Starting phenix.real_space_refine on Thu Jul 2 07:27:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7e2g_30956/07_2026/7e2g_30956.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e2g_30956/07_2026/7e2g_30956.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7e2g_30956/07_2026/7e2g_30956.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e2g_30956/07_2026/7e2g_30956.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7e2g_30956/07_2026/7e2g_30956.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7e2g_30956/07_2026/7e2g_30956.cif" model { file = "/net/cci-nas-00/data/ceres_data/7e2g_30956/07_2026/7e2g_30956.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e2g_30956/07_2026/7e2g_30956.cif" } resolution = 3.61 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= 0.008 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: 4 Type Number sf(0) Gaussians S 59 5.16 5 C 4894 2.51 5 N 1114 2.21 5 O 1309 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 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: 7376 Number of models: 1 Model: "" Number of chains: 2 Chain: "D" Number of atoms: 6935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 901, 6935 Classifications: {'peptide': 901} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 36, 'TRANS': 864} Chain breaks: 4 Unresolved non-hydrogen bonds: 232 Unresolved non-hydrogen angles: 289 Unresolved non-hydrogen dihedrals: 200 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'TYR:plan': 3, 'GLU:plan': 6, 'ASN:plan1': 3, 'PHE:plan': 3, 'GLN:plan1': 4, 'ARG:plan': 5, 'ASP:plan': 6, 'HIS:plan': 5} Unresolved non-hydrogen planarities: 156 Chain: "D" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 441 Unusual residues: {'NAG': 4, 'Y01': 11} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 1.57, per 1000 atoms: 0.21 Number of scatterers: 7376 At special positions: 0 Unit cell: (104.76, 118.8, 114.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 59 16.00 O 1309 8.00 N 1114 7.00 C 4894 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 Links applied NAG-ASN " NAG D1612 " - " ASN D 836 " " NAG D1613 " - " ASN D 476 " " NAG D1614 " - " ASN D 363 " " NAG D1615 " - " ASN D 917 " Time building additional restraints: 0.61 Conformation dependent library (CDL) restraints added in 335.1 milliseconds 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1718 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 3 sheets defined 58.3% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'D' and resid 181 through 186 removed outlier: 3.829A pdb=" N ILE D 185 " --> pdb=" O TYR D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 210 removed outlier: 4.044A pdb=" N VAL D 192 " --> pdb=" O TRP D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 243 Processing helix chain 'D' and resid 315 through 330 Processing helix chain 'D' and resid 353 through 361 removed outlier: 3.913A pdb=" N TYR D 357 " --> pdb=" O THR D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 386 removed outlier: 4.079A pdb=" N SER D 376 " --> pdb=" O GLU D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 389 No H-bonds generated for 'chain 'D' and resid 387 through 389' Processing helix chain 'D' and resid 422 through 430 Processing helix chain 'D' and resid 464 through 472 removed outlier: 3.932A pdb=" N TYR D 468 " --> pdb=" O MET D 464 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP D 470 " --> pdb=" O ASN D 466 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE D 472 " --> pdb=" O TYR D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 503 removed outlier: 3.616A pdb=" N TYR D 499 " --> pdb=" O LEU D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 522 removed outlier: 3.778A pdb=" N ALA D 508 " --> pdb=" O THR D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 548 Processing helix chain 'D' and resid 557 through 560 Processing helix chain 'D' and resid 561 through 587 removed outlier: 3.803A pdb=" N ILE D 565 " --> pdb=" O THR D 561 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ALA D 571 " --> pdb=" O VAL D 567 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N ASN D 572 " --> pdb=" O GLY D 568 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ASN D 573 " --> pdb=" O ILE D 569 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA D 574 " --> pdb=" O GLY D 570 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE D 575 " --> pdb=" O ALA D 571 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N VAL D 576 " --> pdb=" O ASN D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 621 removed outlier: 5.077A pdb=" N LEU D 606 " --> pdb=" O GLN D 602 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N SER D 607 " --> pdb=" O HIS D 603 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR D 615 " --> pdb=" O THR D 611 " (cutoff:3.500A) Processing helix chain 'D' and resid 622 through 624 No H-bonds generated for 'chain 'D' and resid 622 through 624' Processing helix chain 'D' and resid 627 through 659 removed outlier: 3.671A pdb=" N ARG D 631 " --> pdb=" O ILE D 627 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU D 652 " --> pdb=" O MET D 648 " (cutoff:3.500A) Proline residue: D 653 - end of helix Processing helix chain 'D' and resid 688 through 708 Processing helix chain 'D' and resid 708 through 716 removed outlier: 3.600A pdb=" N CYS D 712 " --> pdb=" O LYS D 708 " (cutoff:3.500A) Processing helix chain 'D' and resid 719 through 738 removed outlier: 3.515A pdb=" N PHE D 723 " --> pdb=" O TYR D 719 