Starting phenix.real_space_refine on Fri Oct 23 08:47:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9x0r_66440/10_2026/9x0r_66440.cif Found real_map, /net/cci-nas-00/data/ceres_data/9x0r_66440/10_2026/9x0r_66440.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9x0r_66440/10_2026/9x0r_66440.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9x0r_66440/10_2026/9x0r_66440.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9x0r_66440/10_2026/9x0r_66440.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9x0r_66440/10_2026/9x0r_66440.map" } resolution = 2.69 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 Fe 4 7.16 5 S 37 5.16 5 C 5710 2.51 5 N 1516 2.21 5 O 1701 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8969 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5621 Classifications: {'peptide': 723} Link IDs: {'PCIS': 2, 'PTRANS': 44, 'TRANS': 676} Chain: "B" Number of atoms: 2335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2335 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 23, 'TRANS': 289} Chain breaks: 2 Chain: "C" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 816 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 97} Chain: "A" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 68 Unusual residues: {' CA': 1, 'HEC': 1, 'PQQ': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 129 Unusual residues: {'HEC': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 1.74, per 1000 atoms: 0.19 Number of scatterers: 8969 At special positions: 0 Unit cell: (85.041, 104.798, 104.798, 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) Fe 4 26.01 Ca 1 19.99 S 37 16.00 O 1701 8.00 N 1516 7.00 C 5710 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 141 " - pdb=" SG CYS A 142 " distance=2.04 Simple disulfide: pdb=" SG CYS C 58 " - pdb=" SG CYS C 122 " distance=2.03 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=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 578.6 milliseconds 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2032 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 13 sheets defined 29.2% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 37 through 46 removed outlier: 3.754A pdb=" N ALA A 41 " --> pdb=" O ASP A 37 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASP A 46 " --> pdb=" O ILE A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 80 Processing helix chain 'A' and resid 110 through 112 No H-bonds generated for 'chain 'A' and resid 110 through 112' Processing helix chain 'A' and resid 133 through 140 removed outlier: 3.799A pdb=" N ILE A 136 " --> pdb=" O PRO A 133 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ASP A 138 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY A 140 " --> pdb=" O ALA A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 258 Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 268 through 273 Processing helix chain 'A' and resid 302 through 308 Processing helix chain 'A' and resid 409 through 411 No H-bonds generated for 'chain 'A' and resid 409 through 411' Processing helix chain 'A' and resid 412 through 417 Processing helix chain 'A' and resid 485 through 498 Processing helix chain 'A' and resid 587 through 594 removed outlier: 3.727A pdb=" N GLY A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 599 removed outlier: 4.168A pdb=" N ARG A 598 " --> pdb=" O GLY A 595 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N THR A 599 " --> pdb=" O VAL A 596 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 595 through 599' Processing helix chain 'A' and resid 638 through 640 No H-bonds generated for 'chain 'A' and resid 638 through 640' Processing helix chain 'A' and resid 641 through 653 Processing helix chain 'A' and resid 653 through 658 Processing helix chain 'A' and resid 659 through 662 Processing helix chain 'A' and resid 674 through 677 Processing helix chain 'A' and resid 678 through 687 Processing helix chain 'A' and resid 704 through 730 removed outlier: 5.047A pdb=" N ASP A 724 " --> pdb=" O ASN A 720 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N ASP A 725 " --> pdb=" O GLU A 721 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 55 Processing helix chain 'B' and resid 176 through 187 Processing helix chain 'B' and resid 192 through 197 Processing helix chain 'B' and resid 208 through 212 Processing helix chain 'B' and resid 239 through 249 Processing helix chain 'B' and resid 259 through 268 removed outlier: 3.548A pdb=" N ASP B 263 " --> pdb=" O GLY B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 272 Processing helix chain 'B' and resid 273 through 285 Processing helix chain 'B' and resid 301 through 309 Processing helix chain 'B' and resid 314 through 324 Processing helix chain 'B' and resid 324 through 329 Processing helix chain 'B' and resid 345 through 350 Processing helix chain 'B' and resid 353 through 362 Processing helix chain 'B' and resid 386 through 399 Processing helix chain 'B' and resid 410 through 420 removed outlier: 3.534A pdb=" N ILE B 414 " --> pdb=" O SER B 410 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR B 419 " --> pdb=" O GLN B 415 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N THR B 420 " --> pdb=" O LYS B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 431 removed outlier: 3.621A pdb=" N VAL B 431 " --> pdb=" O GLY B 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 58 Processing helix chain 'C' and resid 69 through 77 removed outlier: 4.152A pdb=" N GLY C 75 " --> pdb=" O PRO C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 97 removed outlier: 4.104A pdb=" N ALA C 93 " --> pdb=" O ASN C 89 