Starting phenix.real_space_refine on Tue Apr 29 10:58:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jup_61833/04_2025/9jup_61833.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jup_61833/04_2025/9jup_61833.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jup_61833/04_2025/9jup_61833.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jup_61833/04_2025/9jup_61833.map" model { file = "/net/cci-nas-00/data/ceres_data/9jup_61833/04_2025/9jup_61833.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jup_61833/04_2025/9jup_61833.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 40 5.16 5 C 5521 2.51 5 N 1483 2.21 5 O 1604 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 8656 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1118, 8592 Classifications: {'peptide': 1118} Link IDs: {'PTRANS': 29, 'TRANS': 1088} Chain breaks: 2 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ANP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 5.11, per 1000 atoms: 0.59 Number of scatterers: 8656 At special positions: 0 Unit cell: (104.16, 83.7, 130.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 40 16.00 P 6 15.00 Mg 2 11.99 O 1604 8.00 N 1483 7.00 C 5521 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.18 Conformation dependent library (CDL) restraints added in 1.1 seconds 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2072 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 5 sheets defined 69.5% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 29 through 34 removed outlier: 3.576A pdb=" N ARG A 34 " --> pdb=" O GLU A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 74 removed outlier: 4.291A pdb=" N LEU A 58 " --> pdb=" O HIS A 54 " (cutoff:3.500A) Proline residue: A 59 - end of helix removed outlier: 4.763A pdb=" N ASN A 70 " --> pdb=" O ALA A 66 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SER A 71 " --> pdb=" O ASP A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 132 removed outlier: 3.747A pdb=" N ILE A 108 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N TRP A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 139 removed outlier: 3.782A pdb=" N PHE A 138 " --> pdb=" O ASP A 134 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP A 139 " --> pdb=" O ILE A 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 134 through 139' Processing helix chain 'A' and resid 143 through 163 removed outlier: 4.042A pdb=" N ASP A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ALA A 155 " --> pdb=" O ILE A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 187 removed outlier: 3.885A pdb=" N GLY A 167 " --> pdb=" O SER A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 195 Processing helix chain 'A' and resid 197 through 236 Processing helix chain 'A' and resid 236 through 243 Processing helix chain 'A' and resid 245 through 299 removed outlier: 3.939A pdb=" N ILE A 259 " --> pdb=" O SER A 255 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 324 removed outlier: 3.592A pdb=" N ALA A 307 " --> pdb=" O ASN A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 346 removed outlier: 3.858A pdb=" N MET A 328 " --> pdb=" O SER A 324 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA A 332 " --> pdb=" O MET A 328 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS A 333 " --> pdb=" O ALA A 329 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE A 344 " --> pdb=" O LYS A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 417 Processing helix chain 'A' and resid 433 through 437 Processing helix chain 'A' and resid 438 through 445 removed outlier: 3.931A pdb=" N LEU A 442 " --> pdb=" O LYS A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 466 Processing helix chain 'A' and resid 472 through 483 Processing helix chain 'A' and resid 485 through 491 removed outlier: 3.525A pdb=" N LYS A 491 " --> pdb=" O SER A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 498 Processing helix chain 'A' and resid 508 through 523 removed outlier: 3.555A pdb=" N LYS A 512 " --> pdb=" O SER A 508 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN A 513 " --> pdb=" O GLY A 509 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS A 523 " --> pdb=" O ARG A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 553 Processing helix chain 'A' and resid 564 through 571 removed outlier: 3.581A pdb=" N LYS A 570 " --> pdb=" O SER A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 693 Processing helix chain 'A' and resid 696 through 728 removed outlier: 3.523A pdb=" N SER A 726 " --> pdb=" O SER A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 787 removed outlier: 3.636A pdb=" N ASN A 787 " --> pdb=" O ALA A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 793 Processing helix chain 'A' and resid 798 through 816 Processing helix chain 'A' and resid 820 through 841 Processing helix chain 'A' and resid 844 through 870 Proline residue: A 854 - end of helix Processing helix chain 'A' and resid 874 through 891 removed outlier: 4.193A pdb=" N HIS A 878 " --> pdb=" O LEU A 874 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY A 881 " --> pdb=" O ALA A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 898 Processing helix chain 'A' and resid 900 through 954 Proline residue: A 914 - end of helix Processing helix chain 'A' and resid 959 through 981 Processing helix chain 'A' and resid 982 through 1002 removed outlier: 3.545A pdb=" N ARG A1002 " --> pdb=" O GLU A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1064 through 1073 removed outlier: 3.605A pdb=" N ILE A1069 " --> pdb=" O LYS A1065 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN A1073 " --> pdb=" O ILE A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1100 removed outlier: 3.578A pdb=" N LYS A1100 " --> pdb=" O LYS A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1115 through 1122 Processing helix chain 'A' and resid 1129 through 1139 Processing helix chain 'A' and resid 1141 through 1148 Processing helix chain 'A' and resid 1150 through 1154 Processing helix chain 'A' and resid 1164 through 1180 removed outlier: 3.839A pdb=" N LYS A1180 " --> pdb=" O ALA A1176 " (cutoff:3.500A) Processing helix chain 'A' and resid 1194 through 1209 Processing sheet with id=AA1, first strand: chain 'A' and resid 384 through 393 removed outlier: 5.121A pdb=" N VAL A 373 " --> pdb=" O ASN A 388 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N CYS A 390 " --> pdb=" O LYS A 371 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LYS A 371 " --> pdb=" O CYS A 390 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N SER A 392 " --> pdb=" O GLU A 369 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLU A 369 " --> pdb=" O SER A 392 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 446 through 449 removed outlier: 6.532A pdb=" N LEU A 528 " --> pdb=" O LEU A 559 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N ILE A 561 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU A 530 " --> pdb=" O ILE A 561 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N THR A 398 " --> pdb=" O LEU A 573 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ALA A 575 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ALA A 400 " --> pdb=" O ALA A 575 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N LEU A 577 " --> pdb=" O ALA A 400 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL A 402 " --> pdb=" O LEU A 577 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1042 through 1048 removed outlier: 6.874A pdb=" N ARG A1043 " --> pdb=" O ASP A1030 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ASP A1030 " --> pdb=" O ARG A1043 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N LEU A1045 " --> pdb=" O HIS A1028 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1055 through 1058 removed outlier: 6.166A pdb=" N ALA A1056 " --> pdb=" O ALA A1231 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ILE A1233 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N VAL A1058 " --> pdb=" O ILE A1233 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ASP A1234 " --> pdb=" O LYS A1237 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1102 through 1103 597 hydrogen bonds defined for protein. 1755 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: 2.93 Time building geometry restraints manager: 2.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2814 1.34 - 1.46: 1813 1.46 - 1.58: 4112 1.58 - 1.69: 10 1.69 - 1.81: 66 Bond restraints: 8815 Sorted by residual: bond pdb=" N3B ANP A1304 " pdb=" PG ANP A1304 " ideal model delta sigma weight residual 1.795 1.632 0.163 2.00e-02 2.50e+03 6.65e+01 bond pdb=" N3B ANP A1303 " pdb=" PG ANP A1303 " ideal model delta sigma weight residual 1.795 1.633 0.162 2.00e-02 2.50e+03 6.56e+01 bond pdb=" O3A ANP A1304 " pdb=" PB ANP A1304 " ideal model delta sigma weight residual 1.700 1.602 0.098 2.00e-02 2.50e+03 2.40e+01 bond pdb=" O3A ANP A1303 " pdb=" PB ANP A1303 " ideal model delta sigma weight residual 1.700 1.605 0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" O5' ANP A1303 " pdb=" PA ANP A1303 " ideal model delta sigma weight residual 1.655 1.603 0.052 2.00e-02 2.50e+03 6.78e+00 ... (remaining 8810 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 11797 1.99 - 3.98: 111 3.98 - 5.97: 30 5.97 - 7.96: 7 7.96 - 9.95: 3 Bond angle restraints: 11948 Sorted by residual: angle pdb=" PA ANP A1303 " pdb=" O3A ANP A1303 " pdb=" PB ANP A1303 " ideal model delta sigma weight residual 125.41 135.36 -9.95 3.00e+00 1.11e-01 1.10e+01 angle pdb=" N3B ANP A1303 " pdb=" PG ANP A1303 " pdb=" O2G ANP A1303 " ideal model delta sigma weight residual 101.05 110.89 -9.84 3.00e+00 1.11e-01 1.08e+01 angle pdb=" N3B ANP A1304 " pdb=" PG ANP A1304 " pdb=" O2G ANP A1304 " ideal model delta sigma weight residual 101.05 109.24 -8.19 3.00e+00 1.11e-01 7.45e+00 angle pdb=" PA ANP A1304 " pdb=" O3A ANP A1304 " pdb=" PB ANP A1304 " ideal model delta sigma weight residual 125.41 132.49 -7.08 3.00e+00 1.11e-01 5.57e+00 angle pdb=" N VAL A 198 " pdb=" CA VAL A 198 " pdb=" C VAL