Starting phenix.real_space_refine on Thu Jul 2 07:42:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jjf_61525/07_2026/9jjf_61525.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jjf_61525/07_2026/9jjf_61525.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jjf_61525/07_2026/9jjf_61525.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jjf_61525/07_2026/9jjf_61525.map" model { file = "/net/cci-nas-00/data/ceres_data/9jjf_61525/07_2026/9jjf_61525.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jjf_61525/07_2026/9jjf_61525.cif" } resolution = 2.65 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= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 P 3 5.49 5 S 41 5.16 5 C 4937 2.51 5 N 1250 2.21 5 O 1386 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7618 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 941, 7549 Classifications: {'peptide': 941} Link IDs: {'PTRANS': 35, 'TRANS': 905} Chain breaks: 5 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'A2R': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Time building chain proxies: 1.54, per 1000 atoms: 0.20 Number of scatterers: 7618 At special positions: 0 Unit cell: (111.28, 71.69, 145.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 S 41 16.00 P 3 15.00 O 1386 8.00 N 1250 7.00 C 4937 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 BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN A1017 " Time building additional restraints: 0.53 Conformation dependent library (CDL) restraints added in 258.4 milliseconds 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1774 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 1 sheets defined 70.0% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 119 through 130 removed outlier: 3.753A pdb=" N VAL A 123 " --> pdb=" O ASP A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 169 removed outlier: 3.654A pdb=" N THR A 169 " --> pdb=" O LYS A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 193 removed outlier: 3.641A pdb=" N HIS A 186 " --> pdb=" O GLY A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 281 removed outlier: 4.150A pdb=" N ILE A 268 " --> pdb=" O TYR A 264 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLY A 269 " --> pdb=" O GLY A 265 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N MET A 270 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU A 275 " --> pdb=" O ARG A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 317 Processing helix chain 'A' and resid 330 through 339 removed outlier: 3.625A pdb=" N VAL A 334 " --> pdb=" O ALA A 330 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY A 335 " --> pdb=" O ALA A 331 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN A 339 " --> pdb=" O GLY A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 369 Processing helix chain 'A' and resid 374 through 386 removed outlier: 4.360A pdb=" N THR A 378 " --> pdb=" O GLY A 374 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU A 386 " --> pdb=" O ILE A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 417 removed outlier: 4.037A pdb=" N ALA A 408 " --> pdb=" O ASP A 404 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN A 417 " --> pdb=" O LEU A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 432 Processing helix chain 'A' and resid 433 through 441 Processing helix chain 'A' and resid 453 through 463 Processing helix chain 'A' and resid 465 through 476 removed outlier: 3.512A pdb=" N GLY A 476 " --> pdb=" O PHE A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 483 Processing helix chain 'A' and resid 484 through 492 Processing helix chain 'A' and resid 500 through 513 Processing helix chain 'A' and resid 518 through 531 Processing helix chain 'A' and resid 536 through 541 removed outlier: 3.728A pdb=" N LYS A 540 " --> pdb=" O SER A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 545 removed outlier: 3.769A pdb=" N PHE A 545 " --> pdb=" O GLY A 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 542 through 545' Processing helix chain 'A' and resid 578 through 590 Processing helix chain 'A' and resid 592 through 603 removed outlier: 3.580A pdb=" N GLY A 603 " --> pdb=" O LEU A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 627 Processing helix chain 'A' and resid 633 through 658 removed outlier: 3.994A pdb=" N GLU A 658 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 667 Processing helix chain 'A' and resid 671 through 675 removed outlier: 3.969A pdb=" N SER A 675 " --> pdb=" O ASP A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 686 removed outlier: 3.521A pdb=" N ALA A 686 " --> pdb=" O LEU A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 693 Processing helix chain 'A' and resid 694 through 706 Processing helix chain 'A' and resid 714 through 721 Processing helix chain 'A' and resid 727 through 732 removed outlier: 4.462A pdb=" N ILE A 731 " --> pdb=" O LEU A 727 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE A 732 " --> pdb=" O ILE A 728 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 727 through 732' Processing helix chain 'A' and resid 827 through 835 Processing helix chain 'A' and resid 836 through 861 Processing helix chain 'A' and resid 870 through 875 removed outlier: 3.771A pdb=" N GLY A 873 " --> pdb=" O LYS A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 899 Processing helix chain 'A' and resid 904 through 913 Processing helix chain 'A' and resid 915 through 935 removed outlier: 3.912A pdb=" N PHE A 919 " --> pdb=" O ASP A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 961 removed outlier: 4.954A pdb=" N ILE A 955 " --> pdb=" O SER A 951 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N PHE A 956 " --> pdb=" O