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLY C 95 " --> pdb=" O ASP C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 133 Proline residue: C 131 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 66 through 67 removed outlier: 4.247A pdb=" N VAL A 534 " --> pdb=" O THR A 530 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N ASP A 548 " --> pdb=" O ASP A 554 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASP A 554 " --> pdb=" O ASP A 548 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 81 through 87 removed outlier: 4.907A pdb=" N LEU A 82 " --> pdb=" O SER A 613 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N SER A 613 " --> pdb=" O LEU A 82 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 99 through 101 removed outlier: 6.251A pdb=" N ASP A 118 " --> pdb=" O LEU A 124 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU A 124 " --> pdb=" O ASP A 118 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 150 through 152 removed outlier: 5.994A pdb=" N ASP A 169 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU A 175 " --> pdb=" O ASP A 169 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 201 through 203 removed outlier: 5.880A pdb=" N ASP A 226 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU A 232 " --> pdb=" O ASP A 226 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 274 through 275 removed outlier: 3.659A pdb=" N GLY A 274 " --> pdb=" O SER A 299 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 282 through 285 Processing sheet with id=AA8, first strand: chain 'A' and resid 350 through 356 removed outlier: 6.031A pdb=" N ASP A 377 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N PHE A 383 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 395 through 398 removed outlier: 5.386A pdb=" N ASN A 406 " --> pdb=" O ASN A 396 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 420 through 422 Processing sheet with id=AB2, first strand: chain 'A' and resid 436 through 438 removed outlier: 7.585A pdb=" N GLY A 501 " --> pdb=" O ASN A 518 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N ASN A 518 " --> pdb=" O GLY A 501 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N THR A 503 " --> pdb=" O THR A 516 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N THR A 516 " --> pdb=" O THR A 503 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ALA A 505 " --> pdb=" O ALA A 514 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA A 512 " --> pdb=" O ASP A 507 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 364 through 366 Processing sheet with id=AB4, first strand: chain 'C' and resid 99 through 101 284 hydrogen bonds defined for protein. 747 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: 1.36 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.36: 2980 1.36 - 1.53: 4943 1.53 - 1.69: 1251 1.69 - 1.85: 62 1.85 - 2.01: 16 Bond restraints: 9252 Sorted by residual: bond pdb=" C2D HEC A 801 " pdb=" C3D HEC A 801 " ideal model delta sigma weight residual 1.544 1.328 0.216 2.00e-02 2.50e+03 1.17e+02 bond pdb=" C2D HEC B 501 " pdb=" C3D HEC B 501 " ideal model delta sigma weight residual 1.544 1.328 0.216 2.00e-02 2.50e+03 1.17e+02 bond pdb=" C2D HEC B 502 " pdb=" C3D HEC B 502 " ideal model delta sigma weight residual 1.544 1.329 0.215 2.00e-02 2.50e+03 1.16e+02 bond pdb=" C2D HEC B 503 " pdb=" C3D HEC B 503 " ideal model delta sigma weight residual 1.544 1.329 0.215 2.00e-02 2.50e+03 1.16e+02 bond pdb=" CAC HEC A 801 " pdb=" CBC HEC A 801 " ideal model delta sigma weight residual 1.544 1.363 0.181 2.00e-02 2.50e+03 8.22e+01 ... (remaining 9247 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.96: 12553 2.96 - 5.91: 108 5.91 - 8.87: 6 8.87 - 11.83: 2 11.83 - 14.79: 1 Bond angle restraints: 12670 Sorted by residual: angle pdb=" C ALA B 58 " pdb=" CA ALA B 58 " pdb=" CB ALA B 58 " ideal model delta sigma weight residual 116.63 110.63 6.00 1.16e+00 7.43e-01 2.67e+01 angle pdb=" C3D HEC B 502 " pdb=" CAD HEC B 502 " pdb=" CBD HEC B 502 " ideal model delta sigma weight residual 109.50 124.29 -14.79 3.00e+00 1.11e-01 2.43e+01 angle pdb=" CA ALA B 58 " pdb=" C ALA B 58 " pdb=" N CYS B 59 " ideal model delta sigma weight residual 119.63 116.67 2.96 8.10e-01 1.52e+00 1.34e+01 angle pdb=" C3D HEC B 503 " pdb=" CAD HEC B 503 " pdb=" CBD HEC B 503 " ideal model delta sigma weight residual 109.50 120.22 -10.72 3.00e+00 1.11e-01 1.28e+01 angle pdb=" C3D HEC B 501 " pdb=" CAD HEC B 501 " pdb=" CBD HEC B 501 " ideal model delta sigma weight residual 109.50 119.22 -9.72 3.00e+00 1.11e-01 1.05e+01 ... (remaining 12665 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 4562 17.92 - 35.85: 525 35.85 - 53.77: 148 53.77 - 71.70: 31 71.70 - 89.62: 14 Dihedral angle restraints: 5280 sinusoidal: 2055 harmonic: 3225 Sorted by residual: dihedral pdb=" CA GLU B 125 " pdb=" C GLU B 125 " pdb=" N PHE B 126 " pdb=" CA PHE B 126 " ideal model delta harmonic sigma weight residual -180.00 -148.77 -31.23 0 5.00e+00 4.00e-02 3.90e+01 dihedral pdb=" CA CYS A 141 " pdb=" C CYS A 141 " pdb=" N CYS A 142 " pdb=" CA CYS A 142 " ideal model delta harmonic sigma weight residual -180.00 -157.66 -22.34 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" C2C HEC A 801 " pdb=" C3C HEC A 801 " pdb=" CAC HEC A 801 " pdb=" CBC HEC A 801 " ideal model delta sinusoidal sigma weight residual 60.00 98.00 -38.00 2 1.00e+01 1.00e-02 1.82e+01 ... (remaining 5277 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 691 0.028 - 0.057: 364 0.057 - 0.085: 135 0.085 - 0.113: 68 0.113 - 0.142: 19 Chirality restraints: 1277 Sorted by residual: chirality pdb=" CA ILE A 423 " pdb=" N ILE A 423 " pdb=" C ILE