Starting phenix.real_space_refine on Wed Feb 4 02:39:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jup_61833/02_2026/9jup_61833.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jup_61833/02_2026/9jup_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_61833/02_2026/9jup_61833.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jup_61833/02_2026/9jup_61833.map" model { file = "/net/cci-nas-00/data/ceres_data/9jup_61833/02_2026/9jup_61833.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jup_61833/02_2026/9jup_61833.cif" } resolution = 3.1 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= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/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: 1.98, per 1000 atoms: 0.23 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: 0.79 Conformation dependent library (CDL) restraints added in 206.0 milliseconds 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: 0.19 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: 1.06 Time building geometry restraints manager: 0.99 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: 1.150 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.150 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.500 ------------------------------------------------------------------------------- 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 : 8.89 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 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: 1.64 (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 ARG 0.005 0.000 ARG A1043 TYR 0.007 0.001 TYR A1076 PHE 0.019 0.001 PHE A 966 TRP 0.016 0.001 TRP A 950 HIS 0.003 0.001 HIS A 171 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 8815) covalent geometry : angle 0.57190 (11948) hydrogen bonds : bond 0.11696 ( 597) hydrogen bonds : angle 4.85634 ( 1755) *********************** 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 : 0.250 Fit side-chains REVERT: A 122 MET cc_start: 0.8757 (ttp) cc_final: 0.8518 (ttm) REVERT: A 491 LYS cc_start: 0.7910 (ttmt) cc_final: 0.7549 (tttt) REVERT: A 558 THR cc_start: 0.8682 (p) cc_final: 0.8311 (p) REVERT: A 864 LYS cc_start: 0.6742 (mtpp) cc_final: 0.6361 (mtmt) REVERT: A 946 TRP cc_start: 0.6160 (t60) cc_final: 0.5857 (t60) REVERT: A 1021 ARG cc_start: 0.6529 (ttm110) cc_final: 0.6312 (ttp-110) REVERT: A 1134 GLN cc_start: 0.7866 (tp-100) cc_final: 0.7309 (tp-100) REVERT: A 1153 LYS cc_start: 0.7813 (mmtm) cc_final: 0.7612 (mptt) REVERT: A 1169 GLN cc_start: 0.7292 (tt0) cc_final: 0.6910 (tt0) REVERT: A 1194 ASP cc_start: 0.6582 (m-30) cc_final: 0.6323 (m-30) REVERT: A 1203 GLU cc_start: 0.7331 (tt0) cc_final: 0.7026 (tp30) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.0801 time to fit residues: 18.4525 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 : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 8.9990 chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 0.1980 overall best weight: 2.6388 ------------------------------------------------------------------------------- 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 797 ASN A1040 GLN A1073 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.145033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.122783 restraints weight = 11130.826| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.54 r_work: 0.3257 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8815 Z= 0.209 Angle : 0.613 7.407 11948 Z= 0.317 Chirality : 0.043 0.143 1383 Planarity : 0.004 0.044 1503 Dihedral : 10.826 173.963 1267 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.50 % Favored : 95.41 % Rotamer: Outliers : 1.43 % Allowed : 8.81 % Favored : 89.76 % 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: 1.34 (0.25), residues: 1112 helix: 1.93 (0.19), residues: 732 sheet: 0.06 (0.86), residues: 45 loop : -1.39 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 688 TYR 0.006 0.001 TYR A 89 PHE 0.023 0.002 PHE A 966 TRP 0.015 0.002 TRP A 843 HIS 0.010 0.001 HIS A 171 Details of bonding type rmsd covalent geometry : bond 0.00472 ( 8815) covalent geometry : angle 0.61274 (11948) hydrogen bonds : bond 0.05757 ( 597) hydrogen bonds : angle 4.07552 ( 1755) *********************** 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: 13 poor density : 145 time to evaluate : 0.275 Fit side-chains REVERT: A 387 ASN cc_start: 0.7883 (p0) cc_final: 0.7652 (p0) REVERT: A 491 LYS cc_start: 0.8062 (ttmt) cc_final: 0.7695 (tttt) REVERT: A 556 ARG cc_start: 0.8465 (ptp-170) cc_final: 