LEU A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 966 removed outlier: 4.009A pdb=" N PHE A 965 " --> pdb=" O SER A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 1008 removed outlier: 3.825A pdb=" N LYS A 974 " --> pdb=" O LEU A 970 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ILE A 990 " --> pdb=" O ALA A 986 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ILE A 991 " --> pdb=" O GLN A 987 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA A1002 " --> pdb=" O ALA A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1035 Proline residue: A1030 - end of helix removed outlier: 3.720A pdb=" N TYR A1035 " --> pdb=" O TYR A1031 " (cutoff:3.500A) Processing helix chain 'A' and resid 1039 through 1044 Processing helix chain 'A' and resid 1057 through 1074 removed outlier: 4.017A pdb=" N LEU A1061 " --> pdb=" O ASP A1057 " (cutoff:3.500A) Proline residue: A1063 - end of helix Processing helix chain 'A' and resid 1076 through 1094 Processing helix chain 'A' and resid 1095 through 1113 removed outlier: 3.813A pdb=" N TYR A1105 " --> pdb=" O LYS A1101 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASP A1106 " --> pdb=" O PHE A1102 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR A1111 " --> pdb=" O LEU A1107 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N SER A1113 " --> pdb=" O GLN A1109 " (cutoff:3.500A) Processing helix chain 'A' and resid 1121 through 1131 Processing helix chain 'A' and resid 1154 through 1182 Processing helix chain 'A' and resid 1183 through 1206 Processing sheet with id=AA1, first strand: chain 'A' and resid 95 through 98 removed outlier: 7.938A pdb=" N LEU A 255 " --> pdb=" O PRO A 110 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU A 112 " --> pdb=" O LEU A 255 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ILE A 174 " --> pdb=" O ILE A 207 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ILE A 209 " --> pdb=" O ILE A 174 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N THR A 176 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N THR A 211 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE A 140 " --> pdb=" O ILE A 175 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N VAL A 139 " --> pdb=" O VAL A 297 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N LEU A 299 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N SER A 141 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N LEU A 301 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N THR A 143 " --> pdb=" O LEU A 301 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N VAL A 322 " --> pdb=" O VAL A 296 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU A 298 " --> pdb=" O VAL A 322 " (cutoff:3.500A) 441 hydrogen bonds defined for protein. 1308 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: 1.09 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2144 1.34 - 1.45: 1361 1.45 - 1.57: 4197 1.57 - 1.69: 7 1.69 - 1.81: 77 Bond restraints: 7786 Sorted by residual: bond pdb="C12' A2R A4001 " pdb="C13' A2R A4001 " ideal model delta sigma weight residual 1.524 1.309 0.215 2.00e-02 2.50e+03 1.15e+02 bond pdb=" C2 A2R A4001 " pdb=" N3 A2R A4001 " ideal model delta sigma weight residual 1.321 1.473 -0.152 2.00e-02 2.50e+03 5.74e+01 bond pdb=" C5 A2R A4001 " pdb=" C6 A2R A4001 " ideal model delta sigma weight residual 1.406 1.532 -0.126 2.00e-02 2.50e+03 3.97e+01 bond pdb=" C2' A2R A4001 " pdb=" O2' A2R A4001 " ideal model delta sigma weight residual 1.375 1.494 -0.119 2.00e-02 2.50e+03 3.53e+01 bond pdb="C14' A2R A4001 " pdb="O14' A2R A4001 " ideal model delta sigma weight residual 1.424 1.541 -0.117 2.00e-02 2.50e+03 3.44e+01 ... (remaining 7781 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 10269 2.70 - 5.40: 243 5.40 - 8.09: 38 8.09 - 10.79: 6 10.79 - 13.49: 6 Bond angle restraints: 10562 Sorted by residual: angle pdb=" O1 A2R A4001 " pdb=" P A2R A4001 " pdb=" O2 A2R A4001 " ideal model delta sigma weight residual 122.24 108.75 13.49 3.00e+00 1.11e-01 2.02e+01 angle pdb=" N PRO A 901 " pdb=" CA PRO A 901 " pdb=" C PRO A 901 " ideal model delta sigma weight residual 110.70 115.97 -5.27 1.22e+00 6.72e-01 1.86e+01 angle pdb=" O3 A2R A4001 " pdb=" P1 A2R A4001 " pdb="O15' A2R A4001 " ideal model delta sigma weight residual 97.52 109.77 -12.25 3.00e+00 1.11e-01 1.67e+01 angle pdb=" O11 A2R A4001 " pdb=" P1 A2R A4001 " pdb=" O12 A2R A4001 " ideal model delta sigma weight residual 122.43 110.19 12.24 3.00e+00 1.11e-01 1.66e+01 angle pdb=" C PHE A 937 " pdb=" N THR A 938 " pdb=" CA THR A 938 " ideal model delta sigma weight residual 122.61 128.61 -6.00 1.56e+00 4.11e-01 1.48e+01 ... (remaining 10557 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.80: 4359 14.80 - 29.60: 238 29.60 - 44.40: 61 44.40 - 59.20: 19 59.20 - 74.00: 19 Dihedral angle restraints: 4696 sinusoidal: 1952 harmonic: 2744 Sorted by residual: dihedral pdb=" CA PRO A 730 " pdb=" C PRO A 730 " pdb=" N ILE A 731 " pdb=" CA ILE A 731 " ideal model delta harmonic sigma weight residual -180.00 -157.92 -22.08 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA VAL A 735 " pdb=" C VAL A 735 " pdb=" N PRO A 736 " pdb=" CA PRO A 736 " ideal model delta harmonic sigma weight residual 180.00 159.99 20.01 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA PRO A1009 " pdb=" C PRO A1009 " pdb=" N SER A1010 " pdb=" CA SER A1010 " ideal model delta harmonic sigma weight residual -180.00 -161.07 -18.93 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 4693 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 1158 0.123 - 0.245: 50 0.245 - 0.368: 1 0.368 - 0.491: 0 0.491 - 0.613: 1 Chirality restraints: 1210 Sorted by residual: chirality pdb=" C2' A2R A4001 " pdb=" C1' A2R A4001 " pdb=" C3' A2R A4001 " pdb=" O2' A2R A4001 " both_signs ideal model delta sigma weight residual False -2.42 -3.04 0.61 2.00e-01 2.50e+01 9.41e+00 chirality pdb="C13' A2R A4001 " pdb="C12' A2R A4001 " pdb="C14' A2R A4001 " pdb="O13' A2R A4001 " both_signs ideal model delta sigma weight residual False -2.74 -2.42 -0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb="C14' A2R A4001 " pdb="C13' A2R A4001 " pdb="C15' A2R A4001 " pdb="O14' A2R A4001 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 1207 not shown) Planarity restraints: 1319 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A1010 " -0.055 5.00e-02 4.00e+02 8.25e-02 1.09e+01 pdb=" N PRO A1011 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO A1011 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A1011 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A1118 " 0.043 5.00e-02 4.00e+02 6.43e-02 6.62e+00 pdb=" N PRO A1119 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO A1119 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A1119 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A1119 " 0.042 5.00e-02 4.00e+02 6.32e-02 6.39e+00 pdb=" N PRO A1120 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO A1120 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A1120 " 0.037 5.00e-02 4.00e+02 ... (remaining 1316 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1772 2.79 - 3.31: 7216 3.31 - 3.84: 13138 3.84 - 4.37: 15684 4.37 - 4.90: 26162 Nonbonded interactions: 63972 Sorted by model distance: nonbonded pdb=" OD2 ASP A 984 " pdb=" OG1 THR A1088 " model vdw 2.258 3.040 nonbonded pdb=" OG SER A 484 " pdb=" OD1 ASP A 486 " model vdw 2.281 3.040 nonbonded pdb=" OE1 GLU A 893 " pdb=" OH TYR A 912 " model vdw 2.293 3.040 nonbonded pdb=" OG1 THR A 176 " pdb=" NE2 HIS A 250 " model vdw 2.304 3.120 nonbonded pdb=" OH TYR A 395 " pdb=" O GLN A 403 " model vdw 2.312 3.040 ... (remaining 63967 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.140 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.310 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:5.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 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 : 0.009 0.215 7788 Z= 0.395 Angle : 1.029 13.492 10568 Z= 0.521 Chirality : 0.061 0.613 1210 Planarity : 0.008 0.082 1318 Dihedral : 11.856 74.002 2922 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % 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: -3.69 (0.21), residues: 929 helix: -2.17 (0.16), residues: 604 sheet: -2.57 (0.58), residues: 53 loop : -2.60 (0.32), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 592 TYR 0.035 0.003 TYR A 638 PHE 0.024 0.003 PHE A 838 TRP 0.029 0.004 TRP A 431 HIS 0.010 0.003 HIS A 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00865 / 0.40 ( 7786) covalent geometry : angle 1.02813 / 0.52 (10562) hydrogen bonds : bond 0.11407 / 7.41 ( 441) hydrogen bonds : angle 6.13207 / 4.23 ( 1308) link_BETA1-4 : bond 0.00383 / 0.20 ( 1) link_BETA1-4 : angle 2.33457 / 1.55 ( 3) link_NAG-ASN : bond 0.00668 / 0.35 ( 1) link_NAG-ASN : angle 2.47463 / 1.64 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.261 Fit side-chains revert: symmetry clash REVERT: A 249 ASN cc_start: 0.8400 (m110) cc_final: 0.8181 (m-40) REVERT: A 273 ARG cc_start: 0.8068 (mtm180) cc_final: 0.7857 (mtm180) REVERT: A 308 VAL cc_start: 0.8599 (p) cc_final: 0.8308 (t) REVERT: A 433 ARG cc_start: 0.8572 (mmt180) cc_final: 0.8328 (mmt180) REVERT: A 438 LYS cc_start: 0.8146 (mtmm) cc_final: 0.7855 (mttt) REVERT: A 479 MET cc_start: 0.8140 (mmt) cc_final: 0.7893 (mmt) REVERT: A 540 LYS cc_start: 0.7939 (mtmt) cc_final: 0.7721 (mtmt) REVERT: A 594 GLU cc_start: 0.7511 (mm-30) cc_final: 0.7284 (mm-30) REVERT: A 709 MET cc_start: 0.7559 (ttp) cc_final: 0.7230 (ttp) REVERT: A 714 ARG cc_start: 0.7587 (mmm-85) cc_final: 0.6666 (mmp-170) REVERT: A 829 ARG cc_start: 0.7159 (mtt-85) cc_final: 0.6462 (mpp-170) REVERT: A 892 GLU cc_start: 0.7342 (tp30) cc_final: 0.6860 (tm-30) REVERT: A 1070 MET cc_start: 0.8800 (mmm) cc_final: 0.8590 (mmm) REVERT: A 1162 ASP cc_start: 0.7215 (m-30) cc_final: 0.6926 (m-30) REVERT: A 1189 ARG cc_start: 0.7615 (ttt180) cc_final: 0.7321 (tpp80) outliers start: 0 outliers final: 3 residues processed: 199 average time/residue: 0.5065 time to fit residues: 106.0440 Evaluate side-chains 144 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 141 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 ASN Chi-restraints excluded: chain A residue 435 ASP Chi-restraints excluded: chain A residue 486 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 0.0370 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.4980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.0980 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 0.5980 overall best weight: 0.3658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 426 ASN A1103 GLN A1160 GLN A1175 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.185447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.148640 restraints weight = 7958.220| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 1.58 r_work: 0.3446 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7788 Z= 0.126 Angle : 0.613 10.268 10568 Z= 0.305 Chirality : 0.042 0.160 1210 Planarity : 0.006 0.062 1318 Dihedral : 8.396 58.982 1124 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.08 % Allowed : 10.27 % Favored : 87.65 % 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: -1.53 (0.25), residues: 929 helix: -0.27 (0.19), residues: 601 sheet: -1.99 (0.66), residues: 52 loop : -2.27 (0.35), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 329 TYR 0.014 0.001 TYR A 395 PHE 0.012 