A 198 " ideal model delta sigma weight residual 108.88 113.70 -4.82 2.16e+00 2.14e-01 4.98e+00 ... (remaining 11943 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.70: 5111 32.70 - 65.39: 155 65.39 - 98.09: 25 98.09 - 130.79: 1 130.79 - 163.49: 1 Dihedral angle restraints: 5293 sinusoidal: 2074 harmonic: 3219 Sorted by residual: dihedral pdb=" O1A ANP A1303 " pdb=" O3A ANP A1303 " pdb=" PA ANP A1303 " pdb=" PB ANP A1303 " ideal model delta sinusoidal sigma weight residual 83.11 -80.38 163.49 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" O1A ANP A1304 " pdb=" O3A ANP A1304 " pdb=" PA ANP A1304 " pdb=" PB ANP A1304 " ideal model delta sinusoidal sigma weight residual 83.11 -17.72 100.83 1 3.00e+01 1.11e-03 1.27e+01 dihedral pdb=" O1B ANP A1304 " pdb=" N3B ANP A1304 " pdb=" PB ANP A1304 " pdb=" PG ANP A1304 " ideal model delta sinusoidal sigma weight residual 35.15 -61.45 96.60 1 3.00e+01 1.11e-03 1.19e+01 ... (remaining 5290 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1246 0.063 - 0.125: 130 0.125 - 0.188: 5 0.188 - 0.251: 0 0.251 - 0.313: 2 Chirality restraints: 1383 Sorted by residual: chirality pdb=" C3' ANP A1304 " pdb=" C2' ANP A1304 " pdb=" C4' ANP A1304 " pdb=" O3' ANP A1304 " both_signs ideal model delta sigma weight residual False -2.36 -2.67 0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" C3' ANP A1303 " pdb=" C2' ANP A1303 " pdb=" C4' ANP A1303 " pdb=" O3' ANP A1303 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" C2' ANP A1303 " pdb=" C1' ANP A1303 " pdb=" C3' ANP A1303 " pdb=" O2' ANP A1303 " both_signs ideal model delta sigma weight residual False -2.72 -2.54 -0.18 2.00e-01 2.50e+01 8.31e-01 ... (remaining 1380 not shown) Planarity restraints: 1503 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 702 " -0.009 2.00e-02 2.50e+03 1.83e-02 3.34e+00 pdb=" C LEU A 702 " 0.032 2.00e-02 2.50e+03 pdb=" O LEU A 702 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY A 703 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 705 " 0.009 2.00e-02 2.50e+03 1.82e-02 3.32e+00 pdb=" C VAL A 705 " -0.032 2.00e-02 2.50e+03 pdb=" O VAL A 705 " 0.012 2.00e-02 2.50e+03 pdb=" N GLY A 706 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 706 " -0.009 2.00e-02 2.50e+03 1.72e-02 2.96e+00 pdb=" C GLY A 706 " 0.030 2.00e-02 2.50e+03 pdb=" O GLY A 706 " -0.011 2.00e-02 2.50e+03 pdb=" N SER A 707 " -0.010 2.00e-02 2.50e+03 ... (remaining 1500 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 56 2.55 - 3.14: 7090 3.14 - 3.73: 14166 3.73 - 4.31: 19285 4.31 - 4.90: 32541 Nonbonded interactions: 73138 Sorted by model distance: nonbonded pdb="MG MG A1301 " pdb=" O3G ANP A1303 " model vdw 1.964 2.170 nonbonded pdb=" OG SER A 410 " pdb="MG MG A1301 " model vdw 2.014 2.170 nonbonded pdb=" OE1 GLN A 451 " pdb="MG MG A1301 " model vdw 2.086 2.170 nonbonded pdb=" OG SER A1066 " pdb="MG MG A1302 " model vdw 2.111 2.170 nonbonded pdb=" NE2 GLN A 513 " pdb=" O THR A 534 " model vdw 2.229 3.120 ... (remaining 73133 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.580 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: 0.000 Extract box with map and model: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 22.600 Find NCS groups from input model: 0.130 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 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 : 0.004 0.163 8815 Z= 0.205 Angle : 0.572 9.948 11948 Z= 0.281 Chirality : 0.040 0.313 1383 Planarity : 0.003 0.037 1503 Dihedral : 16.343 163.486 3221 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % 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: 1.64 (0.26), residues: 1112 helix: 2.13 (0.19), residues: 722 sheet: 0.40 (0.88), residues: 44 loop : -1.13 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 950 HIS 0.003 0.001 HIS A 171 PHE 0.019 0.001 PHE A 966 TYR 0.007 0.001 TYR A1076 ARG 0.005 0.000 ARG A1043 Details of bonding type rmsd hydrogen bonds : bond 0.11696 ( 597) hydrogen bonds : angle 4.85634 ( 1755) covalent geometry : bond 0.00403 ( 8815) covalent geometry : angle 0.57190 (11948) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.930 Fit side-chains REVERT: A 122 MET cc_start: 0.8745 (ttp) cc_final: 0.8508 (ttm) REVERT: A 491 LYS cc_start: 0.7909 (ttmt) cc_final: 0.7544 (tttt) REVERT: A 558 THR cc_start: 0.8681 (p) cc_final: 0.8310 (p) REVERT: A 864 LYS cc_start: 0.6744 (mtpp) cc_final: 0.6362 (mtmt) REVERT: A 946 TRP cc_start: 0.6160 (t60) cc_final: 0.5858 (t60) REVERT: A 1021 ARG cc_start: 0.6529 (ttm110) cc_final: 0.6313 (ttp-110) REVERT: A 1134 GLN cc_start: 0.7862 (tp-100) cc_final: 0.7304 (tp-100) REVERT: A 1153 LYS cc_start: 0.7814 (mmtm) cc_final: 0.7611 (mptt) REVERT: A 1169 GLN cc_start: 0.7291 (tt0) cc_final: 0.6911 (tt0) REVERT: A 1194 ASP cc_start: 0.6583 (m-30) cc_final: 0.6325 (m-30) REVERT: A 1203 GLU cc_start: 0.7335 (tt0) cc_final: 0.7030 (tp30) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.2238 time to fit residues: 51.1074 Evaluate side-chains 139 