2.00e-01 2.50e+01 3.67e+00 chirality pdb=" C3B LMT A1203 " pdb=" C2B LMT A1203 " pdb=" C4B LMT A1203 " pdb=" O3B LMT A1203 " both_signs ideal model delta sigma weight residual False 2.50 2.83 -0.33 2.00e-01 2.50e+01 2.76e+00 ... (remaining 1381 not shown) Planarity restraints: 2369 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A1034 " -0.012 2.00e-02 2.50e+03 2.33e-02 5.41e+00 pdb=" N THR A1035 " 0.040 2.00e-02 2.50e+03 pdb=" CA THR A1035 " -0.011 2.00e-02 2.50e+03 pdb=" H THR A1035 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1032 " -0.011 2.00e-02 2.50e+03 2.11e-02 4.47e+00 pdb=" C LEU A1032 " 0.037 2.00e-02 2.50e+03 pdb=" O LEU A1032 " -0.014 2.00e-02 2.50e+03 pdb=" N ASN A1033 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP A 643 " 0.028 5.00e-02 4.00e+02 4.20e-02 2.82e+00 pdb=" N PRO A 644 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 644 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 644 " 0.023 5.00e-02 4.00e+02 ... (remaining 2366 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 1514 2.24 - 2.83: 35888 2.83 - 3.42: 42583 3.42 - 4.01: 57514 4.01 - 4.60: 89600 Nonbonded interactions: 227099 Sorted by model distance: nonbonded pdb=" O MET A 676 " pdb=" HG SER A 679 " model vdw 1.647 2.450 nonbonded pdb=" HH TYR A 940 " pdb=" OD1 ASP A 967 " model vdw 1.672 2.450 nonbonded pdb=" HG SER A 638 " pdb=" OE1 GLU A 713 " model vdw 1.704 2.450 nonbonded pdb=" HH TYR A 240 " pdb=" O PRO A 470 " model vdw 1.711 2.450 nonbonded pdb="HH21 ARG A 686 " pdb=" O2B ANP A1223 " model vdw 1.721 2.450 ... (remaining 227094 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: 3.510 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: 0.090 Extract box with map and model: 0.160 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.520 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 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 : 0.007 0.199 8469 Z= 0.339 Angle : 1.034 16.175 11513 Z= 0.442 Chirality : 0.142 4.883 1384 Planarity : 0.005 0.042 1403 Dihedral : 17.017 172.071 3490 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 0.12 % Allowed : 0.24 % Favored : 99.64 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.27), residues: 1032 helix: 1.60 (0.24), residues: 464 sheet: -0.42 (0.42), residues: 145 loop : -1.06 (0.32), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 921 TYR 0.011 0.001 TYR A 259 PHE 0.015 0.001 PHE A1128 TRP 0.009 0.001 TRP A 643 HIS 0.005 0.001 HIS A 559 Details of bonding type rmsd/Z covalent geometry : bond 0.00654 / 0.32 ( 8468) covalent geometry : angle 1.03123 / 0.44 (11510) hydrogen bonds : bond 0.13984 / 9.69 ( 433) hydrogen bonds : angle 6.00161 / 4.06 ( 1215) link_NAG-ASN : bond 0.19852 / 10.45 ( 1) link_NAG-ASN : angle 4.55758 / 2.16 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 35 is missing expected H atoms. Skipping. Residue VAL 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue TYR 50 is missing expected H atoms. Skipping. Residue VAL 52 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue MET 56 is missing expected H atoms. Skipping. Residue MET 57 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 612 is missing expected H atoms. Skipping. Residue MET 615 is missing expected H atoms. Skipping. Residue LYS 1156 is missing expected H atoms. Skipping. Evaluate side-chains 80 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 79 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 80 average time/residue: 0.6473 time to fit residues: 57.5795 Evaluate side-chains 52 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1033 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.4980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 497 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.065378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.055311 restraints weight = 100648.149| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 3.21 r_work: 0.2960 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8469 Z= 0.146 Angle : 0.621 10.277 11513 Z= 0.295 Chirality : 0.042 0.180 1384 Planarity : 0.004 0.045 1403 Dihedral : 12.805 170.045 1711 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 0.95 % Allowed : 6.64 % Favored : 92.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.27), residues: 1032 helix: 2.15 (0.24), residues: 468 sheet: -0.53 (0.43), residues: 143 loop : -0.97 (0.32), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1164 TYR 0.009 0.001 TYR A 936 PHE 0.015 0.001 PHE A1128 TRP 0.004 0.001 TRP A1028 HIS 0.004 0.001 HIS A 780 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.15 ( 8468) covalent geometry : angle 0.62008 / 0.29 (11510) hydrogen bonds : bond 0.04272 / 2.87 ( 433) hydrogen bonds : angle 4.74552 / 3.27 ( 1215) link_NAG-ASN : bond 0.00304 / 0.16 ( 1) link_NAG-ASN : angle 2.53833 / 1.11 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 35 is missing expected H atoms. Skipping. Residue VAL 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue TYR 50 is