0.001 PHE A 254 TRP 0.013 0.002 TRP A1100 HIS 0.006 0.001 HIS A 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 ( 7786) covalent geometry : angle 0.61259 / 0.30 (10562) hydrogen bonds : bond 0.04132 / 2.73 ( 441) hydrogen bonds : angle 4.49635 / 3.16 ( 1308) link_BETA1-4 : bond 0.00278 / 0.15 ( 1) link_BETA1-4 : angle 1.31553 / 0.82 ( 3) link_NAG-ASN : bond 0.00290 / 0.15 ( 1) link_NAG-ASN : angle 0.93870 / 0.60 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 245 MET cc_start: 0.6932 (tmt) cc_final: 0.6398 (tmt) REVERT: A 249 ASN cc_start: 0.8713 (m110) cc_final: 0.8499 (m110) REVERT: A 261 GLU cc_start: 0.6387 (mp0) cc_final: 0.5500 (tt0) REVERT: A 273 ARG cc_start: 0.8190 (mtm180) cc_final: 0.7950 (mtm180) REVERT: A 280 LYS cc_start: 0.7960 (mmtp) cc_final: 0.7136 (mtpt) REVERT: A 308 VAL cc_start: 0.8398 (p) cc_final: 0.8132 (t) REVERT: A 336 PHE cc_start: 0.6392 (t80) cc_final: 0.6168 (t80) REVERT: A 463 ASP cc_start: 0.7510 (m-30) cc_final: 0.7130 (m-30) REVERT: A 509 MET cc_start: 0.7435 (OUTLIER) cc_final: 0.5708 (mtp) REVERT: A 528 GLU cc_start: 0.7827 (pp20) cc_final: 0.7595 (mp0) REVERT: A 540 LYS cc_start: 0.7878 (mtmt) cc_final: 0.7670 (mtmt) REVERT: A 623 ARG cc_start: 0.8131 (tpt90) cc_final: 0.7842 (mmm160) REVERT: A 714 ARG cc_start: 0.8119 (mmm-85) cc_final: 0.6778 (mmp-170) REVERT: A 831 MET cc_start: 0.7436 (tpp) cc_final: 0.7067 (ppp) REVERT: A 892 GLU cc_start: 0.8068 (tp30) cc_final: 0.7687 (tm-30) REVERT: A 921 ASP cc_start: 0.8356 (m-30) cc_final: 0.8095 (m-30) REVERT: A 997 ILE cc_start: 0.8812 (OUTLIER) cc_final: 0.8571 (mp) REVERT: A 1157 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.7109 (mt-10) REVERT: A 1189 ARG cc_start: 0.8289 (ttt180) cc_final: 0.7284 (tpp80) outliers start: 17 outliers final: 6 residues processed: 150 average time/residue: 0.5052 time to fit residues: 79.5701 Evaluate side-chains 139 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 130 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 435 ASP Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 664 GLN Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1157 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 62 optimal weight: 0.4980 chunk 92 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 HIS ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1074 ASN A1160 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.182396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.144714 restraints weight = 7893.989| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 1.54 r_work: 0.3406 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 7788 Z= 0.150 Angle : 0.602 9.364 10568 Z= 0.296 Chirality : 0.042 0.154 1210 Planarity : 0.005 0.060 1318 Dihedral : 6.136 48.952 1120 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.83 % Allowed : 11.74 % Favored : 86.43 % 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: -0.50 (0.27), residues: 929 helix: 0.57 (0.20), residues: 605 sheet: -1.89 (0.67), residues: 52 loop : -1.96 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1016 TYR 0.019 0.002 TYR A 855 PHE 0.011 0.001 PHE A1089 TRP 0.013 0.002 TRP A1100 HIS 0.004 0.001 HIS A 876 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 ( 7786) covalent geometry : angle 0.60124 / 0.30 (10562) hydrogen bonds : bond 0.03942 / 2.61 ( 441) hydrogen bonds : angle 4.20848 / 2.99 ( 1308) link_BETA1-4 : bond 0.00103 / 0.05 ( 1) link_BETA1-4 : angle 1.39569 / 0.87 ( 3) link_NAG-ASN : bond 0.00159 / 0.08 ( 1) link_NAG-ASN : angle 1.13916 / 0.68 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 0.174 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 ARG cc_start: 0.4739 (OUTLIER) cc_final: 0.2823 (mpt-90) REVERT: A 267 GLU cc_start: 0.6912 (tm-30) cc_final: 0.6585 (tt0) REVERT: A 280 LYS cc_start: 0.8079 (mmtp) cc_final: 0.7374 (mtpt) REVERT: A 308 VAL cc_start: 0.8388 (p) cc_final: 0.8166 (t) REVERT: A 336 PHE cc_start: 0.6508 (t80) cc_final: 0.6292 (t80) REVERT: A 418 ARG cc_start: 0.8000 (mmm160) cc_final: 0.6998 (mtp85) REVERT: A 447 GLN cc_start: 0.7528 (pm20) cc_final: 0.7124 (mt0) REVERT: A 457 MET cc_start: 0.8935 (tpt) cc_final: 0.8661 (tpt) REVERT: A 463 ASP cc_start: 0.7502 (m-30) cc_final: 0.7032 (m-30) REVERT: A 509 MET cc_start: 0.7604 (OUTLIER) cc_final: 0.6195 (mtp) REVERT: A 512 ARG cc_start: 0.7543 (tpp80) cc_final: 0.7275 (mmm-85) REVERT: A 517 ILE cc_start: 0.7938 (OUTLIER) cc_final: 0.7639 (tp) REVERT: A 528 GLU cc_start: 0.7841 (pp20) cc_final: 0.7627 (mp0) REVERT: A 540 LYS cc_start: 0.7963 (mtmt) cc_final: 0.7611 (mtmt) REVERT: A 623 ARG cc_start: 0.8177 (tpt90) cc_final: 0.7914 (mmm160) REVERT: A 714 ARG cc_start: 0.8193 (mmm-85) cc_final: 0.7216 (mmm160) REVERT: A 831 MET cc_start: 0.7425 (tpp) cc_final: 0.7021 (mpp) REVERT: A 885 TRP cc_start: 0.7349 (t-100) cc_final: 0.6776 (t60) REVERT: A 892 GLU cc_start: 0.8110 (tp30) cc_final: 0.7755 (tm-30) REVERT: A 903 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.8071 (pptt) REVERT: A 921 ASP cc_start: 0.8407 (m-30) cc_final: 0.8095 (m-30) REVERT: A 992 LEU cc_start: 0.8215 (mt) cc_final: 0.7921 (tp) REVERT: A 1157 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.7076 (mt-10) REVERT: A 1189 ARG cc_start: 0.8289 (ttt180) cc_final: 0.7237 (tpp80) outliers start: 15 outliers final: 6 residues processed: 150 average time/residue: 0.4745 time to fit residues: 74.9361 Evaluate side-chains 146 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 135 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 426 ASN Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 664 GLN Chi-restraints excluded: chain A residue 903 LYS Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1157 