Starting phenix.real_space_refine on Sun Apr 27 05:59:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hg7_34737/04_2025/8hg7_34737.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hg7_34737/04_2025/8hg7_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8hg7_34737/04_2025/8hg7_34737.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hg7_34737/04_2025/8hg7_34737.map" model { file = "/net/cci-nas-00/data/ceres_data/8hg7_34737/04_2025/8hg7_34737.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hg7_34737/04_2025/8hg7_34737.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.43, per 1000 atoms: 0.71 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: 1.32 Conformation dependent library (CDL) restraints added in 587.7 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: 0.53 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: 1.31 Time building geometry restraints manager: 1.50 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: 2568 17.40 - 34.80: 241 34.80 - 52.19: 52 52.19 - 69.59: 12 69.59 - 86.99: 3 Dihedral angle restraints: 2876 sinusoidal: 1112 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 2873 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: 0.100 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: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.890 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: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 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 : 14.288 86.989 1740 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.022 0.004 TRP A 487 HIS 0.008 0.002 HIS A 309 PHE 0.022 0.004 PHE A 113 TYR 0.030 0.005 TYR A 128 ARG 0.007 0.001 ARG A 336 Details of bonding type rmsd hydrogen bonds : bond 0.18480 ( 338) hydrogen bonds : angle 8.38574 ( 1005) SS BOND : bond 0.30107 ( 4) SS BOND : angle 5.17466 ( 8) covalent geometry : bond 0.01667 ( 4934) covalent geometry : angle 2.19153 ( 6728) *********************** 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 : 0.523 Fit side-chains REVERT: A 99 GLU cc_start: 0.8350 (mm-30) cc_final: 0.8147 (mm-30) REVERT: A 104 PHE cc_start: 0.7585 (m-80) cc_final: 0.7376 (m-80) REVERT: A 150 TYR cc_start: 0.8535 (m-10) cc_final: 0.8250 (m-10) REVERT: A 167 GLN cc_start: 0.8475 (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: 0.8022 (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: 0.7955 (p) REVERT: A 328 MET cc_start: 0.8610 (mtt) cc_final: 0.8222 (mtt) REVERT: A 382 MET cc_start: 0.8263 (mmm) cc_final: 0.8036 (mmm) REVERT: A 412 ARG cc_start: 0.6987 (ttt180) cc_final: 0.5933 (ttp80) REVERT: A 495 MET cc_start: 0.7652 (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: 0.2679 time to fit residues: 26.9653 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 : 0.490 ------------------------------------------------------------------------------- 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 51 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3259 r_free = 0.3259 target = 0.122846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.102410 restraints weight = 5127.669| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 1.27 r_work: 0.2902 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4938 Z= 0.135 Angle : 0.642 7.426 6736 Z= 0.336 Chirality : 0.042 0.211 782 Planarity : 0.005 0.039 824 Dihedral : 6.981 58.117 739 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.34), residues: 613 helix: 0.88 (0.24), residues: 451 sheet: None (None), residues: 0 loop : -1.22 (0.49), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 42 HIS 0.002 0.000 HIS A 80 PHE 0.011 0.001 PHE A 98 TYR 0.026 0.002 TYR A 256 ARG 0.004 0.000 ARG A 267 Details of bonding type rmsd hydrogen bonds : bond 0.04489 ( 338) hydrogen bonds : angle 5.57909 ( 1005) SS BOND : bond 0.00524 ( 4) SS BOND : angle 1.66062 ( 8) covalent geometry : bond 0.00284 ( 4934) covalent geometry : angle 0.63938 ( 6728) *********************** 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 87 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.520 Fit side-chains REVERT: A 91 SER cc_start: 0.8854 (m) cc_final: 0.8514 (p) REVERT: A 