Starting phenix.real_space_refine on Fri Jul 25 12:01:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e2g_30956/07_2025/7e2g_30956.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e2g_30956/07_2025/7e2g_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_2025/7e2g_30956.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e2g_30956/07_2025/7e2g_30956.map" model { file = "/net/cci-nas-00/data/ceres_data/7e2g_30956/07_2025/7e2g_30956.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e2g_30956/07_2025/7e2g_30956.cif" } resolution = 3.61 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 4, 'HIS:plan': 5, 'TYR:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 6, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG: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 dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 6.26, per 1000 atoms: 0.85 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: 2.33 Conformation dependent library (CDL) restraints added in 920.7 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: 0.74 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: 1.98 Time building geometry restraints manager: 2.59 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 - 22.08: 4703 22.08 - 44.16: 271 44.16 - 66.24: 40 66.24 - 88.32: 3 88.32 - 110.40: 4 Dihedral angle restraints: 5021 sinusoidal: 2372 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 5018 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: 0.420 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 22.980 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 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 : 13.567 110.396 3303 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.015 0.002 TRP D 651 HIS 0.002 0.001 HIS D 551 PHE 0.020 0.001 PHE D 552 TYR 0.009 0.001 TYR D 636 ARG 0.003 0.000 ARG D 661 Details of bonding type rmsd link_NAG-ASN : bond 0.03089 ( 4) link_NAG-ASN : angle 10.42505 ( 12) hydrogen bonds : bond 0.11749 ( 362) hydrogen bonds : angle 5.63765 ( 1071) covalent geometry : bond 0.00469 ( 7587) covalent geometry : angle 0.71674 (10396) *********************** 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 : 0.767 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: 0.8744 (pp20) cc_final: 0.8291 (pp20) outliers start: 1 outliers final: 1 residues processed: 132 average time/residue: 0.1365 time to fit residues: 26.9746 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 : 0.776 ------------------------------------------------------------------------------- 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 75 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 232 GLN D 356 ASN D 422 ASN ** D 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.135733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.103024 restraints weight = 12588.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.103457 restraints weight = 7833.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.104337 restraints weight = 5894.522| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7591 Z= 0.138 Angle : 0.726 19.158 10408 Z= 0.340 Chirality : 0.043 0.379 1234 Planarity : 0.004 0.042 1231 Dihedral : 9.594 74.749 1823 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 1.63 % Allowed : 11.84 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.27), residues: 891 helix: 0.81 (0.24), residues: 473 sheet: -1.54 (0.92), residues: 24 loop : -3.27 (0.27), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 651 HIS 0.003 0.001 HIS D 659 PHE 0.020 0.001 PHE D 856 TYR 0.013 0.001 TYR D 430 ARG 0.001 0.000 ARG D 661 Details of bonding type rmsd link_NAG-ASN : bond 0.00971 ( 4) link_NAG-ASN : angle 8.76653 ( 12) hydrogen bonds : bond 0.04985 ( 362) hydrogen bonds : angle 4.14273 ( 1071) covalent geometry : bond 0.00301 ( 7587) covalent geometry : angle 0.66271 (10396) *********************** 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 121 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.829 Fit side-chains REVERT: D 205 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8085 (mp) REVERT: D 700 GLU cc_start: 0.7896 (pt0) cc_final: 0.7462 (pt0) REVERT: D 739 ASN cc_start: 0.6982 (t0) cc_final: 0.6727 (t0) REVERT: D 768 TYR cc_start: 0.9081 (m-10) cc_final: 0.8688 (m-10) REVERT: D 877 TRP cc_start: 0.8623 (m100) cc_final: 0.8291 (m100) REVERT: D 940 MET cc_start: 0.8901 (mmm) cc_final: 0.8467 (mmp) REVERT: D 960 GLU cc_start: 0.8508 (pp20) cc_final: 0.7662 (pp20) outliers start: 12 outliers final: 7 residues processed: 114 average time/residue: 0.1499 time to fit residues: 25.2784 Evaluate side-chains 103 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.826 ------------------------------------------------------------------------------- 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 590 HIS Chi-restraints excluded: chain D residue 649 VAL Chi-restraints excluded: chain D residue 692 HIS Chi-restraints excluded: chain D residue 728 LEU Chi-restraints excluded: chain D residue 1020 ILE Chi-restraints excluded: chain D residue 1030 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 56 optimal weight: 0.0570 chunk 43 optimal weight: 0.9980 chunk 66 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 89 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 22 optimal weight: 20.0000 chunk 4 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 232 GLN ** D 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3666 r_free = 0.3666 target = 0.134183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.101066 restraints weight = 12869.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.102881 restraints weight = 7499.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.104030 restraints weight = 5474.037| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1420 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= 0.141 Angle : 0.699 18.613 10408 Z= 0.327 Chirality : 0.042 0.355 1234 Planarity : 0.004 0.035 1231 Dihedral : 8.910 58.267 1823 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 2.72 % Allowed : 12.65 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.29), residues: 891 helix: 1.48 (0.24), residues: 474 sheet: -1.24 (0.95), residues: 24 loop : -3.05 (0.28), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 651 HIS 0.002 0.001 HIS D 551 PHE 0.023 0.001 PHE D 856 TYR 0.007 0.001 TYR D 546 ARG 0.002 0.000 ARG D 373 Details of bonding type rmsd link_NAG-ASN : bond 0.01057 ( 4) link_NAG-ASN : angle 8.94964 ( 12) hydrogen bonds : bond 0.04835 ( 362) hydrogen bonds : angle 3.93677 ( 1071) covalent geometry : bond 0.00321 ( 7587) covalent geometry : angle 0.63022 (10396) *********************** 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 125 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.800 Fit side-chains REVERT: D 205 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8029 (mp) REVERT: D 349 CYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7722 (m) REVERT: D 437 MET cc_start: 0.3711 (mmt) cc_final: 0.3434 (tpp) REVERT: D 453 MET cc_start: 0.9095 (ttm) cc_final: 0.8817 (ttt) REVERT: D 700 GLU cc_start: 0.7884 (pt0) cc_final: 0.7409 (pt0) REVERT: D 768 TYR cc_start: 0.9009 (m-10) cc_final: 0.8622 (m-10) REVERT: D 940 MET cc_start: 0.8884 (mmm) cc_final: 0.8653 (mmp) REVERT: D 960 GLU cc_start: 0.8483 (pp20) cc_final: 0.7705 (pp20) outliers start: 20 outliers final: 9 residues processed: 118 average time/residue: 0.1436 time to fit residues: 25.9247 Evaluate side-chains 111 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.836 ------------------------------------------------------------------------------- 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 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 1030 LEU 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 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.0670 chunk 71 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 44 optimal weight: 0.0670 chunk 85 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 overall best weight: 0.8258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 232 GLN ** D 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3706 r_free = 0.3706 target = 0.137173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.104084 restraints weight = 12845.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.106096 restraints weight = 7482.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.107328 restraints weight = 5423.823| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1754 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= 0.115 Angle : 0.654 17.913 10408 Z= 0.307 Chirality : 0.040 0.315 1234 Planarity : 0.003 0.034 1231 Dihedral : 8.741 58.156 1823 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 2.59 % Allowed : 14.42 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.29), residues: 891 helix: 1.79 (0.24), residues: 474 sheet: -0.98 (0.97), residues: 24 loop : -2.96 (0.28), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 651 HIS 0.002 0.000 HIS D 659 PHE 0.025 0.001 PHE D 856 TYR 0.007 0.001 TYR D 257 ARG 0.003 0.000 ARG D 373 Details of bonding type rmsd link_NAG-ASN : bond 0.01239 ( 4) link_NAG-ASN : angle 8.35727 ( 12) hydrogen bonds : bond 0.04149 ( 362) hydrogen bonds : angle 3.80517 ( 1071) covalent geometry : bond 0.00252 ( 7587) covalent geometry : angle 0.58990 (10396) *********************** 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 