A 423 " pdb=" CB ILE A 423 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" CA MET B 329 " pdb=" N MET B 329 " pdb=" C MET B 329 " pdb=" CB MET B 329 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.59e-01 chirality pdb=" CA ILE A 349 " pdb=" N ILE A 349 " pdb=" C ILE A 349 " pdb=" CB ILE A 349 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.53e-01 ... (remaining 1274 not shown) Planarity restraints: 1658 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CBD HEC B 502 " 0.022 2.00e-02 2.50e+03 4.76e-02 2.26e+01 pdb=" CGD HEC B 502 " -0.082 2.00e-02 2.50e+03 pdb=" O1D HEC B 502 " 0.029 2.00e-02 2.50e+03 pdb=" O2D HEC B 502 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CBD HEC B 503 " -0.022 2.00e-02 2.50e+03 4.69e-02 2.20e+01 pdb=" CGD HEC B 503 " 0.081 2.00e-02 2.50e+03 pdb=" O1D HEC B 503 " -0.029 2.00e-02 2.50e+03 pdb=" O2D HEC B 503 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CBA HEC B 502 " -0.019 2.00e-02 2.50e+03 4.21e-02 1.77e+01 pdb=" CGA HEC B 502 " 0.073 2.00e-02 2.50e+03 pdb=" O1A HEC B 502 " -0.027 2.00e-02 2.50e+03 pdb=" O2A HEC B 502 " -0.027 2.00e-02 2.50e+03 ... (remaining 1655 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 149 2.69 - 3.25: 9037 3.25 - 3.80: 15510 3.80 - 4.35: 21707 4.35 - 4.90: 34210 Nonbonded interactions: 80613 Sorted by model distance: nonbonded pdb=" OE2 GLU A 215 " pdb=" O7A PQQ A 802 " model vdw 2.143 3.040 nonbonded pdb=" OD1 ASN A 297 " pdb=" OD1 ASP A 342 " model vdw 2.156 3.040 nonbonded pdb=" N6 PQQ A 802 " pdb="CA CA A 803 " model vdw 2.251 2.590 nonbonded pdb=" O5 PQQ A 802 " pdb="CA CA A 803 " model vdw 2.332 2.510 nonbonded pdb=" OD1 ASP A 342 " pdb="CA CA A 803 " model vdw 2.340 2.510 ... (remaining 80608 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.860 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: 0.020 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.260 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.249 9266 Z= 0.440 Angle : 0.667 14.787 12674 Z= 0.316 Chirality : 0.043 0.142 1277 Planarity : 0.004 0.048 1658 Dihedral : 17.112 89.624 3242 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.64 % Allowed : 25.19 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.43 (0.25), residues: 1133 helix: 0.96 (0.36), residues: 229 sheet: -0.87 (0.40), residues: 153 loop : -0.54 (0.24), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 139 TYR 0.010 0.001 TYR A 593 PHE 0.010 0.001 PHE C 100 TRP 0.014 0.001 TRP A 331 HIS 0.004 0.000 HIS B 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00779 / 0.36 ( 9252) covalent geometry : angle 0.66700 / 0.32 (12670) SS BOND : bond 0.00577 / 0.30 ( 2) SS BOND : angle 1.56983 / 0.89 ( 4) hydrogen bonds : bond 0.12307 / 7.92 ( 284) hydrogen bonds : angle 7.34932 / 5.13 ( 747) Misc. bond : bond 0.11687 / 5.39 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 86 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 ARG cc_start: 0.7828 (mtm180) cc_final: 0.6786 (mpt90) REVERT: A 171 LYS cc_start: 0.9268 (ttmm) cc_final: 0.8947 (tppt) REVERT: A 348 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8457 (tt0) REVERT: A 426 GLU cc_start: 0.9433 (pm20) cc_final: 0.9087 (pm20) REVERT: B 125 GLU cc_start: 0.6170 (mp0) cc_final: 0.5782 (mp0) REVERT: B 199 ARG cc_start: 0.8451 (mmm-85) cc_final: 0.8070 (mmm-85) REVERT: B 240 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7968 (tp30) REVERT: B 261 MET cc_start: 0.8924 (tpt) cc_final: 0.7833 (tpt) REVERT: B 300 ASP cc_start: 0.9333 (OUTLIER) cc_final: 0.9111 (p0) REVERT: C 81 LYS cc_start: 0.8538 (mtmp) cc_final: 0.8014 (mmtt) REVERT: C 115 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8147 (mm-30) outliers start: 24 outliers final: 18 residues processed: 106 average time/residue: 0.5509 time to fit residues: 62.6052 Evaluate side-chains 103 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 653 CYS Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain C residue 115 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: [108, 49, 97, 53, 5, 33, 65, 62, 51, 100, 106] chunk 108 optimal weight: 0.0370 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 overall best weight: 0.6460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 605 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.075866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.058025 restraints weight = 19227.176| |-----------------------------------------------------------------------------| r_work (start): 0.2715 rms_B_bonded: 2.48 r_work: 0.2614 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2494 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.0427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.190 9266 Z= 0.129 Angle : 0.558 6.849 12674 Z= 0.273 Chirality : 0.044 0.141 1277 Planarity : 0.004 0.040 1658 Dihedral : 9.310 84.883 1305 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 4.40 % Allowed : 22.55 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.40 (0.26), residues: 1133 helix: 0.84 (0.34), residues: 249 sheet: -0.99 (0.39), residues: 161 loop : -0.45 (0.24), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 679 TYR 0.011 0.001 TYR A 593 PHE 0.010 0.001 PHE C 100 TRP 0.011 0.001 TRP A 331 HIS 0.004 0.000 HIS B 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.13 ( 9252) covalent geometry : angle 0.55776 / 0.27 (12670) SS BOND : bond 0.00565 / 0.30 ( 2) SS BOND : angle 1.52750 / 0.86 ( 4) hydrogen bonds : bond 0.03265 / 2.20 ( 284) hydrogen bonds : angle 5.92425 / 4.14 ( 747) Misc. bond : bond 0.07984 / 3.89 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 79 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASN cc_start: 0.9140 (OUTLIER) cc_final: 0.8682 (m-40) REVERT: A 139 ARG cc_start: 0.7835 (mtm180) cc_final: 0.6801 (mpt90) REVERT: A 171 LYS cc_start: 0.9279 (ttmm) cc_final: 0.8960 (tppt) REVERT: A 426 GLU cc_start: 0.9383 (pm20) cc_final: 0.9007 (pm20) REVERT: A 734 THR cc_start: 0.9412 (OUTLIER) cc_final: 0.9151 (p) REVERT: B 125 GLU cc_start: 0.5973 (OUTLIER) cc_final: 0.5712 (mp0) REVERT: B 199 ARG cc_start: 0.8437 (mmm-85) cc_final: 0.8087 (mmm-85) REVERT: B 240 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.8032 (tt0) REVERT: B 300 ASP cc_start: 0.9314 (OUTLIER) cc_final: 0.9086 (p0) REVERT: C 81 LYS cc_start: 0.8574 (mtmp) cc_final: 0.8057 (mmtt) REVERT: C 115 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8143 (mm-30) outliers start: 40 outliers final: 15 residues processed: 109 average time/residue: 0.5177 time to fit residues: 60.6939 Evaluate side-chains 99 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 653 CYS Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 738 ASN Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 115 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: [24, 74, 46, 96, 34, 4, 17, 101, 0, 89, 47] chunk 24 optimal weight: 3.9990 chunk 74 optimal weight: 0.4980 chunk 46 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 17 optimal weight: 0.0970 chunk 101 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 89 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.075532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.057610 restraints weight = 19237.300| |-----------------------------------------------------------------------------| r_work (start): 0.2702 rms_B_bonded: 2.51 r_work: 0.2600 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2481 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.0539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.214 9266 Z= 0.143 Angle : 0.560 6.870 12674 Z= 0.275 Chirality : 0.044 0.141 1277 Planarity : 0.004 0.041 1658 Dihedral : 8.760 82.568 1284 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 4.62 % Allowed : 22.55 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.39 (0.26), residues: 1133 helix: 0.90 (0.35), residues: 248 sheet: -1.03 (0.39), residues: 162 loop : -0.44 (0.24), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 106 TYR 0.012 0.001 TYR B 123 PHE 0.010 0.001 PHE C 100 TRP 0.011 0.001 TRP A 331 HIS 0.003 0.001 HIS B 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.14 ( 9252) covalent geometry : angle 0.55911 / 0.27 (12670) SS BOND : bond 0.00532 / 0.28 ( 2) SS BOND : angle 1.54537 / 0.88 ( 4) hydrogen bonds : bond 0.03277 / 2.21 ( 284) hydrogen bonds : angle 5.67518 / 3.97 ( 747) Misc. bond : bond 0.09002 / 4.63 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 81 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 ASN cc_start: 0.9143 (OUTLIER) cc_final: 0.8677 (m-40) REVERT: A 139 ARG cc_start: 0.7822 (mtm180) cc_final: 0.6821 (mpt90) REVERT: A 171 LYS cc_start: 0.9278 (ttmm) cc_final: 0.8956 (tppt) REVERT: A 174 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.8056 (mmtm) REVERT: A 359 GLU cc_start: 0.6828 (OUTLIER) cc_final: 0.6433 (pp20) REVERT: A 426 GLU cc_start: 0.9395 (pm20) cc_final: 0.9146 (pm20) REVERT: A 734 THR cc_start: 0.9411 (OUTLIER) cc_final: 0.9142 (p) REVERT: B 121 MET cc_start: 0.7896 (OUTLIER) cc_final: 0.7480 (mmt) REVERT: B 199 ARG cc_start: 0.8476 (mmm-85) cc_final: 0.8102 (mmm-85) REVERT: B 261 MET cc_start: 0.8997 (tpt) cc_final: 0.7597 (tpt) REVERT: B 300 ASP cc_start: 0.9313 (OUTLIER) cc_final: 0.9081 (p0) REVERT: C 81 LYS cc_start: 0.8586 (mtmp) cc_final: 0.8071 (mmtt) REVERT: C 115 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8134 (mm-30) outliers start: 42 outliers final: 21 residues processed: 114 average time/residue: 0.5302 time to fit residues: 64.8471 Evaluate side-chains 107 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 79 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 653 CYS Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 738 ASN Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 274 ASP Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 115 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: [65, 20, 68, 33, 80, 61, 62, 41, 37, 55, 87] chunk 65 optimal weight: 0.0370 chunk 20 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 62 optimal weight: 0.0070 chunk 41 optimal weight: 0.8980 chunk 37 optimal weight: 0.3980 chunk 55 optimal weight: 1.9990 chunk 87 optimal weight: 0.3980 overall best weight: 0.2876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 370 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.077251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.059375 restraints weight = 19354.083| |-----------------------------------------------------------------------------| r_work (start): 0.2739 rms_B_bonded: 2.52 r_work: 0.2638 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2519 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.0643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.131 9266 Z= 0.099 Angle : 0.536 6.990 12674 Z= 0.263 Chirality : 0.043 0.139 1277 Planarity : 0.003 0.041 1658 Dihedral : 8.389 82.921 1281 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 3.85 % Allowed : 23.65 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.32 (0.26), residues: 1133 helix: 0.97 (0.35), residues: 248 sheet: -0.78 (0.40), residues: 155 loop : -0.47 (0.24), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 730 TYR 0.012 0.001 TYR B 123 PHE 0.010 0.001 PHE C 100 TRP 0.012 0.001 TRP A 331 HIS 0.002 0.000 HIS B 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.10 ( 9252) covalent geometry : angle 0.53565 / 0.26 (12670) SS BOND : bond 0.00677 / 0.36 ( 2) SS BOND : angle 1.56115 / 0.88 ( 4) hydrogen bonds : bond 0.02852 / 1.95 ( 284) hydrogen bonds : angle 5.45285 / 3.81 ( 747) Misc. bond : bond 0.06706 / 3.44 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 84 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 ASN cc_start: 0.9144 (OUTLIER) cc_final: 0.8672 (m-40) REVERT: A 139 ARG cc_start: 0.7766 (mtm180) cc_final: 0.6766 (mpt90) REVERT: A 171 LYS cc_start: 0.9261 (ttmm) cc_final: 0.8936 (tppt) REVERT: A 359 GLU cc_start: 0.6799 (OUTLIER) cc_final: 0.6419 (pp20) REVERT: A 426 GLU cc_start: 0.9361 (pm20) cc_final: 0.9086 (pm20) REVERT: A 734 THR cc_start: 0.9400 (OUTLIER) cc_final: 0.9147 (p) REVERT: B 121 MET cc_start: 0.7785 (mpp) cc_final: 0.7344 (mmt) REVERT: B 199 ARG cc_start: 0.8471 (mmm-85) cc_final: 0.8129 (mmm-85) REVERT: B 261 MET cc_start: 0.8981 (OUTLIER) cc_final: 0.7704 (tpt) REVERT: B 300 ASP cc_start: 0.9312 (OUTLIER) cc_final: 0.9071 (p0) REVERT: C 81 LYS cc_start: 0.8510 (mtmp) cc_final: 0.7936 (mmtt) REVERT: C 115 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8072 (mm-30) outliers start: 35 outliers final: 18 residues processed: 111 average time/residue: 0.5471 time to fit residues: 65.0588 Evaluate side-chains 106 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 82 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 653 CYS Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 738 ASN Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 261 MET Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 115 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: [93, 84, 13, 18, 38, 103, 54, 15, 100, 33, 56] chunk 93 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 103 optimal weight: 0.4980 chunk 54 optimal weight: 0.8980 chunk 15 optimal weight: 0.0020 chunk 100 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 overall best weight: 1.2792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 370 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.074888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.056903 restraints weight = 19481.992| |-----------------------------------------------------------------------------| r_work (start): 0.2681 rms_B_bonded: 2.49 r_work: 0.2579 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2460 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.0712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.244 9266 Z= 0.192 Angle : 0.585 7.455 12674 Z= 0.286 Chirality : 0.046 0.142 1277 Planarity : 0.004 0.042 1658 Dihedral : 8.431 81.843 1281 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 4.84 % Allowed : 22.11 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.40 (0.26), residues: 1133 helix: 0.94 (0.34), residues: 249 sheet: -1.21 (0.37), residues: 178 loop : -0.40 (0.25), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 106 TYR 0.015 0.001 TYR A 329 PHE 0.009 0.001 PHE C 100 TRP 0.011 0.001 TRP A 585 HIS 0.004 0.001 HIS A 657 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.19 ( 9252) covalent geometry : angle 0.58429 / 0.29 (12670) SS BOND : bond 0.00434 / 0.23 ( 2) SS BOND : angle 1.55477 / 0.89 ( 4) hydrogen bonds : bond 0.03390 / 2.29 ( 284) hydrogen bonds : angle 5.55662 / 3.89 ( 747) Misc. bond : bond 0.09662 / 4.95 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 80 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 ASN cc_start: 0.9147 (OUTLIER) cc_final: 0.8678 (m-40) REVERT: A 139 ARG cc_start: 0.7822 (mtm180) cc_final: 0.6841 (mpt90) REVERT: A 171 LYS cc_start: 0.9286 (ttmm) cc_final: 0.8970 (tppt) REVERT: A 174 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.8041 (mmtm) REVERT: A 359 GLU cc_start: 0.6852 (OUTLIER) cc_final: 0.6453 (pp20) REVERT: A 426 GLU cc_start: 0.9387 (pm20) cc_final: 0.9131 (pm20) REVERT: A 528 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8543 (tp) REVERT: A 734 THR cc_start: 0.9413 (OUTLIER) cc_final: 0.9135 (p) REVERT: B 121 MET cc_start: 0.7857 (OUTLIER) cc_final: 0.7369 (mmt) REVERT: B 199 ARG cc_start: 0.8486 (mmm-85) cc_final: 0.8116 (mmm-85) REVERT: B 261 MET cc_start: 0.9012 (OUTLIER) cc_final: 0.7992 (tpt) REVERT: B 300 ASP cc_start: 0.9317 (OUTLIER) cc_final: 0.9083 (p0) REVERT: C 81 LYS cc_start: 0.8628 (mtmp) cc_final: 0.8108 (mmtt) REVERT: C 115 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8153 (mm-30) outliers start: 44 outliers final: 27 residues processed: 113 average time/residue: 0.5245 time to fit residues: 63.6188 Evaluate side-chains 115 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 79 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 653 CYS Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 738 ASN Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 261 MET Chi-restraints excluded: chain B residue 274 ASP Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 115 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: [37, 22, 94, 5, 20, 51, 74, 90, 68, 112, 103] chunk 37 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 20 optimal weight: 0.0170 chunk 51 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 103 optimal weight: 0.1980 overall best weight: 0.8022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 370 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.075552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.057593 restraints weight = 19337.118| |-----------------------------------------------------------------------------| r_work (start): 0.2701 rms_B_bonded: 2.49 r_work: 0.2600 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2482 