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 35 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 chunk 54 optimal weight: 0.4980 chunk 67 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 32 optimal weight: 0.0980 chunk 31 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 HIS ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 ASN A 403 GLN A1160 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.181132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.143674 restraints weight = 7955.214| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 1.55 r_work: 0.3388 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 7788 Z= 0.159 Angle : 0.596 9.198 10568 Z= 0.294 Chirality : 0.043 0.158 1210 Planarity : 0.005 0.054 1318 Dihedral : 5.921 50.909 1118 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.69 % Allowed : 12.71 % Favored : 84.60 % 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: -0.08 (0.27), residues: 929 helix: 0.90 (0.21), residues: 607 sheet: -1.88 (0.64), residues: 52 loop : -1.82 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 273 TYR 0.016 0.002 TYR A 855 PHE 0.010 0.001 PHE A 956 TRP 0.012 0.001 TRP A1100 HIS 0.004 0.001 HIS A 876 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 ( 7786) covalent geometry : angle 0.59511 / 0.29 (10562) hydrogen bonds : bond 0.03914 / 2.58 ( 441) hydrogen bonds : angle 4.16350 / 2.96 ( 1308) link_BETA1-4 : bond 0.00086 / 0.05 ( 1) link_BETA1-4 : angle 1.48871 / 0.92 ( 3) link_NAG-ASN : bond 0.00030 / 0.02 ( 1) link_NAG-ASN : angle 1.12088 / 0.70 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 0.169 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 ARG cc_start: 0.4812 (OUTLIER) cc_final: 0.2818 (mpt-90) REVERT: A 267 GLU cc_start: 0.7082 (tm-30) cc_final: 0.6762 (tt0) REVERT: A 308 VAL cc_start: 0.8378 (p) cc_final: 0.8166 (t) REVERT: A 336 PHE cc_start: 0.6522 (t80) cc_final: 0.6304 (t80) REVERT: A 418 ARG cc_start: 0.7958 (mmm160) cc_final: 0.6884 (mtp85) REVERT: A 447 GLN cc_start: 0.7526 (pm20) cc_final: 0.7104 (mt0) REVERT: A 457 MET cc_start: 0.8955 (tpt) cc_final: 0.8593 (tpt) REVERT: A 512 ARG cc_start: 0.7496 (tpp80) cc_final: 0.7256 (mmm-85) REVERT: A 517 ILE cc_start: 0.7989 (OUTLIER) cc_final: 0.7607 (tp) REVERT: A 528 GLU cc_start: 0.7872 (pp20) cc_final: 0.7651 (mp0) REVERT: A 540 LYS cc_start: 0.7903 (mtmt) cc_final: 0.7550 (mtmt) REVERT: A 623 ARG cc_start: 0.8195 (tpt90) cc_final: 0.7978 (mmm160) REVERT: A 885 TRP cc_start: 0.7435 (t-100) cc_final: 0.6904 (t60) REVERT: A 892 GLU cc_start: 0.8163 (tp30) cc_final: 0.7826 (tm-30) REVERT: A 992 LEU cc_start: 0.8281 (mt) cc_final: 0.7991 (tp) REVERT: A 1157 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.7125 (mt-10) REVERT: A 1159 GLU cc_start: 0.7900 (tp30) cc_final: 0.7681 (tp30) REVERT: A 1189 ARG cc_start: 0.8287 (ttt180) cc_final: 0.7281 (tpp80) outliers start: 22 outliers final: 9 residues processed: 145 average time/residue: 0.4788 time to fit residues: 73.0459 Evaluate side-chains 143 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 131 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 435 ASP Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 664 GLN Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1157 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 17 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 79 optimal weight: 0.5980 chunk 27 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 HIS ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1160 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.180793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.143953 restraints weight = 7939.650| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 1.59 r_work: 0.3393 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 7788 Z= 0.147 Angle : 0.579 6.899 10568 Z= 0.287 Chirality : 0.042 0.163 1210 Planarity : 0.004 0.053 1318 Dihedral : 5.824 50.564 1118 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.96 % Allowed : 14.06 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.22 (0.27), residues: 929 helix: 1.13 (0.21), residues: 606 sheet: -1.84 (0.64), residues: 52 loop : -1.66 (0.37), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 935 TYR 0.014 0.001 TYR A 855 PHE 0.010 0.001 PHE A 956 TRP 0.012 0.001 TRP A1100 HIS 0.004 0.001 HIS A 876 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 ( 7786) covalent geometry : angle 0.57824 / 0.29 (10562) hydrogen bonds : bond 0.03802 / 2.50 ( 441) hydrogen bonds : angle 4.08415 / 2.90 ( 1308) link_BETA1-4 : bond 0.00019 / 0.01 ( 1) link_BETA1-4 : angle 1.47276 / 0.92 ( 3) link_NAG-ASN : bond 0.00004 / 0.00 ( 1) link_NAG-ASN : angle 1.03058 / 0.64 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 0.183 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 ARG cc_start: 0.4848 (OUTLIER) cc_final: 0.2848 (mpt-90) REVERT: A 267 GLU cc_start: 0.7123 (tm-30) cc_final: 0.6814 (tt0) REVERT: A 275 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7997 (mp0) REVERT: A 308 VAL cc_start: 0.8358 (p) cc_final: 0.8156 (t) REVERT: A 336 PHE cc_start: 0.6658 (t80) cc_final: 0.6386 (t80) REVERT: A 418 ARG cc_start: 0.7970 (mmm160) cc_final: 0.6891 (mtp85) REVERT: A 426 ASN cc_start: 0.7953 (p0) cc_final: 0.7648 (m-40) REVERT: A 447 GLN cc_start: 0.7535 (pm20) cc_final: 0.7077 (mt0) REVERT: A 457 MET cc_start: 0.8955 (tpt) cc_final: 0.8571 (tpt) REVERT: A 540 LYS cc_start: 0.7913 (mtmt) cc_final: 0.7571 (mtmt) REVERT: A 885 TRP cc_start: 0.7371 (t-100) cc_final: 0.7026 (t60) REVERT: A 892 GLU cc_start: 0.8144 (tp30) cc_final: 0.7790 (tm-30) REVERT: A 992 LEU cc_start: 0.8276 (mt) cc_final: 0.7999 (tp) REVERT: A 1090 GLU cc_start: 0.8483 (mm-30) cc_final: 