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 752 removed outlier: 3.858A pdb=" N PHE D 752 " --> pdb=" O LEU D 749 " (cutoff:3.500A) Processing helix chain 'D' and resid 759 through 772 removed outlier: 3.684A pdb=" N ASP D 765 " --> pdb=" O PHE D 761 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N LYS D 769 " --> pdb=" O ASP D 765 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N LYS D 770 " --> pdb=" O ALA D 766 " (cutoff:3.500A) Processing helix chain 'D' and resid 772 through 777 Processing helix chain 'D' and resid 820 through 835 Processing helix chain 'D' and resid 851 through 859 removed outlier: 3.989A pdb=" N THR D 855 " --> pdb=" O CYS D 851 " (cutoff:3.500A) Processing helix chain 'D' and resid 885 through 901 removed outlier: 4.211A pdb=" N LYS D 891 " --> pdb=" O GLU D 887 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE D 894 " --> pdb=" O ILE D 890 " (cutoff:3.500A) Processing helix chain 'D' and resid 937 through 953 removed outlier: 4.308A pdb=" N SER D 953 " --> pdb=" O SER D 949 " (cutoff:3.500A) Processing helix chain 'D' and resid 972 through 1004 removed outlier: 3.873A pdb=" N THR D1003 " --> pdb=" O MET D 999 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TRP D1004 " --> pdb=" O LEU D1000 " (cutoff:3.500A) Processing helix chain 'D' and resid 1005 through 1031 removed outlier: 3.669A pdb=" N TYR D1011 " --> pdb=" O ILE D1007 " (cutoff:3.500A) Processing helix chain 'D' and resid 1037 through 1050 removed outlier: 4.014A pdb=" N SER D1043 " --> pdb=" O SER D1039 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N VAL D1046 " --> pdb=" O ILE D1042 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY D1047 " --> pdb=" O SER D1043 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL D1050 " --> pdb=" O VAL D1046 " (cutoff:3.500A) Processing helix chain 'D' and resid 1050 through 1059 removed outlier: 3.853A pdb=" N HIS D1055 " --> pdb=" O ASN D1051 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N TYR D1056 " --> pdb=" O PHE D1052 " (cutoff:3.500A) Processing helix chain 'D' and resid 1072 through 1096 removed outlier: 5.665A pdb=" N SER D1081 " --> pdb=" O SER D1077 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ALA D1082 " --> pdb=" O ARG D1078 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR D1090 " --> pdb=" O ALA D1086 " (cutoff:3.500A) Processing helix chain 'D' and resid 1102 through 1130 removed outlier: 3.717A pdb=" N THR D1106 " --> pdb=" O VAL D1102 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 452 through 459 removed outlier: 4.133A pdb=" N SER D 301 " --> pdb=" O SER D 456 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY D 486 " --> pdb=" O VAL D 304 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N THR D 306 " --> pdb=" O ILE D 484 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ILE D 484 " --> pdb=" O THR D 306 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 789 through 790 Processing sheet with id=AA3, first strand: chain 'D' and resid 913 through 914 362 hydrogen bonds defined for protein. 1071 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.03 Time building geometry restraints manager: 0.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1120 1.32 - 1.44: 2064 1.44 - 1.56: 4310 1.56 - 1.69: 0 1.69 - 1.81: 93 Bond restraints: 7587 Sorted by residual: bond pdb=" C1 NAG D1612 " pdb=" O5 NAG D1612 " ideal model delta sigma weight residual 1.406 1.500 -0.094 2.00e-02 2.50e+03 2.23e+01 bond pdb=" CG ASN D 363 " pdb=" ND2 ASN D 363 " ideal model delta sigma weight residual 1.328 1.375 -0.047 2.10e-02 2.27e+03 5.08e+00 bond pdb=" C1 NAG D1614 " pdb=" O5 NAG D1614 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.18e+00 bond pdb=" C ASN D 739 " pdb=" N PRO D 740 " ideal model delta sigma weight residual 1.334 1.379 -0.045 2.34e-02 1.83e+03 3.75e+00 bond pdb=" CG ASN D 917 " pdb=" ND2 ASN D 917 " ideal model delta sigma weight residual 1.328 1.365 -0.037 2.10e-02 2.27e+03 3.05e+00 ... (remaining 7582 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 9916 1.51 - 3.01: 389 3.01 - 4.52: 72 4.52 - 6.02: 10 6.02 - 7.53: 9 Bond angle restraints: 10396 Sorted by residual: angle pdb=" N LYS D 805 " pdb=" CA LYS D 805 " pdb=" C LYS D 805 " ideal model delta sigma weight residual 113.19 108.39 4.80 1.19e+00 7.06e-01 1.62e+01 angle pdb=" C ASP D 906 " pdb=" N SER D 907 " pdb=" CA SER D 907 " ideal model delta sigma weight residual 121.54 128.85 -7.31 1.91e+00 2.74e-01 1.47e+01 angle pdb=" C ALA D 186 " pdb=" N ASP D 187 " pdb=" CA ASP D 187 " ideal model delta sigma weight residual 121.54 128.25 -6.71 1.91e+00 2.74e-01 1.23e+01 angle pdb=" C THR D 228 " pdb=" N ALA D 229 " pdb=" CA ALA D 229 " ideal model delta sigma weight residual 121.54 127.98 -6.44 1.91e+00 2.74e-01 1.14e+01 angle pdb=" C MET D 437 " pdb=" N THR D 438 " pdb=" CA THR D 438 " ideal model delta sigma weight residual 122.28 118.89 3.39 1.02e+00 9.61e-01 1.10e+01 ... (remaining 10391 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 3914 17.96 - 35.93: 321 35.93 - 53.89: 52 53.89 - 71.85: 9 71.85 - 89.82: 3 Dihedral angle restraints: 4299 sinusoidal: 1650 harmonic: 2649 Sorted by residual: dihedral pdb=" CA ASN D 739 " pdb=" C ASN D 739 " pdb=" N PRO D 740 " pdb=" CA PRO D 740 " ideal model delta harmonic sigma weight residual -180.00 -154.45 -25.55 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA LYS D 256 " pdb=" C LYS D 256 " pdb=" N TYR D 257 " pdb=" CA TYR D 257 " ideal model delta harmonic sigma weight residual -180.00 -154.71 -25.29 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA ASP D 918 " pdb=" C ASP D 918 " pdb=" N THR D 919 " pdb=" CA THR D 919 " ideal model delta harmonic sigma weight residual 180.00 158.37 21.63 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 4296 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.241: 1230 0.241 - 0.482: 0 0.482 - 0.723: 3 0.723 - 0.964: 0 0.964 - 1.205: 1 Chirality restraints: 1234 Sorted by residual: chirality pdb=" C1 NAG D1615 " pdb=" ND2 ASN D 917 " pdb=" C2 NAG D1615 " pdb=" O5 NAG D1615 " both_signs ideal model delta sigma weight residual False -2.40 -1.20 -1.20 2.00e-01 2.50e+01 3.63e+01 chirality pdb=" C1 NAG D1614 " pdb=" ND2 ASN D 363 " pdb=" C2 NAG D1614 " pdb=" O5 NAG D1614 " both_signs ideal model delta sigma weight residual False -2.40 -1.70 -0.70 2.00e-01 2.50e+01 1.23e+01 chirality pdb=" C1 NAG D1613 " pdb=" ND2 ASN D 476 " pdb=" C2 NAG D1613 " pdb=" O5 NAG D1613 " both_signs ideal model delta sigma weight residual False -2.40 -1.71 -0.69 2.00e-01 2.50e+01 1.19e+01 ... (remaining 1231 not shown) Planarity restraints: 1235 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE D 557 " -0.012 2.00e-02 2.50e+03 2.33e-02 5.41e+00 pdb=" C PHE D 557 " 0.040 2.00e-02 2.50e+03 pdb=" O PHE D 557 " -0.015 2.00e-02 2.50e+03 pdb=" N MET D 558 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN D 739 " 0.038 5.00e-02 4.00e+02 5.82e-02 5.41e+00 pdb=" N PRO D 740 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO D 740 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 740 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN D 883 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.93e+00 pdb=" C GLN D 883 " -0.038 2.00e-02 2.50e+03 pdb=" O GLN D 883 " 0.014 2.00e-02 2.50e+03 pdb=" N GLU D 884 " 0.013 2.00e-02 2.50e+03 ... (remaining 1232 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 136 2.69 - 3.24: 7644 3.24 - 3.79: 10657 3.79 - 4.35: 13430 4.35 - 4.90: 22539 Nonbonded interactions: 54406 Sorted by model distance: nonbonded pdb=" CAI Y01 D1610 " pdb=" CAR Y01 D1611 " model vdw 2.132 3.740 nonbonded pdb=" OH TYR D 357 " pdb=" OE1 GLN D 426 " model vdw 2.165 3.040 nonbonded pdb=" CAK Y01 D1610 " pdb=" CAT Y01 D1611 " model vdw 2.196 3.840 nonbonded pdb=" O ASP D 948 " pdb=" OG SER D 952 " model vdw 2.218 3.040 nonbonded pdb=" NZ LYS D 741 " pdb=" OAG Y01 D1607 " model vdw 2.236 3.120 ... (remaining 54401 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.340 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.890 Find NCS groups from input model: 0.030 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:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 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 0.094 7591 Z= 0.220 Angle : 0.799 22.880 10408 Z= 0.399 Chirality : 0.063 1.205 1234 Planarity : 0.004 0.058 1231 Dihedral : 13.601 89.817 2581 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % Rotamer: Outliers : 0.14 % Allowed : 5.99 % Favored : 93.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.91 (0.25), residues: 891 helix: -0.61 (0.23), residues: 474 sheet: -2.20 (0.87), residues: 24 loop : -3.71 (0.25), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 661 TYR 0.009 0.001 TYR D 636 PHE 0.020 0.001 PHE D 552 TRP 0.015 0.002 TRP D 651 HIS 0.002 0.001 HIS D 551 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.22 ( 7587) covalent geometry : angle 0.71674 / 0.38 (10396) hydrogen bonds : bond 0.11749 / 7.19 ( 362) hydrogen bonds : angle 5.63765 / 3.97 ( 1071) link_NAG-ASN : bond 0.03089 / 1.59 ( 4) link_NAG-ASN : angle 10.42505 / 5.36 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 131 time to evaluate : 0.165 Fit side-chains REVERT: D 431 LEU cc_start: 0.8989 (mp) cc_final: 0.8777 (mp) REVERT: D 595 GLU cc_start: 0.8169 (pt0) cc_final: 0.7954 (pt0) REVERT: D 700 GLU cc_start: 0.7949 (pt0) cc_final: 0.7439 (pt0) REVERT: D 738 ILE cc_start: 0.8156 (mm) cc_final: 0.7946 (mt) REVERT: D 926 GLU cc_start: 0.7668 (pp20) cc_final: 0.7266 (pp20) REVERT: D 960 GLU cc_start: 0.8745 (pp20) cc_final: 0.8291 (pp20) outliers start: 1 outliers final: 1 residues processed: 132 average time/residue: 0.0532 time to fit residues: 10.8524 Evaluate side-chains 102 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 101 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 557 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 9.9990 chunk 74 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 232 GLN D 356 ASN D 422 ASN D 497 GLN D 622 ASN D 644 ASN ** D 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 784 HIS ** D1051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1107 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.133699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.099729 restraints weight = 12911.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.101536 restraints weight = 7348.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.102827 restraints weight = 5361.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.103233 restraints weight = 4269.