Starting phenix.real_space_refine on Thu Jul 2 00:36:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hg7_34737/07_2026/8hg7_34737.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hg7_34737/07_2026/8hg7_34737.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 { model { file = "/net/cci-nas-00/data/ceres_data/8hg7_34737/07_2026/8hg7_34737.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hg7_34737/07_2026/8hg7_34737.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hg7_34737/07_2026/8hg7_34737.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hg7_34737/07_2026/8hg7_34737.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8hg7_34737/07_2026/8hg7_34737.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hg7_34737/07_2026/8hg7_34737.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= 0.001 sd= 0.010 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 S 38 5.16 5 Cl 1 4.86 5 Na 1 4.78 5 C 3169 2.51 5 N 786 2.21 5 O 813 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4808 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4532 Classifications: {'peptide': 590} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 562} Chain breaks: 1 Chain: "B" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 231 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 1, 'TRANS': 27} Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 45 Unusual residues: {' NA': 1, 'LFL': 1, 'NAG': 1} Classifications: {'undetermined': 3, 'water': 2} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.04, per 1000 atoms: 0.22 Number of scatterers: 4808 At special positions: 0 Unit cell: (74.1469, 74.1469, 95.1736, 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) Cl 1 17.00 S 38 16.00 Na 1 11.00 O 813 8.00 N 786 7.00 C 3169 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 255 " - pdb=" SG CYS A 511 " distance=2.33 Simple disulfide: pdb=" SG CYS A 345 " - pdb=" SG CYS A 351 " distance=2.41 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 361 " distance=2.30 Simple disulfide: pdb=" SG CYS A 517 " - pdb=" SG CYS A 522 " distance=2.28 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: 0.46 Conformation dependent library (CDL) restraints added in 217.7 milliseconds 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1124 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 0 sheets defined 82.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'A' and resid 22 through 47 Processing helix chain 'A' and resid 51 through 58 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 77 through 92 removed outlier: 3.833A pdb=" N PHE A 81 " --> pdb=" O GLY A 77 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA A 85 " --> pdb=" O PHE A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 120 removed outlier: 4.178A pdb=" N GLU A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA A 102 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU A 103 " --> pdb=" O GLU A 99 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N PHE A 104 " --> pdb=" O TRP A 100 " (cutoff:3.500A) Proline residue: A 115 - end of helix Processing helix chain 'A' and resid 124 through 134 removed outlier: 3.606A pdb=" N LEU A 129 " --> pdb=" O MET A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 154 removed outlier: 3.795A pdb=" N LEU A 140 " --> pdb=" O ARG A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 170 removed outlier: 3.634A pdb=" N ASP A 158 " --> pdb=" O LYS A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 193 removed outlier: 4.490A pdb=" N GLY A 192 " --> pdb=" O TYR A 188 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY A 193 " --> pdb=" O THR A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 224 removed outlier: 3.835A pdb=" N VAL A 203 " --> pdb=" O TYR A 199 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE A 206 " --> pdb=" O THR A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 233 removed outlier: 3.521A pdb=" N LEU A 229 " --> pdb=" O GLY A 225 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE A 230 " --> pdb=" O TYR A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.634A pdb=" N TYR A 256 " --> pdb=" O SER A 252 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG A 257 " --> pdb=" O SER A 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 252 through 257' Processing helix chain 'A' and resid 275 through 293 Processing helix chain 'A' and resid 294 through 299 Processing helix chain 'A' and resid 306 through 321 Processing helix chain 'A' and resid 322 