missing expected H atoms. Skipping. Residue VAL 52 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue MET 56 is missing expected H atoms. Skipping. Residue MET 57 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 612 is missing expected H atoms. Skipping. Residue MET 615 is missing expected H atoms. Skipping. Residue LYS 1156 is missing expected H atoms. Skipping. Evaluate side-chains 59 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 LEU cc_start: 0.9519 (tp) cc_final: 0.9316 (tt) outliers start: 8 outliers final: 3 residues processed: 53 average time/residue: 0.7212 time to fit residues: 42.1559 Evaluate side-chains 52 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 1010 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 15 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 47 optimal weight: 0.0370 chunk 59 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.9862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 281 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.064791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.054729 restraints weight = 101499.576| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 3.23 r_work: 0.2950 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8469 Z= 0.122 Angle : 0.540 6.560 11513 Z= 0.261 Chirality : 0.041 0.151 1384 Planarity : 0.004 0.042 1403 Dihedral : 10.808 174.012 1709 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 0.95 % Allowed : 7.35 % Favored : 91.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.27), residues: 1032 helix: 2.34 (0.24), residues: 469 sheet: -0.53 (0.42), residues: 143 loop : -0.95 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1164 TYR 0.006 0.001 TYR A 871 PHE 0.013 0.001 PHE A1128 TRP 0.004 0.001 TRP A1028 HIS 0.002 0.000 HIS A 836 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 8468) covalent geometry : angle 0.53880 / 0.26 (11510) hydrogen bonds : bond 0.03949 / 2.66 ( 433) hydrogen bonds : angle 4.45973 / 3.09 ( 1215) link_NAG-ASN : bond 0.00907 / 0.48 ( 1) link_NAG-ASN : angle 2.65271 / 1.38 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 35 is missing expected H atoms. Skipping. Residue VAL 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue TYR 50 is missing expected H atoms. Skipping. Residue VAL 52 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue MET 56 is missing expected H atoms. Skipping. Residue MET 57 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 612 is missing expected H atoms. Skipping. Residue MET 615 is missing expected H atoms. Skipping. Residue LYS 1156 is missing expected H atoms. Skipping. Evaluate side-chains 58 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 55 average time/residue: 0.7406 time to fit residues: 44.9545 Evaluate side-chains 55 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 1002 LEU Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1090 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 53 optimal weight: 0.3980 chunk 40 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 51 optimal weight: 0.1980 chunk 30 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.064364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.054275 restraints weight = 100836.925| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 3.21 r_work: 0.2946 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8469 Z= 0.123 Angle : 0.513 6.541 11513 Z= 0.252 Chirality : 0.040 0.141 1384 Planarity : 0.004 0.042 1403 Dihedral : 10.125 176.931 1709 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 0.83 % Allowed : 7.70 % Favored : 91.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.28), residues: 1032 helix: 2.50 (0.24), residues: 472 sheet: -0.48 (0.40), residues: 162 loop : -1.01 (0.33), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 172 TYR 0.006 0.001 TYR A 871 PHE 0.011 0.001 PHE A1159 TRP 0.004 0.001 TRP A1028 HIS 0.003 0.000 HIS A 836 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 8468) covalent geometry : angle 0.51101 / 0.25 (11510) hydrogen bonds : bond 0.03581 / 2.41 ( 433) hydrogen bonds : angle 4.27914 / 2.98 ( 1215) link_NAG-ASN : bond 0.00506 / 0.27 ( 1) link_NAG-ASN : angle 2.78255 / 1.56 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 35 is missing expected H atoms. Skipping. Residue VAL 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue TYR 50 is missing expected H atoms. Skipping. Residue VAL 52 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue MET 56 is missing expected H atoms. Skipping. Residue MET 57 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 612 is missing expected H atoms. Skipping. Residue MET 615 is missing expected H atoms. Skipping. Residue LYS 1156 is missing expected H atoms. Skipping. Evaluate side-chains 58 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 55 average time/residue: 0.7130 time to fit residues: 43.7182 Evaluate side-chains 53 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 CYS Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 