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.103498 restraints weight = 4013.047| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7591 Z= 0.171 Angle : 0.734 19.197 10408 Z= 0.349 Chirality : 0.044 0.363 1234 Planarity : 0.004 0.043 1231 Dihedral : 7.789 56.351 1101 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 1.90 % Allowed : 11.97 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.27), residues: 891 helix: 0.77 (0.24), residues: 473 sheet: -1.64 (0.91), residues: 24 loop : -3.28 (0.27), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 661 TYR 0.015 0.001 TYR D 430 PHE 0.020 0.002 PHE D 552 TRP 0.017 0.001 TRP D 651 HIS 0.003 0.001 HIS D 551 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 ( 7587) covalent geometry : angle 0.67279 / 0.34 (10396) hydrogen bonds : bond 0.05487 / 3.62 ( 362) hydrogen bonds : angle 4.19007 / 2.94 ( 1071) link_NAG-ASN : bond 0.01013 / 0.53 ( 4) link_NAG-ASN : angle 8.66270 / 4.21 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.158 Fit side-chains REVERT: D 205 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8001 (mp) REVERT: D 431 LEU cc_start: 0.9035 (mp) cc_final: 0.8835 (mp) REVERT: D 700 GLU cc_start: 0.7935 (pt0) cc_final: 0.7466 (pt0) REVERT: D 768 TYR cc_start: 0.9107 (m-10) cc_final: 0.8658 (m-10) REVERT: D 877 TRP cc_start: 0.8600 (m100) cc_final: 0.8279 (m100) REVERT: D 940 MET cc_start: 0.8946 (mmm) cc_final: 0.8539 (mmp) REVERT: D 960 GLU cc_start: 0.8552 (pp20) cc_final: 0.7621 (pp20) outliers start: 14 outliers final: 10 residues processed: 109 average time/residue: 0.0447 time to fit residues: 7.4657 Evaluate side-chains 106 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 557 PHE Chi-restraints excluded: chain D residue 590 HIS Chi-restraints excluded: chain D residue 649 VAL Chi-restraints excluded: chain D residue 692 HIS Chi-restraints excluded: chain D residue 709 VAL Chi-restraints excluded: chain D residue 728 LEU Chi-restraints excluded: chain D residue 1020 ILE Chi-restraints excluded: chain D residue 1030 LEU Chi-restraints excluded: chain D residue 1112 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 8 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 82 optimal weight: 0.0070 chunk 58 optimal weight: 5.9990 overall best weight: 0.7002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 232 GLN ** D1051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.136239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.103464 restraints weight = 12863.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.105210 restraints weight = 7510.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.106065 restraints weight = 5422.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.106703 restraints weight = 4440.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.106981 restraints weight = 4160.381| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 7591 Z= 0.118 Angle : 0.671 18.667 10408 Z= 0.315 Chirality : 0.041 0.310 1234 Planarity : 0.004 0.036 1231 Dihedral : 7.355 59.706 1101 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 2.72 % Allowed : 12.52 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.29), residues: 891 helix: 1.48 (0.24), residues: 474 sheet: -1.33 (0.94), residues: 24 loop : -3.05 (0.28), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D1132 TYR 0.012 0.001 TYR D 430 PHE 0.023 0.001 PHE D 856 TRP 0.016 0.001 TRP D 651 HIS 0.002 0.001 HIS D 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 ( 7587) covalent geometry : angle 0.61111 / 0.30 (10396) hydrogen bonds : bond 0.04371 / 2.88 ( 362) hydrogen bonds : angle 3.91704 / 2.74 ( 1071) link_NAG-ASN : bond 0.01125 / 0.58 ( 4) link_NAG-ASN : angle 8.20298 / 3.96 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.264 Fit side-chains REVERT: D 205 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8020 (mp) REVERT: D 437 MET cc_start: 0.3587 (mmt) cc_final: 0.2499 (tpp) REVERT: D 700 GLU cc_start: 0.7799 (pt0) cc_final: 0.7343 (pt0) REVERT: D 768 TYR cc_start: 0.8972 (m-10) cc_final: 0.8631 (m-10) REVERT: D 940 MET cc_start: 0.8845 (mmm) cc_final: 0.8482 (mmp) REVERT: D 960 GLU cc_start: 0.8301 (pp20) cc_final: 0.7539 (pp20) outliers start: 20 outliers final: 8 residues processed: 121 average time/residue: 0.0570 time to fit residues: 10.5382 Evaluate side-chains 115 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 557 PHE Chi-restraints excluded: chain D residue 649 VAL Chi-restraints excluded: chain D residue 692 HIS Chi-restraints excluded: chain D residue 709 VAL Chi-restraints excluded: chain D residue 728 LEU Chi-restraints excluded: chain D residue 966 TRP Chi-restraints excluded: chain D residue 1020 ILE Chi-restraints excluded: chain D residue 1073 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 18 optimal weight: 8.9990 chunk 46 optimal weight: 8.9990 chunk 71 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 28 optimal weight: 0.0870 chunk 2 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 23 optimal weight: 30.0000 chunk 79 optimal weight: 3.9990 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 232 GLN ** D1051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.136757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.103482 restraints weight = 13069.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.105370 restraints weight = 7632.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.106575 restraints weight = 5575.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.107096 restraints weight = 4385.