through 328 removed outlier: 3.999A pdb=" N PHE A 326 " --> pdb=" O LEU A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 339 Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 347 through 356 Processing helix chain 'A' and resid 361 through 363 No H-bonds generated for 'chain 'A' and resid 361 through 363' Processing helix chain 'A' and resid 364 through 374 removed outlier: 3.615A pdb=" N MET A 374 " --> pdb=" O VAL A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 409 Processing helix chain 'A' and resid 409 through 414 Processing helix chain 'A' and resid 420 through 446 removed outlier: 3.592A pdb=" N VAL A 430 " --> pdb=" O GLY A 426 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A 431 " --> pdb=" O ARG A 427 " (cutoff:3.500A) Proline residue: A 442 - end of helix Processing helix chain 'A' and resid 447 through 449 No H-bonds generated for 'chain 'A' and resid 447 through 449' Processing helix chain 'A' and resid 450 through 464 removed outlier: 3.847A pdb=" N ASP A 454 " --> pdb=" O GLY A 450 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN A 457 " --> pdb=" O PHE A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 477 removed outlier: 3.571A pdb=" N LEU A 473 " --> pdb=" O ALA A 469 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL A 477 " --> pdb=" O LEU A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 507 removed outlier: 3.596A pdb=" N ARG A 499 " --> pdb=" O MET A 495 " (cutoff:3.500A) Proline residue: A 502 - end of helix removed outlier: 3.983A pdb=" N PHE A 506 " --> pdb=" O PRO A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 523 removed outlier: 3.577A pdb=" N CYS A 522 " --> pdb=" O PRO A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 548 removed outlier: 3.672A pdb=" N ILE A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 556 Processing helix chain 'A' and resid 560 through 564 removed outlier: 3.671A pdb=" N ARG A 564 " --> pdb=" O PHE A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 671 removed outlier: 3.509A pdb=" N LEU A 658 " --> pdb=" O ASN A 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 55 338 hydrogen bonds defined for protein. 1005 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: 0.52 Time building geometry restraints manager: 0.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 709 1.29 - 1.43: 1412 1.43 - 1.57: 2753 1.57 - 1.72: 1 1.72 - 1.86: 59 Bond restraints: 4934 Sorted by residual: bond pdb=" C MET A 325 " pdb=" O MET A 325 " ideal model delta sigma weight residual 1.237 1.147 0.090 1.19e-02 7.06e+03 5.67e+01 bond pdb=" C PRO A 502 " pdb=" O PRO A 502 " ideal model delta sigma weight residual 1.238 1.149 0.089 1.33e-02 5.65e+03 4.50e+01 bond pdb=" C PRO A 115 " pdb=" O PRO A 115 " ideal model delta sigma weight residual 1.235 1.153 0.082 1.30e-02 5.92e+03 3.94e+01 bond pdb=" C PRO A 324 " pdb=" O PRO A 324 " ideal model delta sigma weight residual 1.238 1.162 0.076 1.33e-02 5.65e+03 3.24e+01 bond pdb=" C TRP A 100 " pdb=" O TRP A 100 " ideal model delta sigma weight residual 1.236 1.308 -0.071 1.29e-02 6.01e+03 3.07e+01 ... (remaining 4929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 4541 2.14 - 4.28: 1850 4.28 - 6.43: 295 6.43 - 8.57: 37 8.57 - 10.71: 5 Bond angle restraints: 6728 Sorted by residual: angle pdb=" N PHE A 113 " pdb=" CA PHE A 113 " pdb=" C PHE A 113 " ideal model delta sigma weight residual 113.55 104.63 8.92 1.26e+00 6.30e-01 5.01e+01 angle pdb=" CA ASP A 261 " pdb=" CB ASP A 261 " pdb=" CG ASP A 261 " ideal model delta sigma weight residual 112.60 119.63 -7.03 1.00e+00 1.00e+00 4.95e+01 angle pdb=" C PHE A 98 " pdb=" CA PHE A 98 " pdb=" CB PHE A 98 " ideal model delta sigma weight residual 110.88 121.59 -10.71 1.57e+00 4.06e-01 4.65e+01 angle pdb=" CA PHE A 148 " pdb=" C PHE A 148 " pdb=" O PHE A 148 " ideal model delta sigma weight residual 120.42 113.58 6.84 1.06e+00 8.90e-01 4.16e+01 angle pdb=" N CYS A 522 " pdb=" CA CYS A 522 " pdb=" C CYS A 522 " ideal model delta sigma weight residual 110.97 118.00 -7.03 1.09e+00 8.42e-01 4.16e+01 ... (remaining 6723 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 2547 17.40 - 34.80: 241 34.80 - 52.19: 52 52.19 - 69.59: 12 69.59 - 86.99: 3 Dihedral angle restraints: 2855 sinusoidal: 1091 harmonic: 1764 Sorted by residual: dihedral pdb=" CB CYS A 255 " pdb=" SG CYS A 255 " pdb=" SG CYS A 511 " pdb=" CB CYS A 511 " ideal model delta sinusoidal sigma weight residual -86.00 -21.88 -64.12 1 1.00e+01 1.00e-02 5.41e+01 dihedral