0.8257 (ptp-170) REVERT: A 757 PHE cc_start: 0.8468 (m-80) cc_final: 0.8075 (m-80) REVERT: A 864 LYS cc_start: 0.6851 (mtpp) cc_final: 0.6308 (mtmt) REVERT: A 946 TRP cc_start: 0.6450 (t60) cc_final: 0.6135 (t60) REVERT: A 993 MET cc_start: 0.8805 (tpp) cc_final: 0.8549 (mmm) REVERT: A 1003 LYS cc_start: 0.7526 (tttm) cc_final: 0.7190 (mttp) REVERT: A 1021 ARG cc_start: 0.6838 (ttm110) cc_final: 0.6611 (ttp-110) REVERT: A 1040 GLN cc_start: 0.8051 (OUTLIER) cc_final: 0.7562 (mm-40) outliers start: 13 outliers final: 12 residues processed: 154 average time/residue: 0.0940 time to fit residues: 19.1857 Evaluate side-chains 149 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 0.201 ------------------------------------------------------------------------------- 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 321 LEU Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 458 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 1214 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 46 optimal weight: 0.6980 chunk 94 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 100 optimal weight: 0.0770 chunk 27 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 71 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- 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 A1073 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.149074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.127100 restraints weight = 10913.539| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.54 r_work: 0.3321 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8815 Z= 0.118 Angle : 0.499 7.609 11948 Z= 0.258 Chirality : 0.039 0.131 1383 Planarity : 0.003 0.038 1503 Dihedral : 9.701 166.484 1267 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.06 % Favored : 96.85 % Rotamer: Outliers : 1.32 % Allowed : 11.01 % Favored : 87.67 % 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: 1.89 (0.26), residues: 1112 helix: 2.37 (0.19), residues: 734 sheet: 0.16 (0.87), residues: 43 loop : -1.23 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1036 TYR 0.008 0.001 TYR A 295 PHE 0.015 0.001 PHE A 966 TRP 0.013 0.001 TRP A 950 HIS 0.002 0.000 HIS A 171 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 8815) covalent geometry : angle 0.49869 (11948) hydrogen bonds : bond 0.04675 ( 597) hydrogen bonds : angle 3.75910 ( 1755) *********************** 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 158 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 146 time to evaluate : 0.315 Fit side-chains REVERT: A 491 LYS cc_start: 0.8046 (ttmt) cc_final: 0.7618 (tttt) REVERT: A 864 LYS cc_start: 0.6744 (mtpp) cc_final: 0.6318 (mtmt) REVERT: A 946 TRP cc_start: 0.6477 (t60) cc_final: 0.6186 (t60) REVERT: A 993 MET cc_start: 0.8761 (tpp) cc_final: 0.8561 (mmm) REVERT: A 1003 LYS cc_start: 0.7587 (tttm) cc_final: 0.7242 (mttp) REVERT: A 1021 ARG cc_start: 0.6823 (ttm110) cc_final: 0.6585 (ttp-110) outliers start: 12 outliers final: 6 residues processed: 153 average time/residue: 0.0847 time to fit residues: 17.6491 Evaluate side-chains 144 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 138 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 494 ASP 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 892 VAL Chi-restraints excluded: chain A residue 1083 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 45 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.147995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.125938 restraints weight = 11074.408| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.54 r_work: 0.3311 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1549 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= 0.131 Angle : 0.514 7.509 11948 Z= 0.264 Chirality : 0.039 0.130 1383 Planarity : 0.003 0.039 1503 Dihedral : 9.405 166.532 1267 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.59 % Favored : 95.32 % Rotamer: Outliers : 2.20 % Allowed : 12.44 % Favored : 85.35 % 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: 1.89 (0.26), residues: 1112 helix: 2.42 (0.19), residues: 726 sheet: 0.13 (0.87), residues: 43 loop : -1.27 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 556 TYR 0.007 0.001 TYR A 295 PHE 0.015 0.002 PHE A 764 TRP 0.012 0.001 TRP A 950 HIS 0.005 0.001 HIS A 171 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 8815) covalent geometry : angle 0.51366 (11948) hydrogen bonds : bond 0.04758 ( 597) hydrogen bonds : angle 3.73186 ( 1755) *********************** 