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.107184 restraints weight = 4141.769| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7591 Z= 0.120 Angle : 0.655 17.843 10408 Z= 0.308 Chirality : 0.040 0.298 1234 Planarity : 0.003 0.035 1231 Dihedral : 7.228 58.414 1101 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 2.59 % Allowed : 14.56 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.29), residues: 891 helix: 1.78 (0.24), residues: 474 sheet: -0.99 (0.96), residues: 24 loop : -2.97 (0.28), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 835 TYR 0.007 0.001 TYR D 257 PHE 0.025 0.001 PHE D 856 TRP 0.015 0.001 TRP D 651 HIS 0.002 0.000 HIS D 551 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 7587) covalent geometry : angle 0.59849 / 0.30 (10396) hydrogen bonds : bond 0.04229 / 2.79 ( 362) hydrogen bonds : angle 3.82266 / 2.67 ( 1071) link_NAG-ASN : bond 0.01190 / 0.61 ( 4) link_NAG-ASN : angle 7.86719 / 3.80 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.252 Fit side-chains REVERT: D 205 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8026 (mp) REVERT: D 349 CYS cc_start: 0.8036 (OUTLIER) cc_final: 0.7597 (m) REVERT: D 437 MET cc_start: 0.3580 (mmt) cc_final: 0.3331 (tpp) REVERT: D 700 GLU cc_start: 0.7859 (pt0) cc_final: 0.7368 (pt0) REVERT: D 768 TYR cc_start: 0.8917 (m-10) cc_final: 0.8595 (m-10) REVERT: D 785 MET cc_start: 0.8945 (OUTLIER) cc_final: 0.8734 (ttp) REVERT: D 940 MET cc_start: 0.8802 (mmm) cc_final: 0.8578 (mmt) REVERT: D 960 GLU cc_start: 0.8247 (pp20) cc_final: 0.7581 (pp20) outliers start: 19 outliers final: 10 residues processed: 127 average time/residue: 0.0464 time to fit residues: 9.0406 Evaluate side-chains 119 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 349 CYS Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 446 THR Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 557 PHE Chi-restraints excluded: chain D residue 649 VAL Chi-restraints excluded: chain D residue 692 HIS Chi-restraints excluded: chain D residue 709 VAL Chi-restraints excluded: chain D residue 728 LEU Chi-restraints excluded: chain D residue 785 MET Chi-restraints excluded: chain D residue 1041 THR Chi-restraints excluded: chain D residue 1073 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 48 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 17 optimal weight: 20.0000 chunk 13 optimal weight: 0.0270 chunk 87 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 60 optimal weight: 7.9990 overall best weight: 1.7844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 232 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.135213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.101569 restraints weight = 12973.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.103336 restraints weight = 7757.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.104465 restraints weight = 5750.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.104957 restraints weight = 4486.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.105074 restraints weight = 4335.923| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7591 Z= 0.145 Angle : 0.665 17.451 10408 Z= 0.313 Chirality : 0.041 0.297 1234 Planarity : 0.003 0.035 1231 Dihedral : 7.209 57.774 1101 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 3.27 % Allowed : 15.92 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.29), residues: 891 helix: 1.87 (0.24), residues: 474 sheet: -0.90 (0.97), residues: 24 loop : -2.95 (0.28), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 373 TYR 0.008 0.001 TYR D 546 PHE 0.025 0.001 PHE D 856 TRP 0.015 0.001 TRP D 651 HIS 0.002 0.000 HIS D 551 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 ( 7587) covalent geometry : angle 0.61129 / 0.30 (10396) hydrogen bonds : bond 0.04564 / 3.04 ( 362) hydrogen bonds : angle 3.81131 / 2.65 ( 1071) link_NAG-ASN : bond 0.01129 / 0.58 ( 4) link_NAG-ASN : angle 7.71723 / 3.75 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 0.260 Fit side-chains REVERT: D 205 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8042 (mp) REVERT: D 349 CYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7615 (m) REVERT: D 401 MET cc_start: 0.7027 (tmm) cc_final: 0.6824 (tmm) REVERT: D 428 LEU cc_start: 0.9439 (mp) cc_final: 0.9032 (mp) REVERT: D 437 MET cc_start: 0.3548 (mmt) cc_final: 0.3320 (tpp) REVERT: D 700 GLU cc_start: 0.7852 (pt0) cc_final: 0.7366 (pt0) REVERT: D 920 ILE cc_start: 0.9057 (mm) cc_final: 0.8707 (tp) REVERT: D 960 GLU cc_start: 0.8278 (pp20) cc_final: 0.7644 (pp20) outliers start: 24 outliers final: 14 residues processed: 119 average time/residue: 0.0602 time to fit residues: 10.9577 Evaluate side-chains 117 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 349 CYS Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 446 THR Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 557 PHE Chi-restraints excluded: chain D residue 649 VAL Chi-restraints excluded: chain D residue 692 HIS Chi-restraints excluded: chain D residue 709 VAL Chi-restraints excluded: chain D residue 728 LEU Chi-restraints excluded: chain D residue 1020 ILE Chi-restraints excluded: chain D residue 1026 SER Chi-restraints excluded: chain D residue 1041 THR Chi-restraints excluded: chain D residue 1042 ILE Chi-restraints excluded: chain D residue 1073 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 24 optimal weight: 7.9990 chunk 19 optimal weight: 40.0000 chunk 73 optimal weight: 3.9990 chunk 37 optimal weight: 8.9990 chunk 85 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D1051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.135797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.102460 restraints weight = 12867.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.103755 restraints weight = 7437.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.104718 restraints weight = 5264.