pdb=" C PRO A 502 " pdb=" N PRO A 502 " pdb=" CA PRO A 502 " pdb=" CB PRO A 502 " ideal model delta harmonic sigma weight residual -120.70 -134.66 13.96 0 2.50e+00 1.60e-01 3.12e+01 dihedral pdb=" CA GLY A 418 " pdb=" C GLY A 418 " pdb=" N ASP A 419 " pdb=" CA ASP A 419 " ideal model delta harmonic sigma weight residual -180.00 -152.13 -27.87 0 5.00e+00 4.00e-02 3.11e+01 ... (remaining 2852 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.132: 664 0.132 - 0.263: 115 0.263 - 0.395: 2 0.395 - 0.526: 0 0.526 - 0.658: 1 Chirality restraints: 782 Sorted by residual: chirality pdb=" CA PRO A 502 " pdb=" N PRO A 502 " pdb=" C PRO A 502 " pdb=" CB PRO A 502 " both_signs ideal model delta sigma weight residual False 2.72 2.06 0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" CA PRO A 367 " pdb=" N PRO A 367 " pdb=" C PRO A 367 " pdb=" CB PRO A 367 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CA ILE A 251 " pdb=" N ILE A 251 " pdb=" C ILE A 251 " pdb=" CB ILE A 251 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.27 2.00e-01 2.50e+01 1.89e+00 ... (remaining 779 not shown) Planarity restraints: 824 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 60 " 0.631 9.50e-02 1.11e+02 2.83e-01 4.89e+01 pdb=" NE ARG A 60 " -0.037 2.00e-02 2.50e+03 pdb=" CZ ARG A 60 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 60 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 60 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 110 " 0.024 2.00e-02 2.50e+03 4.61e-02 2.12e+01 pdb=" C GLY A 110 " -0.080 2.00e-02 2.50e+03 pdb=" O GLY A 110 " 0.029 2.00e-02 2.50e+03 pdb=" N TRP A 111 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 98 " -0.017 2.00e-02 2.50e+03 3.31e-02 1.10e+01 pdb=" C PHE A 98 " 0.057 2.00e-02 2.50e+03 pdb=" O PHE A 98 " -0.021 2.00e-02 2.50e+03 pdb=" N GLU A 99 " -0.020 2.00e-02 2.50e+03 ... (remaining 821 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 84 2.68 - 3.23: 4656 3.23 - 3.79: 7594 3.79 - 4.34: 10798 4.34 - 4.90: 17313 Nonbonded interactions: 40445 Sorted by model distance: nonbonded pdb=" O ALA A 73 " pdb="NA NA A 803 " model vdw 2.121 2.470 nonbonded pdb=" O ILE A 76 " pdb="NA NA A 803 " model vdw 2.133 2.470 nonbonded pdb=" ND2 ASN A 250 " pdb=" C1 NAG A 801 " model vdw 2.200 3.550 nonbonded pdb=" OH TYR A 128 " pdb=" O LEU A 559 " model vdw 2.249 3.040 nonbonded pdb=" O ARG A 259 " pdb=" OG SER A 262 " model vdw 2.358 3.040 ... (remaining 40440 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: 0.090 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.370 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 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 : 0.019 0.375 4938 Z= 1.290 Angle : 2.197 10.711 6736 Z= 1.613 Chirality : 0.094 0.658 782 Planarity : 0.012 0.283 824 Dihedral : 14.363 86.989 1719 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.19 % Allowed : 6.36 % Favored : 91.45 % Cbeta Deviations : 0.36 % 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: -2.67 (0.29), residues: 613 helix: -1.54 (0.20), residues: 443 sheet: None (None), residues: 0 loop : -1.90 (0.44), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 336 TYR 0.030 0.005 TYR A 128 PHE 0.022 0.004 PHE A 113 TRP 0.022 0.004 TRP A 487 HIS 0.008 0.002 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.01667 / 1.22 ( 4934) covalent geometry : angle 2.19153 / 1.61 ( 6728) SS BOND : bond 0.30107 / 14.98 ( 4) SS BOND : angle 5.17466 / 2.80 ( 8) hydrogen bonds : bond 0.18480 / 11.72 ( 338) hydrogen bonds : angle 8.38574 / 6.27 ( 1005) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.135 Fit side-chains REVERT: A 99 GLU cc_start: 0.8350 (mm-30) cc_final: 0.8148 (mm-30) REVERT: A 104 PHE cc_start: 0.7584 (m-80) cc_final: 0.7376 (m-80) REVERT: A 150 TYR cc_start: 0.8535 (m-10) cc_final: 0.8249 (m-10) REVERT: A 167 GLN cc_start: 0.8474 (tt0) cc_final: 0.8229 (tt0) REVERT: A 191 THR cc_start: 0.8067 (m) cc_final: 0.7826 (m) REVERT: A 216 MET cc_start: 0.8021 (ttp) cc_final: 0.7760 (ttp) REVERT: A 244 GLU cc_start: 0.7517 (mm-30) cc_final: 0.7198 (mm-30) REVERT: A 323 THR cc_start: 0.8393 (OUTLIER) cc_final: 0.7956 (p) REVERT: A 328 MET cc_start: 0.8610 (mtt) cc_final: 0.8222 (mtt) REVERT: A 382 MET cc_start: 0.8264 (mmm) cc_final: 0.8037 (mmm) REVERT: A 412 ARG cc_start: 0.6987 (ttt180) cc_final: 0.5933 (ttp80) REVERT: A 495 MET cc_start: 0.7653 (mtp) cc_final: 0.7261 (mtt) REVERT: A 500 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.7392 (tt) REVERT: A 641 GLU