1090 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 281 GLN A 424 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.062085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.052010 restraints weight = 102479.323| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 3.16 r_work: 0.2870 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8469 Z= 0.250 Angle : 0.594 6.694 11513 Z= 0.298 Chirality : 0.042 0.141 1384 Planarity : 0.004 0.049 1403 Dihedral : 10.636 178.058 1709 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 1.18 % Allowed : 8.65 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.27), residues: 1032 helix: 2.28 (0.24), residues: 474 sheet: -0.50 (0.41), residues: 150 loop : -1.02 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 172 TYR 0.012 0.001 TYR A 680 PHE 0.013 0.001 PHE A1159 TRP 0.007 0.001 TRP A1028 HIS 0.005 0.001 HIS A 836 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.25 ( 8468) covalent geometry : angle 0.59255 / 0.30 (11510) hydrogen bonds : bond 0.04264 / 2.88 ( 433) hydrogen bonds : angle 4.51511 / 3.15 ( 1215) link_NAG-ASN : bond 0.00403 / 0.21 ( 1) link_NAG-ASN : angle 2.87736 / 1.61 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 35 is missing expected H atoms. Skipping. Residue VAL 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue TYR 50 is missing expected H atoms. Skipping. Residue VAL 52 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue MET 56 is missing expected H atoms. Skipping. Residue MET 57 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 612 is missing expected H atoms. Skipping. Residue MET 615 is missing expected H atoms. Skipping. Residue LYS 1156 is missing expected H atoms. Skipping. Evaluate side-chains 59 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 LEU cc_start: 0.9554 (tp) cc_final: 0.9350 (tt) outliers start: 10 outliers final: 5 residues processed: 54 average time/residue: 0.6965 time to fit residues: 41.3942 Evaluate side-chains 53 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 CYS Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 1090 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 1 optimal weight: 20.0000 chunk 60 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 2 optimal weight: 20.0000 chunk 16 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 281 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.062448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.052350 restraints weight = 102111.673| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 3.15 r_work: 0.2876 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8469 Z= 0.185 Angle : 0.543 6.600 11513 Z= 0.271 Chirality : 0.041 0.141 1384 Planarity : 0.004 0.044 1403 Dihedral : 10.488 177.933 1709 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 0.83 % Allowed : 9.72 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.28), residues: 1032 helix: 2.45 (0.24), residues: 472 sheet: -0.48 (0.42), residues: 143 loop : -0.95 (0.32), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 172 TYR 0.008 0.001 TYR A 936 PHE 0.010 0.001 PHE A1159 TRP 0.006 0.001 TRP A1028 HIS 0.003 0.001 HIS A 559 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 ( 8468) covalent geometry : angle 0.54062 / 0.27 (11510) hydrogen bonds : bond 0.03883 / 2.62 ( 433) hydrogen bonds : angle 4.40785 / 3.09 ( 1215) link_NAG-ASN : bond 0.00437 / 0.23 ( 1) link_NAG-ASN : angle 3.06388 / 1.71 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 35 is missing expected H atoms. Skipping. Residue VAL 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue TYR 50 is missing expected H atoms. Skipping. Residue VAL 52 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue MET 56 is missing expected H atoms. Skipping. Residue MET 57 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 612 is missing expected H atoms. Skipping. Residue MET 615 is missing expected H atoms. Skipping. Residue LYS 1156 is missing expected H atoms. Skipping. Evaluate side-chains 54 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 LEU cc_start: 0.9550 (tp) cc_final: 0.9329 (tt) REVERT: A 1133 MET cc_start: 0.8394 (mmp) cc_final: 0.8188 (mmp) outliers start: 7 outliers final: 5 residues processed: 51 average time/residue: 0.7564 time to fit residues: 42.3981 Evaluate side-chains 52 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 CYS Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 1090 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 58 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 57 optimal weight: 0.0980 chunk 62 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 281 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.063166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.053085 restraints weight = 100762.046| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 3.16 r_work: 0.2901 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8469 Z= 0.117 Angle : 0.514 6.518 11513 Z= 0.253 Chirality : 0.040 0.136 1384 Planarity : 