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.105226 restraints weight = 4504.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.105434 restraints weight = 4261.219| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7591 Z= 0.128 Angle : 0.643 16.628 10408 Z= 0.303 Chirality : 0.040 0.285 1234 Planarity : 0.004 0.037 1231 Dihedral : 7.197 58.645 1101 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 3.54 % Allowed : 15.78 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.29), residues: 891 helix: 1.97 (0.24), residues: 474 sheet: -0.85 (0.96), residues: 24 loop : -2.88 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 373 TYR 0.007 0.001 TYR D 546 PHE 0.024 0.001 PHE D 856 TRP 0.016 0.001 TRP D 651 HIS 0.002 0.000 HIS D 551 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 7587) covalent geometry : angle 0.59238 / 0.29 (10396) hydrogen bonds : bond 0.04429 / 2.95 ( 362) hydrogen bonds : angle 3.76151 / 2.62 ( 1071) link_NAG-ASN : bond 0.01103 / 0.57 ( 4) link_NAG-ASN : angle 7.38959 / 3.62 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 106 time to evaluate : 0.278 Fit side-chains REVERT: D 205 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8047 (mp) REVERT: D 349 CYS cc_start: 0.7941 (OUTLIER) cc_final: 0.7541 (m) REVERT: D 352 TRP cc_start: 0.8346 (OUTLIER) cc_final: 0.7862 (t-100) REVERT: D 437 MET cc_start: 0.3498 (mmt) cc_final: 0.3223 (tpp) REVERT: D 700 GLU cc_start: 0.7902 (pt0) cc_final: 0.7451 (pt0) REVERT: D 920 ILE cc_start: 0.9007 (mm) cc_final: 0.8685 (tp) REVERT: D 960 GLU cc_start: 0.8322 (pp20) cc_final: 0.7710 (pp20) outliers start: 26 outliers final: 14 residues processed: 125 average time/residue: 0.0611 time to fit residues: 11.6369 Evaluate side-chains 119 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 349 CYS Chi-restraints excluded: chain D residue 352 TRP Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 446 THR Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 557 PHE Chi-restraints excluded: chain D residue 649 VAL Chi-restraints excluded: chain D residue 692 HIS Chi-restraints excluded: chain D residue 709 VAL Chi-restraints excluded: chain D residue 728 LEU Chi-restraints excluded: chain D residue 1020 ILE Chi-restraints excluded: chain D residue 1041 THR Chi-restraints excluded: chain D residue 1073 ILE Chi-restraints excluded: chain D residue 1122 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 81 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 64 optimal weight: 0.0020 chunk 27 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 50 optimal weight: 8.9990 chunk 60 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 84 optimal weight: 0.5980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D1051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.138990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.105990 restraints weight = 12730.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.107631 restraints weight = 7205.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.109004 restraints weight = 5238.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.109296 restraints weight = 4179.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.109361 restraints weight = 4192.728| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 7591 Z= 0.112 Angle : 0.632 15.711 10408 Z= 0.296 Chirality : 0.039 0.272 1234 Planarity : 0.004 0.040 1231 Dihedral : 7.056 59.850 1101 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 2.99 % Allowed : 16.60 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.29), residues: 891 helix: 2.05 (0.24), residues: 474 sheet: -0.63 (1.00), residues: 24 loop : -2.81 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 373 TYR 0.007 0.001 TYR D 257 PHE 0.021 0.001 PHE D 856 TRP 0.015 0.001 TRP D 651 HIS 0.002 0.000 HIS D 941 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 ( 7587) covalent geometry : angle 0.58480 / 0.28 (10396) hydrogen bonds : bond 0.03868 / 2.57 ( 362) hydrogen bonds : angle 3.71840 / 2.59 ( 1071) link_NAG-ASN : bond 0.01129 / 0.58 ( 4) link_NAG-ASN : angle 7.06277 / 3.50 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 0.167 Fit side-chains REVERT: D 205 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8025 (mp) REVERT: D 349 CYS cc_start: 0.7874 (OUTLIER) cc_final: 0.7453 (m) REVERT: D 428 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9026 (mp) REVERT: D 437 MET cc_start: 0.3398 (mmt) cc_final: 0.3192 (tpp) REVERT: D 700 GLU cc_start: 0.7862 (pt0) cc_final: 0.7439 (pt0) REVERT: D 723 PHE cc_start: 0.7804 (t80) cc_final: 0.7314 (t80) REVERT: D 920 ILE cc_start: 0.8963 (mm) cc_final: 0.8711 (tp) REVERT: D 960 GLU cc_start: 0.8220 (pp20) cc_final: 0.7636 (pp20) outliers start: 22 outliers final: 14 residues processed: 125 average time/residue: 0.0524 time to fit residues: 10.1634 Evaluate side-chains 125 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 349 CYS Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain D residue 446 THR Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 557 PHE Chi-restraints excluded: chain D residue 649 VAL Chi-restraints excluded: chain D residue 692 HIS Chi-restraints excluded: chain D residue 709 VAL Chi-restraints excluded: chain D residue 909 THR Chi-restraints excluded: chain D residue 966 TRP Chi-restraints excluded: chain D residue 1020 ILE Chi-restraints excluded: chain D residue 1026 SER Chi-restraints excluded: chain D residue 1041 THR Chi-restraints excluded: chain D residue 1122 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 69 optimal weight: 6.9990 chunk 32 optimal weight: 0.8980 chunk 22 optimal weight: 0.0070 chunk 20 optimal weight: 0.0060 chunk 48 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.5214 ------------------------------------------------------------------------------- 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 = 0.3734 r_free = 0.3734 target = 0.139942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.106566 restraints weight = 12889.