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 10.0000 chunk 84 optimal weight: 1.9990 chunk 46 optimal weight: 0.0270 chunk 28 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 100 optimal weight: 0.0370 overall best weight: 0.7918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 GLN A1040 GLN A1073 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.149917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.128269 restraints weight = 10924.517| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.53 r_work: 0.3354 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.0964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8815 Z= 0.125 Angle : 0.514 7.729 11948 Z= 0.264 Chirality : 0.039 0.132 1383 Planarity : 0.003 0.037 1503 Dihedral : 10.493 178.031 1267 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.69 % Favored : 96.22 % Rotamer: Outliers : 1.10 % Allowed : 6.83 % Favored : 92.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.26), residues: 1112 helix: 2.42 (0.19), residues: 735 sheet: 0.17 (0.87), residues: 43 loop : -1.17 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 843 HIS 0.004 0.001 HIS A 171 PHE 0.020 0.001 PHE A 966 TYR 0.009 0.001 TYR A 295 ARG 0.002 0.000 ARG A1043 Details of bonding type rmsd hydrogen bonds : bond 0.04732 ( 597) hydrogen bonds : angle 3.81475 ( 1755) covalent geometry : bond 0.00249 ( 8815) covalent geometry : angle 0.51351 (11948) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 148 time to evaluate : 0.945 Fit side-chains revert: symmetry clash REVERT: A 122 MET cc_start: 0.9023 (ttp) cc_final: 0.8819 (ttm) REVERT: A 491 LYS cc_start: 0.8020 (ttmt) cc_final: 0.7595 (tttt) REVERT: A 556 ARG cc_start: 0.8416 (ptp-170) cc_final: 0.8213 (ptp-170) REVERT: A 864 LYS cc_start: 0.6787 (mtpp) cc_final: 0.6339 (mtmt) REVERT: A 993 MET cc_start: 0.8755 (tpp) cc_final: 0.8506 (mmm) REVERT: A 1003 LYS cc_start: 0.7517 (tttm) cc_final: 0.7242 (mttp) REVERT: A 1021 ARG cc_start: 0.6788 (ttm110) cc_final: 0.6565 (ttp-110) REVERT: A 1091 ARG cc_start: 0.7577 (mtt-85) cc_final: 0.7315 (mtt90) REVERT: A 1134 GLN cc_start: 0.8072 (tp-100) cc_final: 0.7468 (tp-100) REVERT: A 1203 GLU cc_start: 0.7881 (tt0) cc_final: 0.7385 (tp30) outliers start: 10 outliers final: 7 residues processed: 154 average time/residue: 0.2417 time to fit residues: 49.9222 Evaluate side-chains 145 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 138 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 763 SER Chi-restraints excluded: chain A residue 962 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 71 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 31 optimal weight: 0.3980 chunk 28 optimal weight: 6.9990 chunk 62 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 68 optimal weight: 6.9990 chunk 36 optimal weight: 8.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 GLN A 236 GLN A 499 GLN A 797 ASN A1073 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.147277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.125021 restraints weight = 11095.617| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.54 r_work: 0.3300 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8815 Z= 0.154 Angle : 0.540 7.292 11948 Z= 0.280 Chirality : 0.040 0.142 1383 Planarity : 0.003 0.039 1503 Dihedral : 9.978 172.313 1267 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.23 % Favored : 95.68 % Rotamer: Outliers : 2.31 % Allowed : 8.81 % Favored : 88.88 % 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: 1.78 (0.26), residues: 1112 helix: 2.27 (0.19), residues: 731 sheet: 0.03 (0.85), residues: 45 loop : -1.20 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 843 HIS 0.007 0.001 HIS A 171 PHE 0.028 0.002 PHE A 966 TYR 0.005 0.001 TYR A 292 ARG 0.002 0.000 ARG A 688 Details of bonding type rmsd hydrogen bonds : bond 0.05114 ( 597) hydrogen bonds : angle 3.84265 ( 1755) covalent geometry : bond 0.00338 ( 8815) covalent geometry : angle 0.53995 (11948) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.885 Fit side-chains REVERT: A 122 MET cc_start: 0.9059 (ttp) cc_final: 0.8848 (ttm) REVERT: A 437 LEU cc_start: 0.6994 (OUTLIER) cc_final: 0.6711 (pp) REVERT: A 491 LYS cc_start: 0.8059 (ttmt) cc_final: 0.7639 (tttt) REVERT: A 757 PHE cc_start: 0.8372 (m-80) cc_final: 0.7968 (m-80) REVERT: A 864 LYS cc_start: 0.6834 (mtpp) cc_final: 0.6362 (mtmt) REVERT: A 946 TRP cc_start: 0.6485 (t60) cc_final: 0.6202 (t60) REVERT: A 993 MET cc_start: 0.8760 (tpp) cc_final: 0.8551 (mmm) REVERT: A 1003 LYS cc_start: 0.7499 (tttm) cc_final: 0.7211 (mttp) REVERT: A 1021 ARG cc_start: 0.6828 (ttm110) cc_final: 0.6599 (ttp-110) outliers start: 21 outliers final: 16 residues processed: 161 average time/residue: 0.2290 time to fit residues: 49.8726 Evaluate side-chains 152 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 494 ASP Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 763 SER Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 1040 GLN Chi-restraints excluded: chain A residue 1083 VAL Chi-restraints