0.004 0.040 1403 Dihedral : 10.216 177.602 1709 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 0.95 % Allowed : 9.72 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.28), residues: 1032 helix: 2.63 (0.24), residues: 471 sheet: -0.38 (0.43), residues: 143 loop : -0.91 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 415 TYR 0.007 0.001 TYR A 871 PHE 0.009 0.001 PHE A1132 TRP 0.005 0.001 TRP A1028 HIS 0.002 0.000 HIS A 559 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 ( 8468) covalent geometry : angle 0.51179 / 0.25 (11510) hydrogen bonds : bond 0.03599 / 2.42 ( 433) hydrogen bonds : angle 4.25952 / 2.99 ( 1215) link_NAG-ASN : bond 0.00542 / 0.29 ( 1) link_NAG-ASN : angle 3.00102 / 1.68 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 35 is missing expected H atoms. Skipping. Residue VAL 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue TYR 50 is missing expected H atoms. Skipping. Residue VAL 52 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue MET 56 is missing expected H atoms. Skipping. Residue MET 57 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 612 is missing expected H atoms. Skipping. Residue MET 615 is missing expected H atoms. Skipping. Residue LYS 1156 is missing expected H atoms. Skipping. Evaluate side-chains 56 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 LEU cc_start: 0.9545 (tp) cc_final: 0.9321 (tt) REVERT: A 1133 MET cc_start: 0.8394 (mmp) cc_final: 0.8179 (mmp) outliers start: 8 outliers final: 5 residues processed: 51 average time/residue: 0.6883 time to fit residues: 38.8373 Evaluate side-chains 52 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 CYS Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 679 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 41 optimal weight: 2.9990 chunk 57 optimal weight: 0.0980 chunk 101 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 52 optimal weight: 0.3980 chunk 26 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 281 GLN A 770 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.062400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.052307 restraints weight = 102580.580| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 3.15 r_work: 0.2875 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8469 Z= 0.181 Angle : 0.537 6.630 11513 Z= 0.266 Chirality : 0.041 0.146 1384 Planarity : 0.004 0.043 1403 Dihedral : 10.299 177.586 1709 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 1.07 % Allowed : 9.60 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.28), residues: 1032 helix: 2.58 (0.24), residues: 472 sheet: -0.41 (0.43), residues: 143 loop : -0.94 (0.32), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 172 TYR 0.009 0.001 TYR A 680 PHE 0.010 0.001 PHE A1159 TRP 0.006 0.001 TRP A1028 HIS 0.003 0.001 HIS A 836 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.18 ( 8468) covalent geometry : angle 0.53507 / 0.27 (11510) hydrogen bonds : bond 0.03771 / 2.54 ( 433) hydrogen bonds : angle 4.32577 / 3.03 ( 1215) link_NAG-ASN : bond 0.00427 / 0.22 ( 1) link_NAG-ASN : angle 3.01670 / 1.68 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 35 is missing expected H atoms. Skipping. Residue VAL 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue TYR 50 is missing expected H atoms. Skipping. Residue VAL 52 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue MET 56 is missing expected H atoms. Skipping. Residue MET 57 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 612 is missing expected H atoms. Skipping. Residue MET 615 is missing expected H atoms. Skipping. Residue LYS 1156 is missing expected H atoms. Skipping. Evaluate side-chains 56 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 LEU cc_start: 0.9549 (tp) cc_final: 0.9322 (tt) REVERT: A 1133 MET cc_start: 0.8400 (mmp) cc_final: 0.8187 (mmp) outliers start: 9 outliers final: 6 residues processed: 53 average time/residue: 0.7211 time to fit residues: 42.0906 Evaluate side-chains 53 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 CYS Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 1090 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 95 optimal weight: 0.2980 chunk 72 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 51 optimal weight: 0.0010 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 281 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.063488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.053432 restraints weight = 100718.565| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 3.17 r_work: 0.2910 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8469 Z= 0.094 Angle : 0.504 7.441 11513 Z= 0.246 Chirality : 0.040 0.156 1384 Planarity : 0.004 0.038 1403 Dihedral : 9.923 176.986 1709 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 0.95 % Allowed : 9.83 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.28), residues: 1032 helix: 2.76 (0.24), residues: 472 sheet: -0.33 (0.44), residues: 143 loop : -0.84 (0.33), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1164 