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.108309 restraints weight = 7054.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.109328 restraints weight = 4970.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.109720 restraints weight = 4223.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.109942 restraints weight = 3975.872| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 7591 Z= 0.109 Angle : 0.624 14.604 10408 Z= 0.292 Chirality : 0.039 0.267 1234 Planarity : 0.003 0.033 1231 Dihedral : 6.853 59.682 1101 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 2.72 % Allowed : 17.41 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.29), residues: 891 helix: 2.09 (0.24), residues: 474 sheet: -0.32 (1.04), residues: 24 loop : -2.78 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 302 TYR 0.007 0.001 TYR D 645 PHE 0.025 0.001 PHE D 856 TRP 0.014 0.001 TRP D 651 HIS 0.001 0.000 HIS D 941 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 ( 7587) covalent geometry : angle 0.58144 / 0.28 (10396) hydrogen bonds : bond 0.03723 / 2.47 ( 362) hydrogen bonds : angle 3.73079 / 2.59 ( 1071) link_NAG-ASN : bond 0.01104 / 0.57 ( 4) link_NAG-ASN : angle 6.73040 / 3.39 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.271 Fit side-chains REVERT: D 205 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.7998 (mp) REVERT: D 349 CYS cc_start: 0.7886 (OUTLIER) cc_final: 0.7472 (m) REVERT: D 428 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.8970 (mp) REVERT: D 437 MET cc_start: 0.3398 (mmt) cc_final: 0.3180 (tpp) REVERT: D 700 GLU cc_start: 0.7898 (pt0) cc_final: 0.7598 (pt0) REVERT: D 723 PHE cc_start: 0.7850 (t80) cc_final: 0.7305 (t80) REVERT: D 920 ILE cc_start: 0.8993 (mm) cc_final: 0.8748 (tp) REVERT: D 960 GLU cc_start: 0.8131 (pp20) cc_final: 0.7528 (pp20) outliers start: 20 outliers final: 12 residues processed: 125 average time/residue: 0.0597 time to fit residues: 11.4667 Evaluate side-chains 123 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 349 CYS Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain D residue 446 THR Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 557 PHE Chi-restraints excluded: chain D residue 649 VAL Chi-restraints excluded: chain D residue 692 HIS Chi-restraints excluded: chain D residue 709 VAL Chi-restraints excluded: chain D residue 728 LEU Chi-restraints excluded: chain D residue 909 THR Chi-restraints excluded: chain D residue 968 VAL Chi-restraints excluded: chain D residue 1041 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 4 optimal weight: 0.0870 chunk 86 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 23 optimal weight: 20.0000 chunk 0 optimal weight: 9.9990 chunk 60 optimal weight: 8.9990 chunk 68 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- 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 = 0.3734 r_free = 0.3734 target = 0.139766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.106517 restraints weight = 12769.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.108325 restraints weight = 6928.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.109602 restraints weight = 4988.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.110050 restraints weight = 4083.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.110146 restraints weight = 3930.558| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 7591 Z= 0.111 Angle : 0.648 15.722 10408 Z= 0.297 Chirality : 0.040 0.264 1234 Planarity : 0.003 0.033 1231 Dihedral : 6.886 59.279 1101 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 2.45 % Allowed : 18.10 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.30), residues: 891 helix: 2.14 (0.24), residues: 474 sheet: -0.21 (1.06), residues: 24 loop : -2.77 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 373 TYR 0.007 0.001 TYR D 645 PHE 0.023 0.001 PHE D 856 TRP 0.014 0.001 TRP D 651 HIS 0.001 0.000 HIS D 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 ( 7587) covalent geometry : angle 0.61085 / 0.29 (10396) hydrogen bonds : bond 0.03731 / 2.48 ( 362) hydrogen bonds : angle 3.73898 / 2.60 ( 1071) link_NAG-ASN : bond 0.01072 / 0.55 ( 4) link_NAG-ASN : angle 6.43825 / 3.31 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.272 Fit side-chains REVERT: D 205 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8051 (mp) REVERT: D 349 CYS cc_start: 0.7889 (OUTLIER) cc_final: 0.7467 (m) REVERT: D 352 TRP cc_start: 0.8276 (OUTLIER) cc_final: 0.7999 (t-100) REVERT: D 428 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.8959 (mp) REVERT: D 437 MET cc_start: 0.3364 (mmt) cc_final: 0.3159 (tpp) REVERT: D 453 MET cc_start: 0.8784 (tpp) cc_final: 0.8563 (ttt) REVERT: D 464 MET cc_start: 0.9119 (tpp) cc_final: 0.8683 (tpp) REVERT: D 700 GLU cc_start: 0.7880 (pt0) cc_final: 0.7574 (pt0) REVERT: D 723 PHE cc_start: 0.7847 (t80) cc_final: 0.7295 (t80) REVERT: D 920 ILE cc_start: 0.8995 (mm) cc_final: 0.8756 (tp) REVERT: D 960 GLU cc_start: 0.8096 (pp20) cc_final: 0.7520 (pp20) outliers start: 18 outliers final: 13 