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 165 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: A 171 HIS cc_start: 0.8351 (OUTLIER) cc_final: 0.7020 (t70) REVERT: A 369 GLU cc_start: 0.7434 (mp0) cc_final: 0.7155 (mp0) REVERT: A 491 LYS cc_start: 0.8055 (ttmt) cc_final: 0.7635 (tttt) REVERT: A 757 PHE cc_start: 0.8348 (m-80) cc_final: 0.7963 (m-80) REVERT: A 864 LYS cc_start: 0.6822 (mtpp) cc_final: 0.6367 (mtmt) REVERT: A 946 TRP cc_start: 0.6471 (t60) cc_final: 0.6218 (t60) REVERT: A 993 MET cc_start: 0.8745 (tpp) cc_final: 0.8540 (mmm) REVERT: A 1003 LYS cc_start: 0.7560 (tttm) cc_final: 0.7210 (mttp) REVERT: A 1021 ARG cc_start: 0.6815 (ttm110) cc_final: 0.6575 (ttp-110) outliers start: 20 outliers final: 15 residues processed: 158 average time/residue: 0.0808 time to fit residues: 17.2859 Evaluate side-chains 158 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 0.268 ------------------------------------------------------------------------------- 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 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 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 1153 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 88 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 91 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 GLN ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.148716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.127959 restraints weight = 11044.725| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.36 r_work: 0.3254 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 8815 Z= 0.202 Angle : 0.593 7.289 11948 Z= 0.306 Chirality : 0.043 0.140 1383 Planarity : 0.004 0.044 1503 Dihedral : 9.940 164.568 1267 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.95 % Favored : 94.96 % Rotamer: Outliers : 3.41 % Allowed : 13.00 % Favored : 83.59 % 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: 1.32 (0.25), residues: 1112 helix: 1.98 (0.19), residues: 729 sheet: -0.04 (0.85), residues: 45 loop : -1.54 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1179 TYR 0.008 0.001 TYR A 699 PHE 0.028 0.002 PHE A 966 TRP 0.011 0.001 TRP A 950 HIS 0.007 0.001 HIS A 171 Details of bonding type rmsd covalent geometry : bond 0.00462 ( 8815) covalent geometry : angle 0.59265 (11948) hydrogen bonds : bond 0.05664 ( 597) hydrogen bonds : angle 3.99978 ( 1755) *********************** 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 174 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 143 time to evaluate : 0.180 Fit side-chains REVERT: A 171 HIS cc_start: 0.8580 (OUTLIER) cc_final: 0.7286 (t70) REVERT: A 369 GLU cc_start: 0.7412 (mp0) cc_final: 0.7137 (mp0) REVERT: A 491 LYS cc_start: 0.7995 (ttmt) cc_final: 0.7671 (tttt) REVERT: A 757 PHE cc_start: 0.8451 (m-80) cc_final: 0.8095 (m-80) REVERT: A 864 LYS cc_start: 0.6855 (mtpp) cc_final: 0.6399 (mtmt) REVERT: A 946 TRP cc_start: 0.6428 (t60) cc_final: 0.6134 (t60) REVERT: A 993 MET cc_start: 0.8777 (tpp) cc_final: 0.8575 (mmm) REVERT: A 1021 ARG cc_start: 0.6778 (ttm110) cc_final: 0.6529 (ttp-110) outliers start: 31 outliers final: 23 residues processed: 166 average time/residue: 0.0763 time to fit residues: 17.3234 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 : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 62 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 321 LEU Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 383 VAL 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 1024 VAL Chi-restraints excluded: chain A residue 1032 SER Chi-restraints excluded: chain A residue 1083 VAL 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 47 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 96 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 82 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 GLN ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.145234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.123600 restraints weight = 11084.361| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.43 r_work: 0.3266 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8815 Z= 0.156 Angle : 0.544 7.486 11948 Z= 0.280 Chirality : 0.040 0.136 1383 Planarity : 0.003 0.042 1503 Dihedral : 9.638 160.705 1267 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.50 % Favored : 95.41 % Rotamer: Outliers : 3.30 % Allowed : 14.54 % Favored : 82.16 % 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: 1.45 (0.25), residues: 1112 helix: 2.09 (0.19), residues: 730 