131 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.801 Fit side-chains REVERT: D 205 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8029 (mp) REVERT: D 437 MET cc_start: 0.3578 (mmt) cc_final: 0.3333 (tpp) REVERT: D 700 GLU cc_start: 0.7860 (pt0) cc_final: 0.7374 (pt0) REVERT: D 768 TYR cc_start: 0.8913 (m-10) cc_final: 0.8592 (m-10) REVERT: D 940 MET cc_start: 0.8804 (mmm) cc_final: 0.8586 (mmt) REVERT: D 960 GLU cc_start: 0.8414 (pp20) cc_final: 0.7720 (pp20) outliers start: 19 outliers final: 10 residues processed: 123 average time/residue: 0.1475 time to fit residues: 27.2244 Evaluate side-chains 116 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 0.844 ------------------------------------------------------------------------------- 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 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 966 TRP 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 17 optimal weight: 20.0000 chunk 51 optimal weight: 0.9990 chunk 54 optimal weight: 10.0000 chunk 22 optimal weight: 0.2980 chunk 16 optimal weight: 0.0040 chunk 84 optimal weight: 0.8980 chunk 50 optimal weight: 0.0570 chunk 32 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 overall best weight: 0.4512 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 232 GLN ** D 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 572 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 = 0.3728 r_free = 0.3728 target = 0.138912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.105552 restraints weight = 12758.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.107885 restraints weight = 7206.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.108552 restraints weight = 4652.643| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1987 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= 0.110 Angle : 0.637 17.380 10408 Z= 0.297 Chirality : 0.039 0.302 1234 Planarity : 0.003 0.034 1231 Dihedral : 8.586 58.064 1823 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 2.72 % Allowed : 15.78 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.29), residues: 891 helix: 1.88 (0.24), residues: 474 sheet: -0.63 (1.00), residues: 24 loop : -2.88 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 651 HIS 0.001 0.000 HIS D 941 PHE 0.023 0.001 PHE D 856 TYR 0.007 0.001 TYR D 257 ARG 0.003 0.000 ARG D 373 Details of bonding type rmsd link_NAG-ASN : bond 0.01184 ( 4) link_NAG-ASN : angle 7.99815 ( 12) hydrogen bonds : bond 0.03822 ( 362) hydrogen bonds : angle 3.75091 ( 1071) covalent geometry : bond 0.00227 ( 7587) covalent geometry : angle 0.57694 (10396) *********************** 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 131 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.822 Fit side-chains REVERT: D 205 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8077 (mp) REVERT: D 349 CYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7484 (m) REVERT: D 428 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.8998 (mp) REVERT: D 437 MET cc_start: 0.3419 (mmt) cc_final: 0.2547 (tpp) REVERT: D 451 TYR cc_start: 0.8532 (m-80) cc_final: 0.8196 (m-80) REVERT: D 700 GLU cc_start: 0.7903 (pt0) cc_final: 0.7438 (pt0) REVERT: D 768 TYR cc_start: 0.8835 (m-10) cc_final: 0.8531 (m-10) REVERT: D 940 MET cc_start: 0.8753 (mmm) cc_final: 0.8534 (mmt) REVERT: D 960 GLU cc_start: 0.8392 (pp20) cc_final: 0.7786 (pp20) REVERT: D 1096 MET cc_start: 0.8537 (mmm) cc_final: 0.8332 (tpp) outliers start: 20 outliers final: 11 residues processed: 122 average time/residue: 0.1417 time to fit residues: 25.8555 Evaluate side-chains 121 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 0.858 ------------------------------------------------------------------------------- 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 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 860 MET Chi-restraints excluded: chain D residue 1020 ILE Chi-restraints excluded: chain D residue 1041 THR 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 85 optimal weight: 0.0970 chunk 86 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 71 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 0.0070 chunk 80 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 67 optimal weight: 20.0000 chunk 56 optimal weight: 20.0000 chunk 65 optimal weight: 4.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 497 GLN ** D 572 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 = 0.3711 r_free = 0.3711 target = 0.137455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.103992 restraints weight = 12826.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.105893 restraints weight = 7507.