excluded: chain A residue 1153 LYS Chi-restraints excluded: chain A residue 1214 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 72 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 76 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.148586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.126696 restraints weight = 10870.969| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.50 r_work: 0.3293 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8815 Z= 0.143 Angle : 0.518 7.361 11948 Z= 0.268 Chirality : 0.040 0.134 1383 Planarity : 0.003 0.039 1503 Dihedral : 9.453 162.884 1267 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.87 % Favored : 96.04 % Rotamer: Outliers : 2.64 % Allowed : 11.23 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.79 (0.26), residues: 1112 helix: 2.35 (0.19), residues: 724 sheet: 0.04 (0.87), residues: 43 loop : -1.27 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 950 HIS 0.005 0.001 HIS A 171 PHE 0.027 0.002 PHE A 966 TYR 0.006 0.001 TYR A 295 ARG 0.002 0.000 ARG A 556 Details of bonding type rmsd hydrogen bonds : bond 0.04927 ( 597) hydrogen bonds : angle 3.77819 ( 1755) covalent geometry : bond 0.00312 ( 8815) covalent geometry : angle 0.51815 (11948) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 145 time to evaluate : 0.863 Fit side-chains revert: symmetry clash REVERT: A 122 MET cc_start: 0.9058 (ttp) cc_final: 0.8832 (ttm) REVERT: A 171 HIS cc_start: 0.8361 (OUTLIER) cc_final: 0.7009 (t70) REVERT: A 491 LYS cc_start: 0.8075 (ttmt) cc_final: 0.7624 (tttt) REVERT: A 736 MET cc_start: 0.7706 (ttp) cc_final: 0.7506 (ptm) REVERT: A 757 PHE cc_start: 0.8361 (m-80) cc_final: 0.7948 (m-80) REVERT: A 864 LYS cc_start: 0.6815 (mtpp) cc_final: 0.6346 (mtmt) REVERT: A 946 TRP cc_start: 0.6364 (t60) cc_final: 0.6092 (t60) REVERT: A 993 MET cc_start: 0.8759 (tpp) cc_final: 0.8539 (mmm) REVERT: A 1003 LYS cc_start: 0.7500 (tttm) cc_final: 0.7197 (mttp) REVERT: A 1021 ARG cc_start: 0.6798 (ttm110) cc_final: 0.6527 (ttp-110) outliers start: 24 outliers final: 18 residues processed: 164 average time/residue: 0.2460 time to fit residues: 54.1556 Evaluate side-chains 153 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 171 HIS Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 763 SER Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1032 SER Chi-restraints excluded: chain A residue 1083 VAL Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1153 LYS Chi-restraints excluded: chain A residue 1214 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 57 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 62 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 94 optimal weight: 0.9980 chunk 81 optimal weight: 5.9990 chunk 109 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 2 optimal weight: 8.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 GLN A 499 GLN ** A 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 899 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.142477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.120806 restraints weight = 11073.206| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.41 r_work: 0.3225 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 8815 Z= 0.240 Angle : 0.644 7.517 11948 Z= 0.333 Chirality : 0.045 0.162 1383 Planarity : 0.004 0.044 1503 Dihedral : 10.487 163.514 1267 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.86 % Favored : 95.05 % Rotamer: Outliers : 3.30 % Allowed : 12.56 % Favored : 84.14 % 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: 0.99 (0.25), residues: 1112 helix: 1.69 (0.19), residues: 731 sheet: -0.18 (0.86), residues: 45 loop : -1.59 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 950 HIS 0.008 0.002 HIS A 171 PHE 0.026 0.003 PHE A 764 TYR 0.010 0.002 TYR A 728 ARG 0.003 0.001 ARG A1050 Details of bonding type rmsd hydrogen bonds : bond 0.06126 ( 597) hydrogen bonds : angle 4.16201 ( 1755) covalent geometry : bond 0.00554 ( 8815) covalent geometry : angle 0.64356 (11948) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 134 time to evaluate : 0.886 Fit side-chains revert: symmetry clash REVERT: A 171 HIS cc_start: 0.8695 (OUTLIER) cc_final: 0.7289 (t70) REVERT: A 369 GLU cc_start: 0.7440 (mp0) cc_final: 0.7171 (mp0) REVERT: A 438 LYS cc_start: 0.7745 (pttm) cc_final: 0.7505 (ptpt) REVERT: A 491 LYS cc_start: 0.8010 (ttmt) cc_final: 0.7696 (tttt) REVERT: A 864 LYS cc_start: 0.6861 (mtpp) cc_final: 0.6315 (mtmt) REVERT: A 946 TRP cc_start: 0.6478 (t60) cc_final: 0.6230 (t60) REVERT: A 993 MET cc_start: 0.8841 (tpp) cc_final: 0.8406 (mtm) REVERT: A 1021 ARG cc_start: 0.6875 (ttm110) cc_final: 0.6621 (ttp-110) outliers start: 30 outliers final: 21 residues processed: 158 average time/residue: 0.2331 time to fit residues: 49.8129 Evaluate side-chains 151 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 171 HIS Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 763 SER Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1032 SER Chi-restraints