0.7938 (pt0) REVERT: A 1157 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.7124 (mt-10) REVERT: A 1189 ARG cc_start: 0.8271 (ttt180) cc_final: 0.7274 (tpp80) outliers start: 16 outliers final: 10 residues processed: 147 average time/residue: 0.4672 time to fit residues: 72.4867 Evaluate side-chains 140 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 435 ASP Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 664 GLN Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1157 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 27 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 91 optimal weight: 0.1980 chunk 67 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 HIS ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1160 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.177722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.140671 restraints weight = 7926.384| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 1.54 r_work: 0.3356 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 7788 Z= 0.216 Angle : 0.646 6.661 10568 Z= 0.320 Chirality : 0.045 0.182 1210 Planarity : 0.005 0.054 1318 Dihedral : 6.048 50.004 1118 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.69 % Allowed : 14.67 % Favored : 82.64 % 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: 0.20 (0.27), residues: 929 helix: 1.03 (0.21), residues: 614 sheet: -1.68 (0.66), residues: 52 loop : -1.56 (0.37), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 273 TYR 0.018 0.002 TYR A 855 PHE 0.015 0.002 PHE A 956 TRP 0.014 0.002 TRP A1100 HIS 0.004 0.001 HIS A 832 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.22 ( 7786) covalent geometry : angle 0.64527 / 0.32 (10562) hydrogen bonds : bond 0.04253 / 2.78 ( 441) hydrogen bonds : angle 4.22119 / 2.99 ( 1308) link_BETA1-4 : bond 0.00223 / 0.12 ( 1) link_BETA1-4 : angle 1.78356 / 1.13 ( 3) link_NAG-ASN : bond 0.00271 / 0.14 ( 1) link_NAG-ASN : angle 1.48017 / 0.94 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 0.181 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 ARG cc_start: 0.4951 (OUTLIER) cc_final: 0.2977 (mpt-90) REVERT: A 267 GLU cc_start: 0.7211 (tm-30) cc_final: 0.6836 (tt0) REVERT: A 273 ARG cc_start: 0.8404 (mtm110) cc_final: 0.8086 (mtm180) REVERT: A 274 ILE cc_start: 0.8416 (OUTLIER) cc_final: 0.8185 (mp) REVERT: A 447 GLN cc_start: 0.7633 (pm20) cc_final: 0.7130 (mt0) REVERT: A 511 LYS cc_start: 0.7607 (mttm) cc_final: 0.6849 (mmtt) REVERT: A 540 LYS cc_start: 0.8284 (mtmt) cc_final: 0.7958 (mtmt) REVERT: A 885 TRP cc_start: 0.7534 (t-100) cc_final: 0.7242 (t60) REVERT: A 892 GLU cc_start: 0.8221 (tp30) cc_final: 0.7922 (tm-30) REVERT: A 992 LEU cc_start: 0.8396 (mt) cc_final: 0.8105 (tp) REVERT: A 1157 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7302 (mt-10) REVERT: A 1189 ARG cc_start: 0.8282 (ttt180) cc_final: 0.7257 (tpp80) outliers start: 22 outliers final: 12 residues processed: 144 average time/residue: 0.4807 time to fit residues: 72.8136 Evaluate side-chains 142 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 435 ASP Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 664 GLN Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 828 ASP Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1157 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 82 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 HIS ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1160 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.178418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.142409 restraints weight = 7886.209| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.50 r_work: 0.3381 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 7788 Z= 0.197 Angle : 0.637 7.315 10568 Z= 0.315 Chirality : 0.044 0.225 1210 Planarity : 0.004 0.055 1318 Dihedral : 6.061 49.379 1118 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.93 % Allowed : 14.30 % Favored : 82.76 % 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: 0.29 (0.28), residues: 929 helix: 1.10 (0.21), residues: 614 sheet: -1.62 (0.66), residues: 52 loop : -1.51 (0.37), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 512 TYR 0.016 0.002 TYR A 855 PHE 0.012 0.002 PHE A 956 TRP 0.014 0.002 TRP A1100 HIS 0.003 0.001 HIS A 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.20 ( 7786) covalent geometry : angle 0.63602 / 0.31 (10562) hydrogen bonds : bond 0.04157 / 2.71 ( 441) hydrogen bonds : angle 4.20742 / 2.97 ( 1308) link_BETA1-4 : bond 0.00379 / 0.20 ( 1) link_BETA1-4 : angle 1.73746 / 1.11 ( 3) link_NAG-ASN : bond 0.00208 / 0.11 ( 1) link_NAG-ASN : angle 1.35770 / 0.85 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 ARG cc_start: 0.4915 (OUTLIER) cc_final: 0.2945 (mpt-90) REVERT: A 261 GLU cc_start: 0.6338 (mp0) cc_final: 0.5486 (mm-30) REVERT: A 267 GLU cc_start: 0.7207 (tm-30) cc_final: 0.6801 (tt0) REVERT: A 274 ILE cc_start: 0.8339 (OUTLIER) cc_final: 0.8093 (mp) REVERT: A 276 GLU cc_start: 0.7741 (tt0) cc_final: 0.7470 (tt0) REVERT: A 447 GLN cc_start: 0.7635 (pm20) cc_final: 0.7145 (mt0) REVERT: A 463 ASP cc_start: 0.7608 (m-30) cc_final: 0.7221 (m-30) REVERT: A 511 LYS cc_start: 0.7625 (mttm) cc_final: 0.6871 (mmtt) REVERT: A 540 LYS cc_start: 0.8041 (mtmt) cc_final: 0.7788 (mtmt) REVERT: A 612 MET cc_start: 0.9091 (OUTLIER) cc_final: 0.8580 (ttt) REVERT: A 728 ILE cc_start: 0.6927 (OUTLIER) cc_final: 0.6637 (mt) REVERT: A 831 MET cc_start: 0.7222 (OUTLIER) cc_final: 0.6744 (ppp) REVERT: A 885 TRP cc_start: 0.7517 (t-100) cc_final: 0.7222 (t60) REVERT: A 892 GLU cc_start: 0.8127 (tp30) cc_final: 0.7834 (tm-30) REVERT: A 992 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8085 (tp) REVERT: A 1157 