cc_start: 0.6454 (mm-30) cc_final: 0.5791 (mt-10) outliers start: 11 outliers final: 5 residues processed: 85 average time/residue: 0.0913 time to fit residues: 9.3117 Evaluate side-chains 76 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 PRO Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 466 PRO Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 560 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 0.0970 chunk 56 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 295 GLN A 399 ASN A 656 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.123593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.103226 restraints weight = 5104.522| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 1.27 r_work: 0.2911 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4938 Z= 0.134 Angle : 0.640 7.415 6736 Z= 0.334 Chirality : 0.042 0.219 782 Planarity : 0.005 0.038 824 Dihedral : 6.923 57.922 718 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.59 % Allowed : 8.75 % Favored : 89.66 % 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: 0.48 (0.34), residues: 613 helix: 0.90 (0.24), residues: 451 sheet: None (None), residues: 0 loop : -1.18 (0.49), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 267 TYR 0.025 0.001 TYR A 256 PHE 0.010 0.001 PHE A 98 TRP 0.013 0.001 TRP A 487 HIS 0.002 0.001 HIS A 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 4934) covalent geometry : angle 0.63702 / 0.33 ( 6728) SS BOND : bond 0.00687 / 0.36 ( 4) SS BOND : angle 1.75493 / 0.91 ( 8) hydrogen bonds : bond 0.04436 / 2.85 ( 338) hydrogen bonds : angle 5.56304 / 4.16 ( 1005) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.104 Fit side-chains REVERT: A 91 SER cc_start: 0.8841 (m) cc_final: 0.8519 (p) REVERT: A 191 THR cc_start: 0.8711 (m) cc_final: 0.8475 (m) REVERT: A 198 MET cc_start: 0.8051 (mtt) cc_final: 0.7786 (mtt) REVERT: A 216 MET cc_start: 0.8590 (ttp) cc_final: 0.8234 (ttp) REVERT: A 299 GLN cc_start: 0.8882 (mt0) cc_final: 0.8657 (tt0) REVERT: A 323 THR cc_start: 0.9176 (OUTLIER) cc_final: 0.8938 (p) REVERT: A 352 ARG cc_start: 0.7364 (ttm110) cc_final: 0.7002 (ttm170) REVERT: A 382 MET cc_start: 0.8414 (mmm) cc_final: 0.8140 (mmm) REVERT: A 412 ARG cc_start: 0.7481 (ttt180) cc_final: 0.6924 (ttp80) REVERT: A 445 GLN cc_start: 0.7560 (mm110) cc_final: 0.7357 (mt0) REVERT: A 553 ARG cc_start: 0.7756 (mtp-110) cc_final: 0.7350 (ttp80) REVERT: A 554 LYS cc_start: 0.8129 (pttt) cc_final: 0.7873 (pttm) outliers start: 8 outliers final: 5 residues processed: 84 average time/residue: 0.0888 time to fit residues: 9.0042 Evaluate side-chains 73 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 642 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 56 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 47 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 557 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.116896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.096492 restraints weight = 5258.610| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 1.28 r_work: 0.2815 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 4938 Z= 0.208 Angle : 0.679 7.261 6736 Z= 0.357 Chirality : 0.046 0.169 782 Planarity : 0.006 0.047 824 Dihedral : 6.692 59.458 707 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.19 % Allowed : 10.93 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.78 (0.35), residues: 613 helix: 1.14 (0.25), residues: 450 sheet: None (None), residues: 0 loop : -1.14 (0.51), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 137 TYR 0.020 0.002 TYR A 128 PHE 0.013 0.002 PHE A 666 TRP 0.014 0.002 TRP A 487 HIS 0.004 0.001 HIS A 555 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.21 ( 4934) covalent geometry : angle 0.67673 / 0.36 ( 6728) SS BOND : bond 0.00611 / 0.30 ( 4) SS BOND : angle 1.88082 / 0.98 ( 8) hydrogen bonds : bond 0.05357 / 3.50 ( 338) hydrogen bonds : angle 5.57915 / 4.19 ( 1005) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.114 Fit side-chains REVERT: A 91 SER cc_start: 0.8933 (m) cc_final: 0.8559 (p) REVERT: A 150 TYR cc_start: 0.8483 (m-10) cc_final: 0.7633 (m-10) REVERT: A 191 THR cc_start: 0.8606 (m) cc_final: 0.8247 (m) REVERT: A 216 MET cc_start: 0.8672 (ttp) cc_final: 0.8312 (ttp) REVERT: A 323 THR cc_start: 0.9170 (OUTLIER) cc_final: 0.8942 (p) REVERT: A 382 MET cc_start: 0.8443 (mmm) cc_final: 0.8173 (mmm) REVERT: A 412 ARG cc_start: 0.7452 (ttt180) cc_final: 0.7011 (ttp80) REVERT: A 455 TYR cc_start: 0.8060 (m-10) cc_final: 0.7586 (m-10) REVERT: A 554 LYS cc_start: 0.8167 (pttt) cc_final: 0.7854 (pttm) outliers start: 11 outliers final: 7 residues processed: 76 average time/residue: 0.0891 time to fit residues: 8.3487 Evaluate side-chains 74 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 642 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 13 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 25 optimal weight: 0.0060 chunk 54 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 overall best weight: 1.