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.107049 restraints weight = 5530.866| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2052 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= 0.122 Angle : 0.640 16.913 10408 Z= 0.299 Chirality : 0.039 0.306 1234 Planarity : 0.003 0.033 1231 Dihedral : 8.530 59.610 1823 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 3.40 % Allowed : 15.78 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.29), residues: 891 helix: 2.00 (0.24), residues: 474 sheet: -0.62 (0.99), residues: 24 loop : -2.85 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 651 HIS 0.002 0.000 HIS D 551 PHE 0.026 0.001 PHE D 856 TYR 0.008 0.001 TYR D 430 ARG 0.002 0.000 ARG D 373 Details of bonding type rmsd link_NAG-ASN : bond 0.01106 ( 4) link_NAG-ASN : angle 7.72747 ( 12) hydrogen bonds : bond 0.04190 ( 362) hydrogen bonds : angle 3.75074 ( 1071) covalent geometry : bond 0.00275 ( 7587) covalent geometry : angle 0.58376 (10396) *********************** 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 136 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 0.796 Fit side-chains REVERT: D 205 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8031 (mp) REVERT: D 349 CYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7546 (m) REVERT: D 428 LEU cc_start: 0.9419 (mp) cc_final: 0.9024 (mp) REVERT: D 437 MET cc_start: 0.3448 (mmt) cc_final: 0.3224 (tpp) REVERT: D 700 GLU cc_start: 0.7888 (pt0) cc_final: 0.7453 (pt0) REVERT: D 960 GLU cc_start: 0.8402 (pp20) cc_final: 0.7827 (pp20) outliers start: 25 outliers final: 16 residues processed: 125 average time/residue: 0.1401 time to fit residues: 26.3623 Evaluate side-chains 123 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.801 ------------------------------------------------------------------------------- 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 512 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 855 THR Chi-restraints excluded: chain D residue 909 THR Chi-restraints excluded: chain D residue 966 TRP Chi-restraints excluded: chain D residue 968 VAL Chi-restraints excluded: chain D residue 1020 ILE Chi-restraints excluded: chain D residue 1041 THR Chi-restraints excluded: chain D residue 1073 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 86 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 chunk 52 optimal weight: 0.1980 chunk 68 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 37 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.138991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.105898 restraints weight = 12677.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.107241 restraints weight = 7343.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.108139 restraints weight = 5416.430| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2228 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 : 0.637 16.489 10408 Z= 0.297 Chirality : 0.040 0.295 1234 Planarity : 0.004 0.039 1231 Dihedral : 8.490 58.456 1823 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 2.72 % Allowed : 17.01 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.29), residues: 891 helix: 2.07 (0.24), residues: 474 sheet: -0.56 (1.01), residues: 24 loop : -2.83 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 651 HIS 0.002 0.000 HIS D 941 PHE 0.024 0.001 PHE D 856 TYR 0.007 0.001 TYR D 645 ARG 0.003 0.000 ARG D 373 Details of bonding type rmsd link_NAG-ASN : bond 0.01115 ( 4) link_NAG-ASN : angle 7.51958 ( 12) hydrogen bonds : bond 0.03940 ( 362) hydrogen bonds : angle 3.72395 ( 1071) covalent geometry : bond 0.00237 ( 7587) covalent geometry : angle 0.58359 (10396) *********************** 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 128 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.822 Fit side-chains REVERT: D 205 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8009 (mp) REVERT: D 349 CYS cc_start: 0.7901 (OUTLIER) cc_final: 0.7482 (m) REVERT: D 437 MET cc_start: 0.3548 (mmt) cc_final: 0.3296 (tpp) REVERT: D 700 GLU cc_start: 0.7858 (pt0) cc_final: 0.7431 (pt0) REVERT: D 723 PHE cc_start: 0.7806 (t80) cc_final: 0.7309 (t80) REVERT: D 960 GLU cc_start: 0.8372 (pp20) cc_final: 0.7827 (pp20) outliers start: 20 outliers final: 14 residues processed: 121 average time/residue: 0.1432 time to fit residues: 25.9081 Evaluate side-chains 122 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.758 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain D residue 1073 ILE 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 57 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 22 optimal weight: 0.0870 chunk 44 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 59 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 overall best weight: 1.