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.0706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.212 9266 Z= 0.142 Angle : 0.565 7.821 12674 Z= 0.276 Chirality : 0.044 0.139 1277 Planarity : 0.004 0.042 1658 Dihedral : 8.408 81.719 1281 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 4.18 % Allowed : 22.99 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.26), residues: 1133 helix: 0.95 (0.34), residues: 249 sheet: -1.01 (0.39), residues: 162 loop : -0.45 (0.24), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 106 TYR 0.012 0.001 TYR A 593 PHE 0.009 0.001 PHE C 100 TRP 0.011 0.001 TRP A 331 HIS 0.003 0.000 HIS A 657 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.14 ( 9252) covalent geometry : angle 0.56399 / 0.28 (12670) SS BOND : bond 0.00529 / 0.28 ( 2) SS BOND : angle 1.55299 / 0.88 ( 4) hydrogen bonds : bond 0.03162 / 2.14 ( 284) hydrogen bonds : angle 5.48894 / 3.84 ( 747) Misc. bond : bond 0.08649 / 4.40 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 80 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 ASN cc_start: 0.9133 (OUTLIER) cc_final: 0.8661 (m-40) REVERT: A 139 ARG cc_start: 0.7808 (mtm180) cc_final: 0.6835 (mpt90) REVERT: A 171 LYS cc_start: 0.9278 (ttmm) cc_final: 0.8959 (tppt) REVERT: A 185 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7413 (pm20) REVERT: A 340 GLU cc_start: 0.9187 (OUTLIER) cc_final: 0.8619 (pt0) REVERT: A 359 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.6459 (pp20) REVERT: A 426 GLU cc_start: 0.9391 (pm20) cc_final: 0.9131 (pm20) REVERT: A 528 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8519 (tp) REVERT: A 734 THR cc_start: 0.9414 (OUTLIER) cc_final: 0.9142 (p) REVERT: B 121 MET cc_start: 0.7818 (OUTLIER) cc_final: 0.7321 (mmt) REVERT: B 199 ARG cc_start: 0.8483 (mmm-85) cc_final: 0.8112 (mmm-85) REVERT: B 261 MET cc_start: 0.9021 (OUTLIER) cc_final: 0.7977 (tpt) REVERT: B 300 ASP cc_start: 0.9324 (OUTLIER) cc_final: 0.9073 (p0) REVERT: C 81 LYS cc_start: 0.8608 (mtmp) cc_final: 0.8090 (mmtt) REVERT: C 115 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8183 (mm-30) outliers start: 38 outliers final: 24 residues processed: 110 average time/residue: 0.5565 time to fit residues: 65.7001 Evaluate side-chains 112 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 79 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 653 CYS Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 738 ASN Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 261 MET Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain C residue 115 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: [11, 16, 40, 57, 84, 65, 111, 83, 32, 67, 78] chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 65 optimal weight: 0.0980 chunk 111 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 78 optimal weight: 0.1980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 370 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.076389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.058411 restraints weight = 19420.929| |-----------------------------------------------------------------------------| r_work (start): 0.2719 rms_B_bonded: 2.51 r_work: 0.2617 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2498 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.0661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.162 9266 Z= 0.116 Angle : 0.551 8.828 12674 Z= 0.269 Chirality : 0.044 0.140 1277 Planarity : 0.004 0.042 1658 Dihedral : 8.336 82.243 1281 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 3.52 % Allowed : 23.65 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.34 (0.26), residues: 1133 helix: 1.00 (0.34), residues: 248 sheet: -0.98 (0.39), residues: 162 loop : -0.44 (0.24), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 235 TYR 0.011 0.001 TYR A 593 PHE 0.009 0.001 PHE C 100 TRP 0.011 0.001 TRP A 331 HIS 0.002 0.000 HIS B 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.11 ( 9252) covalent geometry : angle 0.55081 / 0.27 (12670) SS BOND : bond 0.00597 / 0.31 ( 2) SS BOND : angle 1.56845 / 0.89 ( 4) hydrogen bonds : bond 0.02944 / 2.00 ( 284) hydrogen bonds : angle 5.41068 / 3.79 ( 747) Misc. bond : bond 0.07163 / 3.62 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 83 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 ASN cc_start: 0.9137 (OUTLIER) cc_final: 0.8671 (m-40) REVERT: A 139 ARG cc_start: 0.7751 (mtm180) cc_final: 0.6796 (mpt90) REVERT: A 171 LYS cc_start: 0.9269 (ttmm) cc_final: 0.8944 (tppt) REVERT: A 359 GLU cc_start: 0.6807 (OUTLIER) cc_final: 0.6429 (pp20) REVERT: A 426 GLU cc_start: 0.9393 (pm20) cc_final: 0.9117 (pm20) REVERT: A 528 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8442 (tp) REVERT: A 734 THR cc_start: 0.9401 (OUTLIER) cc_final: 0.9140 (p) REVERT: B 121 MET cc_start: 0.7785 (OUTLIER) cc_final: 0.7338 (mmt) REVERT: B 199 ARG cc_start: 0.8486 (mmm-85) cc_final: 0.8130 (mmm-85) REVERT: B 261 MET cc_start: 0.8994 (OUTLIER) cc_final: 0.7925 (tpt) REVERT: B 300 ASP cc_start: 0.9321 (OUTLIER) cc_final: 0.9076 (p0) REVERT: C 81 LYS cc_start: 0.8563 (mtmp) cc_final: 0.8041 (mmtt) REVERT: C 115 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8124 (mm-30) outliers start: 32 outliers final: 19 residues processed: 109 average time/residue: 0.5477 time to fit residues: 63.9331 Evaluate side-chains 108 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 81 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 653 CYS Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 738 ASN Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 261 MET Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain C residue 115 