excluded: chain A residue 1083 VAL Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1153 LYS Chi-restraints excluded: chain A residue 1217 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 85 optimal weight: 0.9990 chunk 50 optimal weight: 6.9990 chunk 30 optimal weight: 0.7980 chunk 86 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 GLN A 228 ASN A 499 GLN ** A 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.147289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.125931 restraints weight = 10926.601| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.41 r_work: 0.3296 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8815 Z= 0.121 Angle : 0.503 7.538 11948 Z= 0.260 Chirality : 0.039 0.135 1383 Planarity : 0.003 0.039 1503 Dihedral : 9.374 157.988 1267 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.60 % Favored : 96.31 % Rotamer: Outliers : 2.20 % Allowed : 14.98 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.26), residues: 1112 helix: 2.28 (0.19), residues: 728 sheet: -0.06 (0.88), residues: 43 loop : -1.30 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 950 HIS 0.002 0.000 HIS A 171 PHE 0.017 0.001 PHE A 853 TYR 0.008 0.001 TYR A 295 ARG 0.003 0.000 ARG A 556 Details of bonding type rmsd hydrogen bonds : bond 0.04725 ( 597) hydrogen bonds : angle 3.77523 ( 1755) covalent geometry : bond 0.00245 ( 8815) covalent geometry : angle 0.50306 (11948) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.938 Fit side-chains REVERT: A 171 HIS cc_start: 0.8422 (OUTLIER) cc_final: 0.7194 (t70) REVERT: A 354 ASN cc_start: 0.7649 (m110) cc_final: 0.7405 (m-40) REVERT: A 369 GLU cc_start: 0.7402 (mp0) cc_final: 0.7102 (mp0) REVERT: A 438 LYS cc_start: 0.7636 (pttm) cc_final: 0.7214 (ptpt) REVERT: A 491 LYS cc_start: 0.7949 (ttmt) cc_final: 0.7645 (tttt) REVERT: A 757 PHE cc_start: 0.8360 (m-80) cc_final: 0.7992 (m-80) REVERT: A 864 LYS cc_start: 0.6790 (mtpp) cc_final: 0.6388 (mtmt) REVERT: A 946 TRP cc_start: 0.6353 (t60) cc_final: 0.6099 (t60) REVERT: A 993 MET cc_start: 0.8879 (tpp) cc_final: 0.8443 (mtt) REVERT: A 1021 ARG cc_start: 0.6762 (ttm110) cc_final: 0.6523 (ttp-110) outliers start: 20 outliers final: 15 residues processed: 148 average time/residue: 0.2307 time to fit residues: 46.1065 Evaluate side-chains 144 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 HIS Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 763 SER Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1032 SER Chi-restraints excluded: chain A residue 1083 VAL Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1153 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 99 optimal weight: 0.3980 chunk 106 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 109 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 GLN ** A 513 GLN ** 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 = 0.3652 r_free = 0.3652 target = 0.147847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.126895 restraints weight = 10976.066| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.37 r_work: 0.3283 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8815 Z= 0.141 Angle : 0.525 7.513 11948 Z= 0.269 Chirality : 0.040 0.135 1383 Planarity : 0.003 0.039 1503 Dihedral : 9.298 158.388 1267 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.23 % Favored : 95.68 % Rotamer: Outliers : 2.64 % Allowed : 14.98 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.26), residues: 1112 helix: 2.29 (0.19), residues: 726 sheet: -0.11 (0.87), residues: 43 loop : -1.32 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 950 HIS 0.005 0.001 HIS A 171 PHE 0.015 0.002 PHE A 764 TYR 0.007 0.001 TYR A 295 ARG 0.002 0.000 ARG A 556 Details of bonding type rmsd hydrogen bonds : bond 0.04913 ( 597) hydrogen bonds : angle 3.80666 ( 1755) covalent geometry : bond 0.00307 ( 8815) covalent geometry : angle 0.52473 (11948) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 0.973 Fit side-chains REVERT: A 171 HIS cc_start: 0.8418 (OUTLIER) cc_final: 0.7123 (t70) REVERT: A 360 GLU cc_start: 0.7711 (tp30) cc_final: 0.7419 (tp30) REVERT: A 369 GLU cc_start: 0.7335 (mp0) cc_final: 0.7018 (mp0) REVERT: A 438 LYS cc_start: 0.7664 (pttm) cc_final: 0.7290 (ptpt) REVERT: A 491 LYS cc_start: 0.7931 (ttmt) cc_final: 0.7632 (tttt) REVERT: A 757 PHE cc_start: 0.8357 (m-80) cc_final: 0.8002 (m-80) REVERT: A 864 LYS cc_start: 0.6847 (mtpp) cc_final: 0.6445 (mtmt) REVERT: A 946 TRP cc_start: 0.6388 (t60) cc_final: 0.6111 (t60) REVERT: A 993 MET cc_start: 0.8860 (tpp) cc_final: 0.8541 (mtm) REVERT: A 997 PHE cc_start: 0.8477 (m-80) cc_final: 0.8231 (m-80) REVERT: A 1021 ARG cc_start: 0.6768 (ttm110) cc_final: 0.6535 (ttp-110) REVERT: A 1084 MET cc_start: 0.7502 (mmm) cc_final: 0.7261 (mtm) outliers start: 24 outliers final: 20 residues processed: 152 average time/residue: 0.2338 time to fit residues: 48.2002 Evaluate side-chains 152 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 HIS Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 763 