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 363 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.119752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.099631 restraints weight = 5231.331| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 1.27 r_work: 0.2862 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4938 Z= 0.140 Angle : 0.601 7.029 6736 Z= 0.313 Chirality : 0.042 0.158 782 Planarity : 0.005 0.045 824 Dihedral : 6.383 57.595 707 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.99 % Allowed : 11.93 % Favored : 86.08 % 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: 1.13 (0.35), residues: 613 helix: 1.40 (0.25), residues: 451 sheet: None (None), residues: 0 loop : -1.02 (0.51), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 553 TYR 0.019 0.001 TYR A 256 PHE 0.010 0.001 PHE A 534 TRP 0.012 0.001 TRP A 487 HIS 0.003 0.001 HIS A 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 4934) covalent geometry : angle 0.59881 / 0.31 ( 6728) SS BOND : bond 0.00570 / 0.27 ( 4) SS BOND : angle 1.63248 / 1.08 ( 8) hydrogen bonds : bond 0.04418 / 2.85 ( 338) hydrogen bonds : angle 5.29394 / 3.97 ( 1005) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.108 Fit side-chains REVERT: A 91 SER cc_start: 0.9062 (m) cc_final: 0.8735 (p) REVERT: A 191 THR cc_start: 0.8580 (m) cc_final: 0.8253 (m) REVERT: A 216 MET cc_start: 0.8664 (ttp) cc_final: 0.8350 (ttp) REVERT: A 323 THR cc_start: 0.9180 (OUTLIER) cc_final: 0.8953 (p) REVERT: A 382 MET cc_start: 0.8359 (mmm) cc_final: 0.8143 (mmm) REVERT: A 412 ARG cc_start: 0.7453 (ttt180) cc_final: 0.7009 (ttp80) REVERT: A 455 TYR cc_start: 0.7885 (m-10) cc_final: 0.7405 (m-10) REVERT: A 553 ARG cc_start: 0.7792 (mtp-110) cc_final: 0.7320 (ttp80) REVERT: A 554 LYS cc_start: 0.8108 (pttt) cc_final: 0.7807 (pttm) outliers start: 10 outliers final: 6 residues processed: 74 average time/residue: 0.0827 time to fit residues: 7.5063 Evaluate side-chains 73 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 642 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 32 optimal weight: 8.9990 chunk 41 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 445 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.119243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.099786 restraints weight = 5277.201| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 1.25 r_work: 0.2864 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4938 Z= 0.138 Angle : 0.597 8.229 6736 Z= 0.307 Chirality : 0.042 0.159 782 Planarity : 0.005 0.045 824 Dihedral : 6.202 56.589 706 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.78 % Allowed : 10.93 % Favored : 85.29 % 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: 1.28 (0.35), residues: 613 helix: 1.48 (0.25), residues: 452 sheet: None (None), residues: 0 loop : -0.91 (0.50), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 267 TYR 0.019 0.001 TYR A 256 PHE 0.010 0.001 PHE A 534 TRP 0.012 0.001 TRP A 487 HIS 0.003 0.001 HIS A 555 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 4934) covalent geometry : angle 0.59553 / 0.31 ( 6728) SS BOND : bond 0.00420 / 0.21 ( 4) SS BOND : angle 1.27477 / 0.63 ( 8) hydrogen bonds : bond 0.04360 / 2.81 ( 338) hydrogen bonds : angle 5.21222 / 3.92 ( 1005) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.123 Fit side-chains REVERT: A 91 SER cc_start: 0.9072 (m) cc_final: 0.8742 (p) REVERT: A 99 GLU cc_start: 0.8405 (mm-30) cc_final: 0.8133 (mm-30) REVERT: A 150 TYR cc_start: 0.8467 (m-10) cc_final: 0.7660 (m-10) REVERT: A 191 THR cc_start: 0.8560 (m) cc_final: 0.8248 (m) REVERT: A 216 MET cc_start: 0.8675 (ttp) cc_final: 0.8339 (ttp) REVERT: A 323 THR cc_start: 0.9204 (OUTLIER) cc_final: 0.8971 (p) REVERT: A 328 MET cc_start: 0.8690 (mtt) cc_final: 0.8291 (mtt) REVERT: A 382 MET cc_start: 0.8443 (mmm) cc_final: 0.8203 (mmm) REVERT: A 412 ARG cc_start: 0.7481 (ttt180) cc_final: 0.6661 (tmt-80) REVERT: A 455 TYR cc_start: 0.8007 (m-10) cc_final: 0.7561 (m-10) REVERT: A 553 ARG cc_start: 0.7761 (mtp-110) cc_final: 0.7306 (ttp80) REVERT: A 554 LYS cc_start: 0.8058 (pttt) cc_final: 0.7767 (pttm) REVERT: A 660 MET cc_start: 0.8588 (ttp) cc_final: 0.8355 (ttp) outliers start: 19 outliers final: 11 residues processed: 84 average time/residue: 0.0690 time to fit residues: 7.4054 Evaluate side-chains 82 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 642 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 10 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.3197 r_free = 0.3197 target = 0.117751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.098315 restraints weight = 5275.231| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 1.24 r_work: 0.2840 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4938 Z= 0.162 Angle : 0.631 12.380 6736 Z= 0.322 Chirality : 0.043 0.162 782 Planarity : 0.005 0.046 824 Dihedral : 6.209 56.364 706 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.98 % Allowed : 11.93 % Favored : 85.09 % 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: 1.28 (0.35), residues: 613 helix: 1.47 (0.25), residues: 451 sheet: None (None), residues: 0 loop : -0.86 (0.50), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 267 TYR 0.018 0.002 TYR A 256 PHE 0.012 0.001 PHE A 534 TRP 0.012 0.001 TRP A 487 HIS 0.003 0.001 HIS A 555 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 ( 4934) covalent geometry : angle 0.62776 / 0.32 ( 6728) SS BOND : bond 0.00584 / 0.28 ( 4) SS BOND : angle 1.87245 / 1.23 ( 8) hydrogen bonds : bond 0.04684 / 3.03 ( 338) hydrogen bonds : angle 5.29019 / 3.98 ( 1005) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.145 Fit side-chains REVERT: A 91 SER cc_start: 0.8973 (m) cc_final: 0.8613 (p) REVERT: A 99 GLU cc_start: 0.8377 (mm-30) cc_final: 0.8094 (mm-30) REVERT: A 150 TYR cc_start: 0.8481 (m-10) cc_final: 0.7666 (m-10) REVERT: A 191 THR cc_start: 0.8656 (m) cc_final: 0.8325 (m) REVERT: A 216 MET cc_start: 0.8684 (ttp) cc_final: 0.8315 (ttp) REVERT: A 323 THR cc_start: 0.9197 (OUTLIER) cc_final: 0.8959 (p) REVERT: A 328 MET cc_start: 0.8694 (mtt) cc_final: 0.8287 (mtt) REVERT: A 382 MET cc_start: 0.8462 (mmm) cc_final: 0.8205 (mmm) REVERT: A 412 ARG cc_start: 0.7470 (ttt180) cc_final: 0.6641 (tmt-80) REVERT: A 455 TYR cc_start: 0.8034 (m-10) cc_final: 0.7579 (m-10) REVERT: A 553 ARG cc_start: 0.7775 (mtp-110) cc_final: 0.7313 (ttp80) REVERT: A 554 LYS cc_start: 0.8038 (pttt) cc_final: 0.7736 (pttm) outliers start: 15 outliers final: 12 residues processed: 79 average time/residue: 0.0606 time to fit residues: 6.1195 Evaluate side-chains 80 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 642 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 9 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 32 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 27 optimal weight: 0.6980 chunk 15 optimal weight: 5.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 376 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.116970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.097516 restraints weight = 5301.591| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 1.25 r_work: 0.2828 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4938 Z= 0.177 Angle : 0.650 15.049 6736 Z= 0.329 Chirality : 0.044 0.161 782 Planarity : 0.005 0.047 824 Dihedral : 6.220 56.126 706 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.98 % Allowed : 12.52 % Favored : 84.49 % 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: 1.20 (0.35), residues: 613 helix: 1.39 (0.25), residues: 452 sheet: None (None), residues: 0 loop : -0.81 (0.51), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 267 TYR 0.017 0.002 TYR A 256 PHE 0.013 0.001 PHE A 534 TRP 0.013 0.001 TRP A 487 HIS 0.003 0.001 HIS A 555 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 ( 4934) covalent geometry : angle 0.64804 / 0.33 ( 6728) SS BOND : bond 0.00586 / 0.29 ( 4) SS BOND : angle 1.68007 / 0.96 ( 8) hydrogen bonds : bond 0.04870 / 3.15 ( 338) hydrogen bonds : angle 5.34415 / 4.02 ( 1005) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.138 Fit side-chains REVERT: A 91 SER cc_start: 0.8932 (m) cc_final: 0.8602 (p) REVERT: A 150 TYR cc_start: 0.8496 (m-10) cc_final: 0.7676 (m-10) REVERT: A 191 THR cc_start: 0.8663 (m) cc_final: 0.8355 (m) REVERT: A 216 MET cc_start: 0.8701 (ttp) cc_final: 0.8340 (ttp) REVERT: A 323 THR cc_start: 0.9158 (OUTLIER) cc_final: 0.8939 (p) REVERT: A 328 MET cc_start: 0.8713 (mtt) cc_final: 0.8322 (mtt) REVERT: A 382 MET cc_start: 0.8471 (mmm) cc_final: 0.8188 (mmm) REVERT: A 412 ARG cc_start: 0.7459 (ttt180) cc_final: 0.6629 (tmt-80) REVERT: A 455 TYR cc_start: 0.8057 (m-10) cc_final: 0.7593 (m-10) REVERT: A 553 ARG cc_start: 0.7783 (mtp-110) cc_final: 0.7316 (ttp80) outliers start: 15 outliers final: 13 residues processed: 83 average time/residue: 0.0748 time to fit residues: 7.8097 Evaluate side-chains 83 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 642 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 5 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 49 optimal weight: 0.2980 chunk 2 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 50 optimal weight: 8.9990 chunk 6 optimal weight: 7.9990 overall best weight: 3.0586 ------------------------------------------------------------------------------- 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 = 0.3176 r_free = 0.3176 target = 0.116066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.096415 restraints weight = 5358.993| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 1.26 r_work: 0.2811 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 4938 Z= 0.200 Angle : 0.683 16.512 6736 Z= 0.344 Chirality : 0.045 0.161 782 Planarity : 0.005 0.048 824 Dihedral : 6.282 56.130 706 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.38 % Allowed : 12.13 % Favored : 84.49 % 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: 1.08 (0.35), residues: 613 helix: 1.29 (0.25), residues: 452 sheet: None (None), residues: 0 loop : -0.83 (0.51), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 267 TYR 0.017 0.002 TYR A 256 PHE 0.014 0.002 PHE A 534 TRP 0.011 0.002 TRP A 487 HIS 0.003 0.001 HIS A 555 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.20 ( 4934) covalent geometry : angle 0.67860 / 0.34 ( 6728) SS BOND : bond 0.00692 / 0.34 ( 4) SS BOND : angle 2.38711 / 1.71 ( 8) hydrogen bonds : bond 0.05112 / 3.33 ( 338) hydrogen bonds : angle 5.43205 / 4.09 ( 1005) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.116 Fit side-chains REVERT: A 91 SER cc_start: 0.9032 (m) cc_final: 0.8669 (p) REVERT: A 150 TYR cc_start: 0.8515 (m-10) cc_final: 0.7687 (m-10) REVERT: A 191 THR cc_start: 0.8735 (m) cc_final: 0.8423 (m) REVERT: A 216 MET cc_start: 0.8725 (ttp) cc_final: 0.8360 (ttp) REVERT: A 323 THR cc_start: 0.9158 (OUTLIER) cc_final: 0.8938 (p) REVERT: A 328 MET cc_start: 0.8736 (mtt) cc_final: 0.8357 (mtt) REVERT: A 382 MET cc_start: 0.8558 (mmm) cc_final: 0.8264 (mmm) REVERT: A 412 ARG cc_start: 0.7477 (ttt180) cc_final: 0.6655 (tmt-80) REVERT: A 455 TYR cc_start: 0.8157 (m-10) cc_final: 0.7692 (m-10) REVERT: A 553 ARG cc_start: 0.7861 (mtp-110) cc_final: 0.7283 (ttp80) outliers start: 17 outliers final: 13 residues processed: 81 average time/residue: 0.0612 time to fit residues: 6.2029 Evaluate side-chains 82 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 642 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 42 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 2 optimal weight: 8.9990 chunk 55 optimal weight: 9.9990 chunk 29 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 22 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.120605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.101651 restraints weight = 5210.145| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 1.23 r_work: 0.2892 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 4938 Z= 0.121 Angle : 0.592 14.637 6736 Z= 0.298 Chirality : 0.040 0.162 782 Planarity : 0.005 0.047 824 Dihedral : 5.979 54.197 706 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.99 % Allowed : 13.72 % Favored : 84.29 % 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: 1.50 (0.35), residues: 613 helix: 1.59 (0.25), residues: 452 sheet: None (None), residues: 0 loop : -0.64 (0.51), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 267 TYR 0.019 0.001 TYR A 256 PHE 0.010 0.001 PHE A 534 TRP 0.010 0.001 TRP A 487 HIS 0.003 0.001 HIS A 555 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 4934) covalent geometry : angle 0.58945 / 0.30 ( 6728) SS BOND : bond 0.00354 / 0.17 ( 4) SS BOND : angle 1.60400 / 1.12 ( 8) hydrogen bonds : bond 0.03979 / 2.56 ( 338) hydrogen bonds : angle 5.08235 / 3.81 ( 1005) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.182 Fit side-chains REVERT: A 150 TYR cc_start: 0.8403 (m-10) cc_final: 0.7603 (m-10) REVERT: A 191 THR cc_start: 0.8618 (m) cc_final: 0.8327 (m) REVERT: A 216 MET cc_start: 0.8642 (ttp) cc_final: 