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: [83, 104, 38, 59, 94, 75, 90, 30, 102, 35, 3] chunk 83 optimal weight: 0.5980 chunk 104 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 59 optimal weight: 0.3980 chunk 94 optimal weight: 0.7980 chunk 75 optimal weight: 0.0270 chunk 90 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 102 optimal weight: 0.1980 chunk 35 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.076970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.059013 restraints weight = 19300.147| |-----------------------------------------------------------------------------| r_work (start): 0.2734 rms_B_bonded: 2.51 r_work: 0.2634 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2516 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.0739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.150 9266 Z= 0.107 Angle : 0.550 8.477 12674 Z= 0.268 Chirality : 0.043 0.141 1277 Planarity : 0.004 0.042 1658 Dihedral : 8.281 83.638 1281 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 3.52 % Allowed : 23.76 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.26), residues: 1133 helix: 1.11 (0.35), residues: 242 sheet: -0.92 (0.39), residues: 160 loop : -0.44 (0.24), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 235 TYR 0.011 0.001 TYR B 123 PHE 0.010 0.001 PHE C 100 TRP 0.012 0.001 TRP A 331 HIS 0.002 0.000 HIS B 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 ( 9252) covalent geometry : angle 0.54889 / 0.27 (12670) SS BOND : bond 0.00633 / 0.33 ( 2) SS BOND : angle 1.57893 / 0.89 ( 4) hydrogen bonds : bond 0.02870 / 1.96 ( 284) hydrogen bonds : angle 5.35552 / 3.75 ( 747) Misc. bond : bond 0.06537 / 3.27 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 81 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASN cc_start: 0.9124 (OUTLIER) cc_final: 0.8661 (m-40) REVERT: A 139 ARG cc_start: 0.7751 (mtm180) cc_final: 0.6792 (mpt90) REVERT: A 171 LYS cc_start: 0.9269 (ttmm) cc_final: 0.8944 (tppt) REVERT: A 350 MET cc_start: 0.9140 (ttm) cc_final: 0.8903 (ttm) REVERT: A 359 GLU cc_start: 0.6817 (OUTLIER) cc_final: 0.6438 (pp20) REVERT: A 426 GLU cc_start: 0.9386 (pm20) cc_final: 0.9116 (pm20) REVERT: A 528 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8429 (tp) REVERT: A 734 THR cc_start: 0.9402 (OUTLIER) cc_final: 0.9148 (p) REVERT: B 121 MET cc_start: 0.7897 (OUTLIER) cc_final: 0.7344 (mmt) REVERT: B 199 ARG cc_start: 0.8444 (mmm-85) cc_final: 0.8104 (mmm-85) REVERT: B 261 MET cc_start: 0.8997 (OUTLIER) cc_final: 0.7925 (tpt) REVERT: B 300 ASP cc_start: 0.9324 (OUTLIER) cc_final: 0.9085 (p0) REVERT: C 81 LYS cc_start: 0.8540 (mtmp) cc_final: 0.8018 (mmtt) REVERT: C 115 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8098 (mm-30) outliers start: 32 outliers final: 21 residues processed: 107 average time/residue: 0.5462 time to fit residues: 62.6445 Evaluate side-chains 108 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 79 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 653 CYS Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 738 ASN Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 192 CYS Chi-restraints excluded: chain B residue 261 MET Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 383 ASN Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain C residue 115 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: [71, 84, 70, 90, 93, 8, 10, 3, 74, 110, 64] chunk 71 optimal weight: 0.0670 chunk 84 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 3 optimal weight: 0.0570 chunk 74 optimal weight: 10.0000 chunk 110 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.7838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.075998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.058008 restraints weight = 19344.919| |-----------------------------------------------------------------------------| r_work (start): 0.2713 rms_B_bonded: 2.52 r_work: 0.2613 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2495 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.0727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.216 9266 Z= 0.140 Angle : 0.572 9.112 12674 Z= 0.276 Chirality : 0.044 0.142 1277 Planarity : 0.004 0.042 1658 Dihedral : 8.295 83.489 1281 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 3.74 % Allowed : 23.32 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.38 (0.26), residues: 1133 helix: 0.97 (0.34), residues: 248 sheet: -1.01 (0.39), residues: 164 loop : -0.47 (0.24), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 235 TYR 0.012 0.001 TYR A 329 PHE 0.010 0.001 PHE C 100 TRP 0.010 0.001 TRP A 331 HIS 0.003 0.000 HIS A 657 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.14 ( 9252) covalent geometry : angle 0.57136 / 0.28 (12670) SS BOND : bond 0.00559 / 0.29 ( 2) SS BOND : angle 1.56145 / 0.89 ( 4) hydrogen bonds : bond 0.03065 / 2.08 ( 284) hydrogen bonds : angle 5.39653 / 3.78 ( 747) Misc. bond : bond 0.08115 / 4.07 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 80 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASN cc_start: 0.9149 (OUTLIER) cc_final: 0.8678 (m-40) REVERT: A 139 ARG cc_start: 0.7776 (mtm180) cc_final: 0.6830 (mpt90) REVERT: A 171 LYS cc_start: 0.9282 (ttmm) cc_final: 0.8965 (tppt) REVERT: A 350 MET cc_start: 0.9176 (ttm) cc_final: 0.8948 (ttm) REVERT: A 359 GLU cc_start: 0.6877 (OUTLIER) cc_final: 0.6496 (pp20) REVERT: A 426 GLU cc_start: 0.9409 (pm20) cc_final: 0.9135 (pm20) REVERT: A 528 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8499 (tp) REVERT: A 734 THR cc_start: 0.9412 (OUTLIER) cc_final: 0.9150 (p) REVERT: B 121 MET cc_start: 0.7879 (OUTLIER) cc_final: 0.7257 (mmt) REVERT: B 199 ARG cc_start: 0.8462 (mmm-85) cc_final: 0.8120 (mmm-85) REVERT: B 261 MET cc_start: 0.9020 (OUTLIER) cc_final: 0.7971 (tpt) REVERT: B 300 ASP cc_start: 0.9331 (OUTLIER) cc_final: 0.9095 (p0) REVERT: C 81 LYS cc_start: 0.8592 (mtmp) cc_final: 0.8068 (mmtt) REVERT: C 115 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8107 (mm-30) outliers start: 34 outliers final: 22 residues processed: 108 average time/residue: 0.5421 time to fit residues: 62.8997 Evaluate side-chains 109 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 79 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 653 CYS Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 738 ASN Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 192 CYS Chi-restraints excluded: chain B residue 261 MET Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 115 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: [91, 105, 94, 23, 38, 41, 83, 24, 60, 27, 69] chunk 91 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 83 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 69 optimal weight: 0.0370 overall best weight: 0.9260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.075452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.057490 restraints weight = 19240.038| |-----------------------------------------------------------------------------| r_work (start): 0.2698 rms_B_bonded: 2.49 r_work: 0.2596 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2478 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.0778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.236 9266 Z= 0.155 Angle : 0.584 9.489 12674 Z= 0.282 Chirality : 0.045 0.140 1277 Planarity : 0.004 0.042 1658 Dihedral : 8.338 82.731 1281 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 3.63 % Allowed : 23.43 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.39 (0.26), residues: 1133 helix: 0.91 (0.34), residues: 250 sheet: -1.02 (0.39), residues: 164 loop : -0.45 (0.24), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 235 TYR 0.013 0.001 TYR A 329 PHE 0.009 0.001 PHE C 100 TRP 0.010 0.001 TRP A 585 HIS 0.003 0.000 HIS A 657 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.15 ( 9252) covalent geometry : angle 0.58352 / 0.28 (12670) SS BOND : bond 0.00508 / 0.27 ( 2) SS BOND : angle 1.57785 / 0.90 ( 4) hydrogen bonds : bond 0.03180 / 2.16 ( 284) hydrogen bonds : angle 5.44542 / 3.82 ( 747) Misc. bond : bond 0.08734 / 4.39 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 77 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASN cc_start: 0.9130 (OUTLIER) cc_final: 0.8666 (m-40) REVERT: A 139 ARG cc_start: 0.7775 (mtm180) cc_final: 0.6812 (mpt90) REVERT: A 171 LYS cc_start: 0.9275 (ttmm) cc_final: 0.8957 (tppt) REVERT: A 359 GLU cc_start: 0.6814 (OUTLIER) cc_final: 0.6436 (pp20) REVERT: A 426 GLU cc_start: 0.9395 (pm20) cc_final: 0.9127 (pm20) REVERT: A 528 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8474 (tp) REVERT: A 734 THR cc_start: 0.9402 (OUTLIER) cc_final: 0.9130 (p) REVERT: B 121 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.7236 (mmt) REVERT: B 199 ARG cc_start: 0.8484 (mmm-85) cc_final: 0.8139 (mmm-85) REVERT: B 261 MET cc_start: 0.8995 (OUTLIER) cc_final: 0.7551 (tpt) REVERT: B 300 ASP cc_start: 0.9333 (OUTLIER) cc_final: 0.9083 (p0) REVERT: C 81 LYS cc_start: 0.8590 (mtmp) cc_final: 0.8073 (mmtt) REVERT: C 115 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8174 (mm-30) outliers start: 33 outliers final: 22 residues processed: 106 average time/residue: 0.5456 time to fit residues: 61.9853 Evaluate side-chains 108 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 78 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 653 CYS Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 738 ASN Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 192 CYS Chi-restraints excluded: chain B residue 261 MET Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain C residue 115 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: [94, 76, 96, 83, 105, 106, 28, 38, 79, 86, 27] chunk 94 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 105 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 38 optimal weight: 0.0470 chunk 79 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.076280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.058330 restraints weight = 19065.332| |-----------------------------------------------------------------------------| r_work (start): 0.2718 rms_B_bonded: 2.50 r_work: 0.2617 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2498 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.0724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.204 9266 Z= 0.123 Angle : 0.573 8.966 12674 Z= 0.276 Chirality : 0.044 0.149 1277 Planarity : 0.004 0.042 1658 Dihedral : 8.301 82.564 1281 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 3.30 % Allowed : 23.98 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.36 (0.26), residues: 1133 helix: 0.98 (0.34), residues: 249 sheet: -0.99 (0.39), residues: 164 loop : -0.45 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 235 TYR 0.011 0.001 TYR A 593 PHE 0.010 0.001 PHE C 100 TRP 0.011 0.001 TRP A 331 HIS 0.002 0.000 HIS B 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.12 ( 9252) covalent geometry : angle 0.57233 / 0.28 (12670) SS BOND : bond 0.00590 / 0.31 ( 2) SS BOND : angle 1.61510 / 0.91 ( 4) hydrogen bonds : bond 0.02968 / 2.02 ( 284) hydrogen bonds : angle 5.40442 / 3.79 ( 747) Misc. bond : bond 0.07676 / 3.83 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3123.69 seconds wall clock time: 54 minutes 1.46 seconds (3241.46 seconds total)