SER Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1032 SER Chi-restraints excluded: chain A residue 1083 VAL Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1153 LYS Chi-restraints excluded: chain A residue 1216 VAL Chi-restraints excluded: chain A residue 1217 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 18 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 GLN ** A 513 GLN ** 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 = 0.3609 r_free = 0.3609 target = 0.144075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.122531 restraints weight = 11168.117| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.42 r_work: 0.3242 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 8815 Z= 0.205 Angle : 0.604 7.771 11948 Z= 0.310 Chirality : 0.043 0.157 1383 Planarity : 0.004 0.042 1503 Dihedral : 9.680 158.914 1267 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.86 % Favored : 95.05 % Rotamer: Outliers : 3.19 % Allowed : 15.09 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.25), residues: 1112 helix: 1.92 (0.19), residues: 730 sheet: -0.18 (0.88), residues: 43 loop : -1.56 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 950 HIS 0.008 0.001 HIS A 171 PHE 0.021 0.002 PHE A 764 TYR 0.008 0.001 TYR A 728 ARG 0.003 0.000 ARG A 820 Details of bonding type rmsd hydrogen bonds : bond 0.05631 ( 597) hydrogen bonds : angle 4.01326 ( 1755) covalent geometry : bond 0.00472 ( 8815) covalent geometry : angle 0.60424 (11948) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 134 time to evaluate : 0.930 Fit side-chains REVERT: A 171 HIS cc_start: 0.8621 (OUTLIER) cc_final: 0.7311 (t70) REVERT: A 267 THR cc_start: 0.8596 (OUTLIER) cc_final: 0.8377 (m) REVERT: A 369 GLU cc_start: 0.7379 (mp0) cc_final: 0.7077 (mp0) REVERT: A 438 LYS cc_start: 0.7759 (pttm) cc_final: 0.7512 (ptpt) REVERT: A 491 LYS cc_start: 0.7999 (ttmt) cc_final: 0.7700 (tttt) REVERT: A 757 PHE cc_start: 0.8454 (m-80) cc_final: 0.8097 (m-80) REVERT: A 864 LYS cc_start: 0.6856 (mtpp) cc_final: 0.6399 (mtmt) REVERT: A 946 TRP cc_start: 0.6357 (t60) cc_final: 0.6118 (t60) REVERT: A 993 MET cc_start: 0.8836 (tpp) cc_final: 0.8528 (mtm) REVERT: A 1021 ARG cc_start: 0.6812 (ttm170) cc_final: 0.6556 (ttp-110) outliers start: 29 outliers final: 25 residues processed: 157 average time/residue: 0.2231 time to fit residues: 47.6082 Evaluate side-chains 158 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 171 HIS Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 736 MET Chi-restraints excluded: chain A residue 763 SER Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1032 SER Chi-restraints excluded: chain A residue 1083 VAL Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1153 LYS Chi-restraints excluded: chain A residue 1216 VAL Chi-restraints excluded: chain A residue 1217 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 92 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 34 optimal weight: 7.9990 chunk 73 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 101 optimal weight: 0.0980 chunk 75 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 GLN ** A 513 GLN ** 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 = 0.3640 r_free = 0.3640 target = 0.146785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.125892 restraints weight = 10983.170| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.36 r_work: 0.3280 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8815 Z= 0.148 Angle : 0.547 7.996 11948 Z= 0.280 Chirality : 0.040 0.178 1383 Planarity : 0.003 0.041 1503 Dihedral : 9.409 156.223 1267 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.96 % Favored : 95.95 % Rotamer: Outliers : 3.08 % Allowed : 15.53 % Favored : 81.39 % 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: 1.51 (0.25), residues: 1112 helix: 2.15 (0.19), residues: 725 sheet: -0.22 (0.86), residues: 43 loop : -1.43 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 950 HIS 0.005 0.001 HIS A 171 PHE 0.015 0.002 PHE A 764 TYR 0.006 0.001 TYR A 295 ARG 0.003 0.000 ARG A 556 Details of bonding type rmsd hydrogen bonds : bond 0.05089 ( 597) hydrogen bonds : angle 3.88417 ( 1755) covalent geometry : bond 0.00324 ( 8815) covalent geometry : angle 0.54721 (11948) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 136 time to evaluate : 0.925 Fit side-chains revert: symmetry clash REVERT: A 171 HIS cc_start: 0.8438 (OUTLIER) cc_final: 0.7157 (t70) REVERT: A 369 GLU cc_start: 0.7359 (mp0) cc_final: 0.7048 (mp0) REVERT: A 438 LYS cc_start: 0.7741 (pttm) cc_final: 0.7424 (ptpt) REVERT: A 491 LYS cc_start: 0.7967 (ttmt) cc_final: 0.7663 (tttt) REVERT: A 757 PHE cc_start: 0.8390 (m-80) cc_final: 0.8033 (m-80) REVERT: A 864 LYS cc_start: 0.6848 (mtpp) cc_final: 0.6430 (mtmt) REVERT: A 946 TRP cc_start: 0.6354 (t60) cc_final: 0.6119 (t60) REVERT: A 993 MET cc_start: 0.8880 (tpp) cc_final: 0.8571 (mtm) REVERT: A 997 PHE cc_start: 0.8530 (m-80) cc_final: 0.8309 (m-80) REVERT: A 1021 ARG cc_start: 0.6783 (ttm170) cc_final: 0.6535 (ttp-110) REVERT: A 1084 MET cc_start: 0.7510 (mmm) cc_final: 0.7222 (mtm) outliers start: 28 outliers final: 26 residues processed: 158 average time/residue: 0.2296 time to fit residues: 49.6137 Evaluate side-chains 159 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 171 HIS Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 736 MET Chi-restraints excluded: chain A residue 763 SER Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1032 SER Chi-restraints excluded: chain A residue 1083 VAL Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1153 LYS Chi-restraints excluded: chain A residue 1216 VAL Chi-restraints excluded: chain A residue 1217 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 48 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 29 optimal weight: 7.9990 chunk 105 optimal weight: 5.9990 chunk 9 optimal weight: 0.0980 chunk 19 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 GLN ** A 513 GLN ** 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 = 0.3636 r_free = 0.3636 target = 0.146489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.125100 restraints weight = 11106.520| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.42 r_work: 0.3275 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8815 Z= 0.139 Angle : 0.535 8.345 11948 Z= 0.273 Chirality : 0.040 0.179 1383 Planarity : 0.003 0.040 1503 Dihedral : 9.171 155.158 1267 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.14 % Favored : 95.77 % Rotamer: Outliers : 3.19 % Allowed : 15.53 % Favored : 81.28 % 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: 1.66 (0.26), residues: 1112 helix: 2.26 (0.19), residues: 726 sheet: -0.24 (0.86), residues: 43 loop : -1.36 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 950 HIS 0.005 0.001 HIS A 171 PHE 0.014 0.002 PHE A 764 TYR 0.006 0.001 TYR A 295 ARG 0.003 0.000 ARG A 556 Details of bonding type rmsd hydrogen bonds : bond 0.04886 ( 597) hydrogen bonds : angle 3.81903 ( 1755) covalent geometry : bond 0.00300 ( 8815) covalent geometry : angle 0.53454 (11948) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 137 time to evaluate : 0.936 Fit side-chains REVERT: A 171 HIS cc_start: 0.8412 (OUTLIER) cc_final: 0.7113 (t70) REVERT: A 369 GLU cc_start: 0.7377 (mp0) cc_final: 0.7057 (mp0) REVERT: A 438 LYS cc_start: 0.7714 (pttm) cc_final: 0.7374 (ptpt) REVERT: A 491 LYS cc_start: 0.7986 (ttmt) cc_final: 0.7657 (tttt) REVERT: A 757 PHE cc_start: 0.8367 (m-80) cc_final: 0.7988 (m-80) REVERT: A 864 LYS cc_start: 0.6800 (mtpp) cc_final: 0.6401 (mtmt) REVERT: A 946 TRP cc_start: 0.6392 (t60) cc_final: 0.6150 (t60) REVERT: A 993 MET cc_start: 0.8874 (tpp) cc_final: 0.8564 (mtm) REVERT: A 997 PHE cc_start: 0.8513 (m-80) cc_final: 0.8305 (m-80) REVERT: A 1021 ARG cc_start: 0.6784 (ttm170) cc_final: 0.6535 (ttp-110) outliers start: 29 outliers final: 25 residues processed: 160 average time/residue: 0.2258 time to fit residues: 49.2696 Evaluate side-chains 159 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 171 HIS Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 563 HIS Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 736 MET Chi-restraints excluded: chain A residue 763 SER Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1032 SER Chi-restraints excluded: chain A residue 1083 VAL Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1153 LYS Chi-restraints excluded: chain A residue 1216 VAL Chi-restraints excluded: chain A residue 1217 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 42 optimal weight: 0.1980 chunk 82 optimal weight: 7.9990 chunk 45 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 70 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 105 optimal weight: 3.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 GLN ** A 513 GLN ** 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 = 0.3614 r_free = 0.3614 target = 0.144477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.123025 restraints weight = 11121.421| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.42 r_work: 0.3245 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8815 Z= 0.188 Angle : 0.593 8.452 11948 Z= 0.304 Chirality : 0.042 0.180 1383 Planarity : 0.004 0.042 1503 Dihedral : 9.452 156.901 1267 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.68 % Favored : 95.23 % Rotamer: Outliers : 3.30 % Allowed : 15.64 % Favored : 81.06 % 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: 1.27 (0.25), residues: 1112 helix: 1.96 (0.19), residues: 730 sheet: -0.37 (0.85), residues: 43 loop : -1.56 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 950 HIS 0.007 0.001 HIS A 171 PHE 0.019 0.002 PHE A 764 TYR 0.007 0.001 TYR A 728 ARG 0.002 0.000 ARG A 556 Details of bonding type rmsd hydrogen bonds : bond 0.05501 ( 597) hydrogen bonds : angle 3.98262 ( 1755) covalent geometry : bond 0.00429 ( 8815) covalent geometry : angle 0.59264 (11948) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4752.46 seconds wall clock time: 82 minutes 1.03 seconds (4921.03 seconds total)