sheet: -0.14 (0.85), residues: 43 loop : -1.51 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 556 TYR 0.007 0.001 TYR A 699 PHE 0.016 0.002 PHE A 764 TRP 0.011 0.001 TRP A 950 HIS 0.006 0.001 HIS A 171 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 8815) covalent geometry : angle 0.54425 (11948) hydrogen bonds : bond 0.05206 ( 597) hydrogen bonds : angle 3.89213 ( 1755) *********************** 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 163 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 133 time to evaluate : 0.260 Fit side-chains revert: symmetry clash REVERT: A 171 HIS cc_start: 0.8482 (OUTLIER) cc_final: 0.7196 (t70) REVERT: A 369 GLU cc_start: 0.7432 (mp0) cc_final: 0.7152 (mp0) REVERT: A 491 LYS cc_start: 0.7966 (ttmt) cc_final: 0.7652 (tttt) REVERT: A 757 PHE cc_start: 0.8403 (m-80) cc_final: 0.8039 (m-80) REVERT: A 864 LYS cc_start: 0.6854 (mtpp) cc_final: 0.6417 (mtmt) REVERT: A 946 TRP cc_start: 0.6463 (t60) cc_final: 0.6213 (t60) REVERT: A 993 MET cc_start: 0.8783 (tpp) cc_final: 0.8314 (mtt) REVERT: A 1021 ARG cc_start: 0.6754 (ttm170) cc_final: 0.6508 (ttp-110) outliers start: 30 outliers final: 23 residues processed: 157 average time/residue: 0.0853 time to fit residues: 18.1950 Evaluate side-chains 157 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 0.247 ------------------------------------------------------------------------------- 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 324 SER 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 1153 LYS Chi-restraints excluded: chain A residue 1216 VAL Chi-restraints excluded: chain A residue 1217 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.9990 chunk 55 optimal weight: 10.0000 chunk 46 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 80 optimal weight: 6.9990 chunk 85 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 GLN ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.147986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.126880 restraints weight = 11088.041| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.39 r_work: 0.3282 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1871 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= 0.142 Angle : 0.526 7.584 11948 Z= 0.271 Chirality : 0.040 0.137 1383 Planarity : 0.003 0.040 1503 Dihedral : 9.339 158.300 1267 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.32 % Favored : 95.59 % Rotamer: Outliers : 3.63 % Allowed : 14.65 % 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 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: 1.65 (0.25), residues: 1112 helix: 2.26 (0.19), residues: 726 sheet: -0.14 (0.85), residues: 43 loop : -1.39 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 556 TYR 0.007 0.001 TYR A 295 PHE 0.015 0.002 PHE A 764 TRP 0.010 0.001 TRP A 950 HIS 0.005 0.001 HIS A 171 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 8815) covalent geometry : angle 0.52639 (11948) hydrogen bonds : bond 0.04975 ( 597) hydrogen bonds : angle 3.81793 ( 1755) *********************** 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 168 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 135 time to evaluate : 0.317 Fit side-chains REVERT: A 171 HIS cc_start: 0.8423 (OUTLIER) cc_final: 0.7131 (t70) REVERT: A 369 GLU cc_start: 0.7358 (mp0) cc_final: 0.7055 (mp0) REVERT: A 491 LYS cc_start: 0.7938 (ttmt) cc_final: 0.7626 (tttt) REVERT: A 757 PHE cc_start: 0.8362 (m-80) cc_final: 0.7990 (m-80) REVERT: A 789 MET cc_start: 0.8545 (mmp) cc_final: 0.8298 (tpp) REVERT: A 864 LYS cc_start: 0.6839 (mtpp) cc_final: 0.6427 (mtmt) REVERT: A 946 TRP cc_start: 0.6440 (t60) cc_final: 0.6166 (t60) REVERT: A 993 MET cc_start: 0.8852 (tpp) cc_final: 0.8510 (mtm) REVERT: A 997 PHE cc_start: 0.8481 (m-80) cc_final: 0.8270 (m-80) REVERT: A 1021 ARG cc_start: 0.6759 (ttm170) cc_final: 0.6524 (ttp-110) outliers start: 33 outliers final: 27 residues processed: 159 average time/residue: 0.0815 time to fit residues: 17.6669 Evaluate side-chains 161 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 62 LEU 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 324 SER 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 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 104 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 GLN ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 899 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.143509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.122408 restraints weight = 