TYR 0.007 0.001 TYR A 166 PHE 0.008 0.001 PHE A1128 TRP 0.004 0.001 TRP A 251 HIS 0.002 0.000 HIS A 559 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.09 ( 8468) covalent geometry : angle 0.50211 / 0.25 (11510) hydrogen bonds : bond 0.03436 / 2.32 ( 433) hydrogen bonds : angle 4.16115 / 2.92 ( 1215) link_NAG-ASN : bond 0.00584 / 0.31 ( 1) link_NAG-ASN : angle 2.97884 / 1.66 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 35 is missing expected H atoms. Skipping. Residue VAL 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue TYR 50 is missing expected H atoms. Skipping. Residue VAL 52 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue MET 56 is missing expected H atoms. Skipping. Residue MET 57 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 612 is missing expected H atoms. Skipping. Residue MET 615 is missing expected H atoms. Skipping. Residue LYS 1156 is missing expected H atoms. Skipping. Evaluate side-chains 56 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 LEU cc_start: 0.9549 (tp) cc_final: 0.9319 (tt) outliers start: 8 outliers final: 6 residues processed: 53 average time/residue: 0.7374 time to fit residues: 43.1972 Evaluate side-chains 54 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 CYS Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1090 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 54 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 281 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.063230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.053248 restraints weight = 100948.179| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 3.16 r_work: 0.2904 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8469 Z= 0.117 Angle : 0.508 6.703 11513 Z= 0.248 Chirality : 0.040 0.159 1384 Planarity : 0.004 0.039 1403 Dihedral : 9.773 176.307 1709 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 0.71 % Allowed : 10.07 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.28), residues: 1032 helix: 2.71 (0.24), residues: 476 sheet: -0.29 (0.44), residues: 143 loop : -0.84 (0.33), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 172 TYR 0.006 0.001 TYR A 871 PHE 0.013 0.001 PHE A 428 TRP 0.004 0.001 TRP A1028 HIS 0.002 0.000 HIS A 836 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 8468) covalent geometry : angle 0.50631 / 0.25 (11510) hydrogen bonds : bond 0.03447 / 2.33 ( 433) hydrogen bonds : angle 4.14507 / 2.92 ( 1215) link_NAG-ASN : bond 0.00498 / 0.26 ( 1) link_NAG-ASN : angle 2.92556 / 1.63 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 35 is missing expected H atoms. Skipping. Residue VAL 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue TYR 50 is missing expected H atoms. Skipping. Residue VAL 52 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue MET 56 is missing expected H atoms. Skipping. Residue MET 57 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 612 is missing expected H atoms. Skipping. Residue MET 615 is missing expected H atoms. Skipping. Residue LYS 1156 is missing expected H atoms. Skipping. Evaluate side-chains 53 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 LEU cc_start: 0.9555 (tp) cc_final: 0.9324 (tt) outliers start: 6 outliers final: 5 residues processed: 51 average time/residue: 0.7073 time to fit residues: 39.9724 Evaluate side-chains 52 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 CYS Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 1090 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 9 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 80 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 68 optimal weight: 0.0870 chunk 36 optimal weight: 0.5980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 281 GLN A 957 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.063792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.053739 restraints weight = 100831.874| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 3.18 r_work: 0.2922 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8469 Z= 0.094 Angle : 0.494 6.429 11513 Z= 0.241 Chirality : 0.040 0.165 1384 Planarity : 0.004 0.038 1403 Dihedral : 9.585 174.950 1709 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 0.59 % Allowed : 10.31 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.28), residues: 1032 helix: 2.78 (0.24), residues: 475 sheet: -0.23 (0.44), residues: 143 loop : -0.79 (0.33), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A1164 TYR 0.007 0.001 TYR A 166 PHE 0.013 0.001 PHE A 428 TRP 0.004 0.001 TRP A 643 HIS 0.001 0.000 HIS A 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.09 ( 8468) covalent geometry : angle 0.49156 / 0.24 (11510) hydrogen bonds : bond 0.03282 / 2.21 ( 433) hydrogen bonds : angle 4.06005 / 2.86 ( 1215) link_NAG-ASN : bond 0.00543 / 0.29 ( 1) link_NAG-ASN : angle 2.88831 / 1.61 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3445.10 seconds wall clock time: 59 minutes 9.57 seconds (3549.57 seconds total)