0.8271 (ttp) REVERT: A 328 MET cc_start: 0.8644 (mtt) cc_final: 0.8258 (mtt) REVERT: A 352 ARG cc_start: 0.7198 (ttp80) cc_final: 0.6845 (ttm170) REVERT: A 382 MET cc_start: 0.8471 (mmm) cc_final: 0.7979 (mmm) REVERT: A 412 ARG cc_start: 0.7429 (ttt180) cc_final: 0.6997 (ttp80) REVERT: A 455 TYR cc_start: 0.8067 (m-10) cc_final: 0.7605 (m-10) REVERT: A 553 ARG cc_start: 0.7819 (mtp-110) cc_final: 0.7304 (ttp80) outliers start: 10 outliers final: 8 residues processed: 77 average time/residue: 0.0928 time to fit residues: 8.9558 Evaluate side-chains 75 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 475 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 26 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 49 optimal weight: 30.0000 overall best weight: 1.3188 ------------------------------------------------------------------------------- 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 = 0.3221 r_free = 0.3221 target = 0.119558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.100117 restraints weight = 5247.264| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 1.25 r_work: 0.2867 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 4938 Z= 0.131 Angle : 0.606 14.829 6736 Z= 0.304 Chirality : 0.041 0.172 782 Planarity : 0.005 0.048 824 Dihedral : 5.716 53.888 705 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.19 % Allowed : 14.12 % Favored : 83.70 % 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: 1.54 (0.35), residues: 613 helix: 1.61 (0.25), residues: 452 sheet: None (None), residues: 0 loop : -0.59 (0.51), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 130 TYR 0.017 0.001 TYR A 256 PHE 0.010 0.001 PHE A 534 TRP 0.012 0.001 TRP A 487 HIS 0.002 0.001 HIS A 555 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 4934) covalent geometry : angle 0.60395 / 0.30 ( 6728) SS BOND : bond 0.00406 / 0.20 ( 4) SS BOND : angle 1.65197 / 1.10 ( 8) hydrogen bonds : bond 0.04158 / 2.68 ( 338) hydrogen bonds : angle 5.10739 / 3.83 ( 1005) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.138 Fit side-chains REVERT: A 150 TYR cc_start: 0.8459 (m-10) cc_final: 0.7644 (m-10) REVERT: A 191 THR cc_start: 0.8681 (m) cc_final: 0.8396 (m) REVERT: A 216 MET cc_start: 0.8680 (ttp) cc_final: 0.8316 (ttp) REVERT: A 328 MET cc_start: 0.8672 (mtt) cc_final: 0.8289 (mtt) REVERT: A 352 ARG cc_start: 0.7208 (ttp80) cc_final: 0.6838 (ttm170) REVERT: A 382 MET cc_start: 0.8522 (mmm) cc_final: 0.8261 (mmm) REVERT: A 412 ARG cc_start: 0.7447 (ttt180) cc_final: 0.7003 (ttp80) REVERT: A 455 TYR cc_start: 0.8104 (m-10) cc_final: 0.7620 (m-10) REVERT: A 553 ARG cc_start: 0.7819 (mtp-110) cc_final: 0.7298 (ttp80) REVERT: A 660 MET cc_start: 0.8589 (ttp) cc_final: 0.8337 (ttp) outliers start: 11 outliers final: 11 residues processed: 74 average time/residue: 0.0884 time to fit residues: 8.1413 Evaluate side-chains 78 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 661 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 36 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 23 optimal weight: 0.0870 chunk 53 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.8164 ------------------------------------------------------------------------------- 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 = 0.3253 r_free = 0.3253 target = 0.122192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.103209 restraints weight = 5189.997| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 1.22 r_work: 0.2913 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 4938 Z= 0.117 Angle : 0.580 13.797 6736 Z= 0.292 Chirality : 0.040 0.174 782 Planarity : 0.005 0.047 824 Dihedral : 5.598 53.263 705 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.19 % Allowed : 14.12 % Favored : 83.70 % 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 (0.35), residues: 613 helix: 1.71 (0.25), residues: 455 sheet: None (None), residues: 0 loop : -0.65 (0.51), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 267 TYR 0.018 0.001 TYR A 256 PHE 0.009 0.001 PHE A 534 TRP 0.011 0.001 TRP A 487 HIS 0.002 0.000 HIS A 555 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 4934) covalent geometry : angle 0.57880 / 0.29 ( 6728) SS BOND : bond 0.00300 / 0.15 ( 4) SS BOND : angle 1.37819 / 0.90 ( 8) hydrogen bonds : bond 0.03802 / 2.44 ( 338) hydrogen bonds : angle 4.97782 / 3.74 ( 1005) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1121.91 seconds wall clock time: 19 minutes 52.72 seconds (1192.72 seconds total)