11092.408| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.37 r_work: 0.3225 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 8815 Z= 0.240 Angle : 0.638 7.695 11948 Z= 0.328 Chirality : 0.045 0.165 1383 Planarity : 0.004 0.044 1503 Dihedral : 10.047 160.034 1267 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.04 % Favored : 94.87 % Rotamer: Outliers : 3.74 % Allowed : 15.09 % 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: 0.99 (0.25), residues: 1112 helix: 1.74 (0.19), residues: 728 sheet: -0.35 (0.84), residues: 43 loop : -1.66 (0.31), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1048 TYR 0.009 0.002 TYR A 89 PHE 0.023 0.002 PHE A 764 TRP 0.006 0.002 TRP A 441 HIS 0.008 0.001 HIS A 171 Details of bonding type rmsd covalent geometry : bond 0.00560 ( 8815) covalent geometry : angle 0.63785 (11948) hydrogen bonds : bond 0.05984 ( 597) hydrogen bonds : angle 4.13117 ( 1755) *********************** 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 168 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 134 time to evaluate : 0.287 Fit side-chains REVERT: A 171 HIS cc_start: 0.8652 (OUTLIER) cc_final: 0.7254 (t70) REVERT: A 369 GLU cc_start: 0.7417 (mp0) cc_final: 0.7131 (mp0) REVERT: A 438 LYS cc_start: 0.8003 (OUTLIER) cc_final: 0.7457 (ptpt) REVERT: A 491 LYS cc_start: 0.8005 (ttmt) cc_final: 0.7689 (tttt) REVERT: A 864 LYS cc_start: 0.6876 (mtpp) cc_final: 0.6393 (mtmt) REVERT: A 946 TRP cc_start: 0.6348 (t60) cc_final: 0.6108 (t60) REVERT: A 993 MET cc_start: 0.8785 (tpp) cc_final: 0.8500 (mtm) REVERT: A 1021 ARG cc_start: 0.6864 (ttm170) cc_final: 0.6606 (ttp-110) outliers start: 34 outliers final: 29 residues processed: 162 average time/residue: 0.0849 time to fit residues: 18.8857 Evaluate side-chains 162 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 131 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 62 LEU 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 297 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 324 SER 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 438 LYS 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 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 64 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 90 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 GLN ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.147608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.126730 restraints weight = 10973.594| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.37 r_work: 0.3286 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1973 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= 0.133 Angle : 0.533 8.072 11948 Z= 0.273 Chirality : 0.040 0.178 1383 Planarity : 0.003 0.040 1503 Dihedral : 9.343 156.577 1267 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.60 % Favored : 96.31 % 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 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: 1.56 (0.25), residues: 1112 helix: 2.21 (0.19), residues: 726 sheet: -0.28 (0.96), residues: 33 loop : -1.45 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1048 TYR 0.008 0.001 TYR A 295 PHE 0.015 0.002 PHE A 764 TRP 0.014 0.001 TRP A 950 HIS 0.004 0.001 HIS A 171 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 8815) covalent geometry : angle 0.53307 (11948) hydrogen bonds : bond 0.04899 ( 597) hydrogen bonds : angle 3.85073 ( 1755) *********************** 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 166 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 136 time to evaluate : 0.322 Fit side-chains REVERT: A 171 HIS cc_start: 0.8370 (OUTLIER) cc_final: 0.7107 (t70) REVERT: A 369 GLU cc_start: 0.7378 (mp0) cc_final: 0.7084 (mp0) REVERT: A 438 LYS cc_start: 0.7816 (OUTLIER) cc_final: 0.7412 (ptpt) REVERT: A 491 LYS cc_start: 0.7944 (ttmt) cc_final: 0.7641 (tttt) REVERT: A 757 PHE cc_start: 0.8345 (m-80) cc_final: 0.7979 (m-80) REVERT: A 789 MET cc_start: 0.8558 (mmp) cc_final: 0.8322 (tpp) REVERT: A 864 LYS cc_start: 0.6834 (mtpp) cc_final: 0.6433 (mtmt) REVERT: A 946 TRP cc_start: 0.6365 (t60) cc_final: 0.6129 (t60) REVERT: A 993 MET cc_start: 0.8835 (tpp) cc_final: 0.8528 (mtm) REVERT: A 1021 ARG cc_start: 0.6743 (ttm170) cc_final: 0.6510 (ttp-110) outliers start: 30 outliers final: 25 residues processed: 161 average time/residue: 0.0869 time to fit residues: 19.1419 Evaluate side-chains 163 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU 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 324 SER 