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3715 r_free = 0.3715 target = 0.138256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.104550 restraints weight = 12712.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.106352 restraints weight = 7194.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.107706 restraints weight = 5108.372| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 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 : 0.003 0.043 7591 Z= 0.123 Angle : 0.649 16.176 10408 Z= 0.302 Chirality : 0.040 0.325 1234 Planarity : 0.004 0.033 1231 Dihedral : 8.499 59.001 1823 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 2.86 % Allowed : 17.01 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.29), residues: 891 helix: 2.07 (0.24), residues: 474 sheet: -0.67 (1.03), residues: 24 loop : -2.78 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 651 HIS 0.001 0.000 HIS D 551 PHE 0.024 0.001 PHE D 856 TYR 0.008 0.001 TYR D 546 ARG 0.004 0.000 ARG D 373 Details of bonding type rmsd link_NAG-ASN : bond 0.01075 ( 4) link_NAG-ASN : angle 7.37453 ( 12) hydrogen bonds : bond 0.04161 ( 362) hydrogen bonds : angle 3.77543 ( 1071) covalent geometry : bond 0.00275 ( 7587) covalent geometry : angle 0.59877 (10396) *********************** 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 128 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.841 Fit side-chains REVERT: D 205 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8066 (mp) REVERT: D 349 CYS cc_start: 0.7951 (OUTLIER) cc_final: 0.7540 (m) REVERT: D 428 LEU cc_start: 0.9407 (mp) cc_final: 0.9029 (mp) REVERT: D 437 MET cc_start: 0.3531 (mmt) cc_final: 0.3331 (tpp) REVERT: D 453 MET cc_start: 0.9001 (ttm) cc_final: 0.8436 (ttt) REVERT: D 700 GLU cc_start: 0.7916 (pt0) cc_final: 0.7471 (pt0) REVERT: D 723 PHE cc_start: 0.7872 (t80) cc_final: 0.7321 (t80) REVERT: D 960 GLU cc_start: 0.8385 (pp20) cc_final: 0.7830 (pp20) outliers start: 21 outliers final: 17 residues processed: 121 average time/residue: 0.1389 time to fit residues: 25.2344 Evaluate side-chains 123 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.742 ------------------------------------------------------------------------------- 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 549 VAL Chi-restraints excluded: chain D residue 557 PHE Chi-restraints excluded: chain D residue 647 LEU 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 855 THR 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 Chi-restraints excluded: chain D residue 1073 ILE Chi-restraints excluded: chain D residue 1122 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 29 optimal weight: 2.9990 chunk 44 optimal weight: 0.3980 chunk 81 optimal weight: 0.4980 chunk 15 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3738 r_free = 0.3738 target = 0.140052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.107009 restraints weight = 12814.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.108461 restraints weight = 7303.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.109328 restraints weight = 5390.392| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2432 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= 0.110 Angle : 0.660 16.021 10408 Z= 0.301 Chirality : 0.040 0.359 1234 Planarity : 0.004 0.034 1231 Dihedral : 8.485 58.717 1823 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 2.72 % Allowed : 16.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.29), residues: 891 helix: 2.09 (0.24), residues: 474 sheet: -0.51 (1.05), residues: 24 loop : -2.79 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 651 HIS 0.002 0.000 HIS D 941 PHE 0.023 0.001 PHE D 856 TYR 0.006 0.001 TYR D 645 ARG 0.004 0.000 ARG D 373 Details of bonding type rmsd link_NAG-ASN : bond 0.01116 ( 4) link_NAG-ASN : angle 7.14277 ( 12) hydrogen bonds : bond 0.03800 ( 362) hydrogen bonds : angle 3.73493 ( 1071) covalent geometry : bond 0.00233 ( 7587) covalent geometry : angle 0.61430 (10396) *********************** 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 127 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.759 Fit side-chains REVERT: D 205 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8053 (mp) REVERT: D 349 CYS cc_start: 0.7876 (OUTLIER) cc_final: 0.7468 (m) REVERT: D 428 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.8997 (mp) REVERT: D 437 MET cc_start: 0.3435 (mmt) cc_final: 0.3206 (tpp) REVERT: D 453 MET cc_start: 0.8846 (ttm) cc_final: 0.8296 (ttt) REVERT: D 700 GLU cc_start: 0.7841 (pt0) cc_final: 0.7543 (pt0) REVERT: D 723 PHE cc_start: 0.7767 (t80) cc_final: 0.7277 (t80) REVERT: D 960 GLU cc_start: 0.8335 (pp20) cc_final: 0.7814 (pp20) outliers start: 20 outliers