residues processed: 126 average time/residue: 0.0609 time to fit residues: 11.7688 Evaluate side-chains 126 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 349 CYS Chi-restraints excluded: chain D residue 352 TRP Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain D residue 446 THR Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 557 PHE Chi-restraints excluded: chain D residue 649 VAL Chi-restraints excluded: chain D residue 692 HIS Chi-restraints excluded: chain D residue 709 VAL Chi-restraints excluded: chain D residue 728 LEU Chi-restraints excluded: chain D residue 909 THR Chi-restraints excluded: chain D residue 968 VAL Chi-restraints excluded: chain D residue 1020 ILE Chi-restraints excluded: chain D residue 1041 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 41 optimal weight: 4.9990 chunk 69 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 46 optimal weight: 8.9990 chunk 19 optimal weight: 30.0000 chunk 26 optimal weight: 4.9990 chunk 17 optimal weight: 20.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 = 0.3688 r_free = 0.3688 target = 0.136025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.102540 restraints weight = 12798.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.103525 restraints weight = 8010.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.104949 restraints weight = 6034.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.105669 restraints weight = 4746.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.105755 restraints weight = 4537.764| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7591 Z= 0.161 Angle : 0.686 14.336 10408 Z= 0.320 Chirality : 0.042 0.354 1234 Planarity : 0.004 0.034 1231 Dihedral : 6.945 57.626 1101 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 2.72 % Allowed : 18.37 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.30), residues: 891 helix: 2.10 (0.24), residues: 475 sheet: -0.40 (1.04), residues: 24 loop : -2.76 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 373 TYR 0.011 0.001 TYR D 546 PHE 0.023 0.001 PHE D 856 TRP 0.015 0.001 TRP D 651 HIS 0.002 0.001 HIS D 551 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 ( 7587) covalent geometry : angle 0.65184 / 0.31 (10396) hydrogen bonds : bond 0.04653 / 3.12 ( 362) hydrogen bonds : angle 3.85473 / 2.69 ( 1071) link_NAG-ASN : bond 0.00975 / 0.50 ( 4) link_NAG-ASN : angle 6.30749 / 3.28 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.275 Fit side-chains REVERT: D 205 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8112 (mp) REVERT: D 349 CYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7566 (m) REVERT: D 428 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.9020 (mp) REVERT: D 437 MET cc_start: 0.3380 (mmt) cc_final: 0.3163 (tpp) REVERT: D 700 GLU cc_start: 0.7849 (pt0) cc_final: 0.7553 (pt0) REVERT: D 723 PHE cc_start: 0.7809 (t80) cc_final: 0.7354 (t80) REVERT: D 920 ILE cc_start: 0.9000 (mm) cc_final: 0.8723 (tp) REVERT: D 960 GLU cc_start: 0.8222 (pp20) cc_final: 0.7664 (pp20) REVERT: D 1112 MET cc_start: 0.8162 (OUTLIER) cc_final: 0.7862 (ttm) outliers start: 20 outliers final: 13 residues processed: 122 average time/residue: 0.0646 time to fit residues: 12.0465 Evaluate side-chains 123 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 349 CYS Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain D residue 446 THR Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 557 PHE Chi-restraints excluded: chain D residue 649 VAL Chi-restraints excluded: chain D residue 692 HIS Chi-restraints excluded: chain D residue 709 VAL Chi-restraints excluded: chain D residue 728 LEU Chi-restraints excluded: chain D residue 1020 ILE Chi-restraints excluded: chain D residue 1026 SER Chi-restraints excluded: chain D residue 1041 THR Chi-restraints excluded: chain D residue 1112 MET Chi-restraints excluded: chain D residue 1122 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 13 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 chunk 12 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3712 r_free = 0.3712 target = 0.138020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.104928 restraints weight = 12753.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.105270 restraints weight = 8259.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.106487 restraints weight = 5985.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.106614 restraints weight = 5198.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.108918 restraints weight = 4727.695| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7591 Z= 0.120 Angle : 0.673 14.756 10408 Z= 0.309 Chirality : 0.041 0.339 1234 Planarity : 0.003 0.034 1231 Dihedral : 6.949 59.477 1101 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 2.45 % Allowed : 18.91 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.29), residues: 891 helix: 2.12 (0.24), residues: 475 sheet: -0.42 (1.04), residues: 24 loop : -2.71 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 373 TYR 0.007 0.001 TYR D 645 PHE 0.022 0.001 PHE D 856 TRP 0.015 0.001 TRP D 651 HIS 0.002 0.000 HIS D 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 7587) covalent geometry : angle 0.64167 / 0.30 (10396) hydrogen bonds : bond 0.04124 / 2.76 ( 362) hydrogen bonds : angle 3.78730 / 2.64 ( 1071) link_NAG-ASN : bond 0.01035 / 0.53 ( 4) link_NAG-ASN : angle 6.02493 / 3.20 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1235.49 seconds wall clock time: 22 minutes 5.07 seconds (1325.07 seconds total)