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 438 LYS 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 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 100 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 96 optimal weight: 0.8980 chunk 93 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 94 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 GLN A1241 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.149775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.129038 restraints weight = 10954.427| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.36 r_work: 0.3292 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8815 Z= 0.138 Angle : 0.533 8.311 11948 Z= 0.273 Chirality : 0.040 0.171 1383 Planarity : 0.003 0.041 1503 Dihedral : 9.189 156.537 1267 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.32 % Favored : 95.59 % 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 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: 1.64 (0.25), residues: 1112 helix: 2.28 (0.19), residues: 725 sheet: -0.26 (0.97), residues: 33 loop : -1.41 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1048 TYR 0.007 0.001 TYR A 295 PHE 0.014 0.002 PHE A 966 TRP 0.013 0.001 TRP A 950 HIS 0.005 0.001 HIS A 171 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 8815) covalent geometry : angle 0.53301 (11948) hydrogen bonds : bond 0.04890 ( 597) hydrogen bonds : angle 3.82693 ( 1755) ********************** 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 169 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 0.231 Fit side-chains revert: symmetry clash REVERT: A 171 HIS cc_start: 0.8402 (OUTLIER) cc_final: 0.7129 (t70) REVERT: A 369 GLU cc_start: 0.7412 (mp0) cc_final: 0.7118 (mp0) REVERT: A 438 LYS cc_start: 0.7688 (OUTLIER) cc_final: 0.7094 (ptpt) REVERT: A 491 LYS cc_start: 0.7943 (ttmt) cc_final: 0.7637 (tttt) REVERT: A 757 PHE cc_start: 0.8355 (m-80) cc_final: 0.7987 (m-80) REVERT: A 789 MET cc_start: 0.8569 (mmp) cc_final: 0.8323 (tpp) REVERT: A 864 LYS cc_start: 0.6785 (mtpp) cc_final: 0.6398 (mtmt) REVERT: A 946 TRP cc_start: 0.6404 (t60) cc_final: 0.6167 (t60) REVERT: A 993 MET cc_start: 0.8863 (tpp) cc_final: 0.8504 (mtm) REVERT: A 1021 ARG cc_start: 0.6746 (ttm170) cc_final: 0.6510 (ttp-110) REVERT: A 1084 MET cc_start: 0.7498 (mmm) cc_final: 0.7224 (mtm) outliers start: 30 outliers final: 28 residues processed: 163 average time/residue: 0.0832 time to fit residues: 18.6235 Evaluate side-chains 167 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 137 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU 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 324 SER 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 438 LYS 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 1216 VAL Chi-restraints excluded: chain A residue 1217 VAL Chi-restraints excluded: chain A residue 1224 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 34 optimal weight: 7.9990 chunk 109 optimal weight: 9.9990 chunk 28 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 82 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 41 optimal weight: 0.0570 overall best weight: 2.5704 ------------------------------------------------------------------------------- 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 = 0.3651 r_free = 0.3651 target = 0.147835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.127171 restraints weight = 10900.855| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.35 r_work: 0.3251 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2110 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= 0.194 Angle : 0.593 8.448 11948 Z= 0.306 Chirality : 0.043 0.175 1383 Planarity : 0.004 0.042 1503 Dihedral : 9.490 158.028 1267 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.86 % Favored : 95.05 % Rotamer: Outliers : 3.52 % Allowed : 15.75 % Favored : 80.73 % 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: 1.23 (0.25), residues: 1112 helix: 1.96 (0.19), residues: 729 sheet: -0.39 (0.96), residues: 33 loop : -1.62 (0.30), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1048 TYR 0.007 0.001 TYR A 89 PHE 0.019 0.002 PHE A 764 TRP 0.011 0.001 TRP A 950 HIS 0.007 0.001 HIS A 171 Details of bonding type rmsd covalent geometry : bond 0.00446 ( 8815) covalent geometry : angle 0.59306 (11948) hydrogen bonds : bond 0.05519 ( 597) hydrogen bonds : angle 3.99498 ( 1755) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1801.37 seconds wall clock time: 31 minutes 25.67 seconds (1885.67 seconds total)