final: 15 residues processed: 119 average time/residue: 0.1369 time to fit residues: 24.4697 Evaluate side-chains 124 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.836 ------------------------------------------------------------------------------- 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 557 PHE Chi-restraints excluded: chain D residue 647 LEU 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 855 THR Chi-restraints excluded: chain D residue 909 THR Chi-restraints excluded: chain D residue 968 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 54 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 20 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3730 r_free = 0.3730 target = 0.139420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.106304 restraints weight = 12923.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.107828 restraints weight = 7359.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.109063 restraints weight = 5469.367| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2496 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= 0.113 Angle : 0.652 15.344 10408 Z= 0.299 Chirality : 0.040 0.365 1234 Planarity : 0.004 0.034 1231 Dihedral : 8.535 59.705 1823 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 2.59 % Allowed : 17.28 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.29), residues: 891 helix: 2.11 (0.24), residues: 476 sheet: -0.40 (1.05), residues: 24 loop : -2.73 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 651 HIS 0.001 0.000 HIS D1055 PHE 0.022 0.001 PHE D 856 TYR 0.007 0.001 TYR D 546 ARG 0.005 0.000 ARG D 373 Details of bonding type rmsd link_NAG-ASN : bond 0.01087 ( 4) link_NAG-ASN : angle 7.05105 ( 12) hydrogen bonds : bond 0.03909 ( 362) hydrogen bonds : angle 3.78222 ( 1071) covalent geometry : bond 0.00249 ( 7587) covalent geometry : angle 0.60631 (10396) ********************** 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 125 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.828 Fit side-chains REVERT: D 205 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8085 (mp) REVERT: D 349 CYS cc_start: 0.7893 (OUTLIER) cc_final: 0.7511 (m) REVERT: D 428 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.8988 (mp) REVERT: D 437 MET cc_start: 0.3381 (mmt) cc_final: 0.2005 (tpp) REVERT: D 453 MET cc_start: 0.8855 (ttm) cc_final: 0.8300 (ttt) REVERT: D 700 GLU cc_start: 0.7820 (pt0) cc_final: 0.7520 (pt0) REVERT: D 723 PHE cc_start: 0.7793 (t80) cc_final: 0.7323 (t80) REVERT: D 960 GLU cc_start: 0.8288 (pp20) cc_final: 0.7785 (pp20) outliers start: 19 outliers final: 15 residues processed: 120 average time/residue: 0.1390 time to fit residues: 24.9742 Evaluate side-chains 121 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 0.759 ------------------------------------------------------------------------------- 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 557 PHE Chi-restraints excluded: chain D residue 647 LEU 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 855 THR Chi-restraints excluded: chain D residue 909 THR Chi-restraints excluded: chain D residue 968 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 4 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 3 optimal weight: 0.2980 chunk 30 optimal weight: 0.7980 chunk 19 optimal weight: 30.0000 chunk 5 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3705 r_free = 0.3705 target = 0.137292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.104090 restraints weight = 12779.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.104440 restraints weight = 8451.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.105592 restraints weight = 6121.307| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2443 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= 0.135 Angle : 0.674 15.171 10408 Z= 0.312 Chirality : 0.041 0.358 1234 Planarity : 0.004 0.034 1231 Dihedral : 8.613 59.597 1823 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 3.13 % Allowed : 16.87 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.30), residues: 891 helix: 2.12 (0.24), residues: 475 sheet: -0.53 (1.04), residues: 24 loop : -2.74 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 651 HIS 0.001 0.000 HIS D 551 PHE 0.022 0.001 PHE D 856 TYR 0.009 0.001 TYR D 546 ARG 0.001 0.000 ARG D 921 Details of bonding type rmsd link_NAG-ASN : bond 0.01010 ( 4) link_NAG-ASN : angle 6.98332 ( 12) hydrogen bonds : bond 0.04370 ( 362) hydrogen bonds : angle 3.78471 ( 1071) covalent geometry : bond 0.00314 ( 7587) covalent geometry : angle 0.63144 (10396) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2432.56 seconds wall clock time: 42 minutes 58.79 seconds (2578.79 seconds total)