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7281 (mt-10) REVERT: A 1189 ARG cc_start: 0.8199 (ttt180) cc_final: 0.7227 (tpp80) outliers start: 24 outliers final: 12 residues processed: 142 average time/residue: 0.4454 time to fit residues: 66.7021 Evaluate side-chains 147 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 435 ASP Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 612 MET Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 664 GLN Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 728 ILE Chi-restraints excluded: chain A residue 831 MET Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1157 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 29 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 39 optimal weight: 0.5980 chunk 79 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 116 HIS A 186 HIS ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 ASN A1160 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.180078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.142960 restraints weight = 7956.441| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 1.52 r_work: 0.3398 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 7788 Z= 0.149 Angle : 0.599 7.231 10568 Z= 0.297 Chirality : 0.043 0.247 1210 Planarity : 0.004 0.052 1318 Dihedral : 5.887 49.215 1118 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.20 % Allowed : 15.65 % Favored : 82.15 % 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: 0.53 (0.28), residues: 929 helix: 1.30 (0.21), residues: 612 sheet: -1.74 (0.66), residues: 52 loop : -1.42 (0.38), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 512 TYR 0.015 0.001 TYR A 395 PHE 0.009 0.001 PHE A 956 TRP 0.012 0.001 TRP A1100 HIS 0.003 0.001 HIS A 832 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 ( 7786) covalent geometry : angle 0.59880 / 0.30 (10562) hydrogen bonds : bond 0.03783 / 2.47 ( 441) hydrogen bonds : angle 4.09650 / 2.89 ( 1308) link_BETA1-4 : bond 0.00013 / 0.01 ( 1) link_BETA1-4 : angle 1.53972 / 0.97 ( 3) link_NAG-ASN : bond 0.00022 / 0.01 ( 1) link_NAG-ASN : angle 0.97868 / 0.60 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 139 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 ARG cc_start: 0.4981 (OUTLIER) cc_final: 0.2930 (mpt-90) REVERT: A 261 GLU cc_start: 0.6352 (mp0) cc_final: 0.5563 (tt0) REVERT: A 267 GLU cc_start: 0.7201 (tm-30) cc_final: 0.6829 (tt0) REVERT: A 276 GLU cc_start: 0.7753 (tt0) cc_final: 0.7477 (tt0) REVERT: A 336 PHE cc_start: 0.6638 (t80) cc_final: 0.6426 (t80) REVERT: A 447 GLN cc_start: 0.7618 (pm20) cc_final: 0.7128 (mt0) REVERT: A 463 ASP cc_start: 0.7644 (m-30) cc_final: 0.7250 (m-30) REVERT: A 494 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.7129 (mp0) REVERT: A 540 LYS cc_start: 0.7954 (mtmt) cc_final: 0.7679 (mtmt) REVERT: A 728 ILE cc_start: 0.6950 (OUTLIER) cc_final: 0.6712 (mt) REVERT: A 828 ASP cc_start: 0.6047 (t70) cc_final: 0.5655 (p0) REVERT: A 885 TRP cc_start: 0.7438 (t-100) cc_final: 0.7161 (t60) REVERT: A 892 GLU cc_start: 0.8126 (tp30) cc_final: 0.7800 (tm-30) REVERT: A 992 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.8037 (tp) REVERT: A 1090 GLU cc_start: 0.8441 (mm-30) cc_final: 0.7927 (pt0) REVERT: A 1157 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7252 (mt-10) REVERT: A 1189 ARG cc_start: 0.8123 (ttt180) cc_final: 0.7281 (tpp80) outliers start: 18 outliers final: 9 residues processed: 146 average time/residue: 0.4488 time to fit residues: 69.2547 Evaluate side-chains 145 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 435 ASP Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 664 GLN Chi-restraints excluded: chain A residue 728 ILE Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1157 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 28 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 92 optimal weight: 5.9990 chunk 39 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 58 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 HIS ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1160 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.180313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.143335 restraints weight = 7913.871| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 1.52 r_work: 0.3401 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 7788 Z= 0.144 Angle : 0.604 7.393 10568 Z= 0.297 Chirality : 0.044 0.484 1210 Planarity : 0.004 0.051 1318 Dihedral : 5.814 49.683 1118 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.32 % Allowed : 15.89 % Favored : 81.78 % 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: 0.60 (0.28), residues: 929 helix: 1.36 (0.21), residues: 618 sheet: -1.72 (0.66), residues: 52 loop : -1.43 (0.38), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 273 TYR 0.012 0.001 TYR A 395 PHE 0.009 0.001 PHE A 956 TRP 0.011 0.001 TRP A1100 HIS 0.002 0.001 HIS A 876 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.14 ( 7786) covalent geometry : angle 0.60304 / 0.30 (10562) hydrogen bonds : bond 0.03728 / 2.43 ( 441) hydrogen bonds : angle 4.06588 / 2.88 ( 1308) link_BETA1-4 : bond 0.00057 / 0.03 ( 1) link_BETA1-4 : angle 1.49474 / 0.94 ( 3) link_NAG-ASN : bond 0.00010 / 0.01 ( 1) link_NAG-ASN : angle 0.98927 / 0.60 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 ARG cc_start: 0.5109 (OUTLIER) cc_final: 0.3024 (mpt-90) REVERT: A 261 GLU cc_start: 0.6373 (mp0) cc_final: 0.5569 (tt0) REVERT: A 267 GLU cc_start: 0.7257 (tm-30) cc_final: 0.6900 (tt0) REVERT: A 275 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.8027 (mp0) REVERT: A 336 PHE cc_start: 0.6653 (t80) cc_final: 0.6440 (t80) REVERT: A 447 GLN cc_start: 0.7613 (pm20) cc_final: 0.7132 (mt0) REVERT: A 463 ASP cc_start: 0.7628 (m-30) cc_final: 0.7246 (m-30) REVERT: A 494 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.7081 (mp0) REVERT: A 540 LYS cc_start: 0.7959 (mtmt) cc_final: 0.7617 (mtmt) REVERT: A 828 ASP cc_start: 0.6198 (t70) cc_final: 0.5838 (p0) REVERT: A 892 GLU cc_start: 0.8177 (tp30) cc_final: 0.7835 (tm-30) REVERT: A 992 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.8035 (tp) REVERT: A 1090 GLU cc_start: 0.8450 (mm-30) cc_final: 0.7938 (pt0) REVERT: A 1157 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7260 (mt-10) REVERT: A 1189 ARG cc_start: 0.8078 (ttt180) cc_final: 0.7242 (tpp80) outliers start: 19 outliers final: 9 residues processed: 145 average time/residue: 0.4916 time to fit residues: 75.1519 Evaluate side-chains 146 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 132 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 435 ASP Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 664 GLN Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1157 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 93 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 86 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 63 optimal weight: 0.2980 chunk 39 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 HIS ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1160 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.180416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.145026 restraints weight = 7912.832| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 1.59 r_work: 0.3412 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 7788 Z= 0.139 Angle : 0.596 7.147 10568 Z= 0.296 Chirality : 0.042 0.165 1210 Planarity : 0.004 0.050 1318 Dihedral : 5.737 49.720 1118 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.83 % Allowed : 16.99 % Favored : 81.17 % 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: 0.73 (0.28), residues: 929 helix: 1.46 (0.21), residues: 616 sheet: -1.71 (0.66), residues: 52 loop : -1.37 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 273 TYR 0.012 0.001 TYR A 855 PHE 0.009 0.001 PHE A 545 TRP 0.020 0.001 TRP A 885 HIS 0.002 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 7786) covalent geometry : angle 0.59556 / 0.30 (10562) hydrogen bonds : bond 0.03680 / 2.40 ( 441) hydrogen bonds : angle 4.05340 / 2.86 ( 1308) link_BETA1-4 : bond 0.00005 / 0.00 ( 1) link_BETA1-4 : angle 1.44798 / 0.91 ( 3) link_NAG-ASN : bond 0.00045 / 0.02 ( 1) link_NAG-ASN : angle 0.93872 / 0.57 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 0.173 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 ARG cc_start: 0.5021 (OUTLIER) cc_final: 0.2988 (mpt-90) REVERT: A 261 GLU cc_start: 0.6424 (mp0) cc_final: 0.5525 (tt0) REVERT: A 267 GLU cc_start: 0.7246 (tm-30) cc_final: 0.6925 (tt0) REVERT: A 275 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8010 (mp0) REVERT: A 447 GLN cc_start: 0.7600 (pm20) cc_final: 0.7115 (mt0) REVERT: A 463 ASP cc_start: 0.7549 (m-30) cc_final: 0.7160 (m-30) REVERT: A 494 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7090 (mp0) REVERT: A 540 LYS cc_start: 0.7939 (mtmt) cc_final: 0.7603 (mtmt) REVERT: A 612 MET cc_start: 0.9056 (OUTLIER) cc_final: 0.8517 (ttt) REVERT: A 828 ASP cc_start: 0.6183 (t70) cc_final: 0.5905 (p0) REVERT: A 892 GLU cc_start: 0.8202 (tp30) cc_final: 0.7884 (tm-30) REVERT: A 992 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.8023 (tp) REVERT: A 1090 GLU cc_start: 0.8450 (mm-30) cc_final: 0.7922 (pt0) REVERT: A 1157 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.7232 (mt-10) REVERT: A 1161 MET cc_start: 0.7723 (mmp) cc_final: 0.7301 (mmp) REVERT: A 1189 ARG cc_start: 0.8037 (ttt180) cc_final: 0.7231 (tpp80) outliers start: 15 outliers final: 10 residues processed: 137 average time/residue: 0.4542 time to fit residues: 65.5890 Evaluate side-chains 146 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 435 ASP Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 612 MET Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 664 GLN Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1157 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 43 optimal weight: 0.7980 chunk 8 optimal weight: 0.0980 chunk 60 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 HIS ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 ASN A1160 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.180020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.144319 restraints weight = 7933.685| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 1.70 r_work: 0.3400 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7788 Z= 0.150 Angle : 0.610 7.164 10568 Z= 0.303 Chirality : 0.043 0.166 1210 Planarity : 0.004 0.051 1318 Dihedral : 5.740 49.855 1118 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.96 % Allowed : 16.63 % Favored : 81.42 % 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: 0.71 (0.28), residues: 929 helix: 1.47 (0.21), residues: 611 sheet: -1.62 (0.67), residues: 52 loop : -1.40 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 935 TYR 0.013 0.001 TYR A 395 PHE 0.010 0.001 PHE A 956 TRP 0.020 0.001 TRP A 885 HIS 0.002 0.001 HIS A 876 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 ( 7786) covalent geometry : angle 0.60980 / 0.30 (10562) hydrogen bonds : bond 0.03765 / 2.47 ( 441) hydrogen bonds : angle 4.08808 / 2.88 ( 1308) link_BETA1-4 : bond 0.00027 / 0.01 ( 1) link_BETA1-4 : angle 1.49321 / 0.93 ( 3) link_NAG-ASN : bond 0.00027 / 0.01 ( 1) link_NAG-ASN : angle 1.01013 / 0.61 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2693.10 seconds wall clock time: 46 minutes 24.77 seconds (2784.77 seconds total)