191 THR cc_start: 0.8665 (m) cc_final: 0.8454 (m) REVERT: A 216 MET cc_start: 0.8600 (ttp) cc_final: 0.8229 (ttp) REVERT: A 323 THR cc_start: 0.9177 (OUTLIER) cc_final: 0.8938 (p) REVERT: A 382 MET cc_start: 0.8422 (mmm) cc_final: 0.8153 (mmm) REVERT: A 412 ARG cc_start: 0.7481 (ttt180) cc_final: 0.6920 (ttp80) REVERT: A 445 GLN cc_start: 0.7583 (mm110) cc_final: 0.7371 (mt0) REVERT: A 553 ARG cc_start: 0.7784 (mtp-110) cc_final: 0.7342 (ttp80) REVERT: A 554 LYS cc_start: 0.8136 (pttt) cc_final: 0.7880 (pttm) outliers start: 8 outliers final: 5 residues processed: 82 average time/residue: 0.2579 time to fit residues: 25.1739 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 : 0.470 ------------------------------------------------------------------------------- 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 34 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 2 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 53 optimal weight: 0.0060 chunk 23 optimal weight: 0.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 557 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.124419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.104183 restraints weight = 5159.865| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 1.26 r_work: 0.2924 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4938 Z= 0.116 Angle : 0.573 7.206 6736 Z= 0.298 Chirality : 0.040 0.161 782 Planarity : 0.005 0.041 824 Dihedral : 6.310 57.240 728 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.39 % Allowed : 11.73 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.35), residues: 613 helix: 1.50 (0.25), residues: 453 sheet: None (None), residues: 0 loop : -0.95 (0.51), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 42 HIS 0.002 0.000 HIS A 80 PHE 0.008 0.001 PHE A 534 TYR 0.022 0.001 TYR A 256 ARG 0.002 0.000 ARG A 267 Details of bonding type rmsd hydrogen bonds : bond 0.03935 ( 338) hydrogen bonds : angle 5.15664 ( 1005) SS BOND : bond 0.00172 ( 4) SS BOND : angle 1.36346 ( 8) covalent geometry : bond 0.00242 ( 4934) covalent geometry : angle 0.57093 ( 6728) *********************** 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 77 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.482 Fit side-chains REVERT: A 44 MET cc_start: 0.7581 (mtp) cc_final: 0.7378 (mtp) REVERT: A 191 THR cc_start: 0.8616 (m) cc_final: 0.8366 (m) REVERT: A 216 MET cc_start: 0.8659 (ttp) cc_final: 0.8352 (ttp) REVERT: A 323 THR cc_start: 0.9184 (OUTLIER) cc_final: 0.8953 (p) REVERT: A 352 ARG cc_start: 0.7413 (ttm110) cc_final: 0.7063 (ttm170) REVERT: A 382 MET cc_start: 0.8244 (mmm) cc_final: 0.8035 (mmm) REVERT: A 412 ARG cc_start: 0.7411 (ttt180) cc_final: 0.6980 (ttp80) REVERT: A 553 ARG cc_start: 0.7758 (mtp-110) cc_final: 0.7344 (ttp80) outliers start: 7 outliers final: 2 residues processed: 73 average time/residue: 0.2204 time to fit residues: 19.7702 Evaluate side-chains 65 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 323 THR 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 48 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 54 optimal weight: 8.9990 chunk 52 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 44 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.124316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.104173 restraints weight = 5139.407| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 1.28 r_work: 0.2926 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4938 Z= 0.115 Angle : 0.566 7.780 6736 Z= 0.290 Chirality : 0.040 0.167 782 Planarity : 0.005 0.042 824 Dihedral : 6.073 56.001 727 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.39 % Allowed : 12.13 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.35), residues: 613 helix: 1.72 (0.25), residues: 452 sheet: None (None), residues: 0 loop : -0.85 (0.51), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 487 HIS 0.002 0.000 HIS A 80 PHE 0.008 0.001 PHE A 534 TYR 0.020 0.001 TYR A 256 ARG 0.003 0.000 ARG A 130 Details of bonding type rmsd hydrogen bonds : bond 0.03812 ( 338) hydrogen bonds : angle 5.05193 ( 1005) SS BOND : bond 0.00370 ( 4) SS BOND : angle 0.95614 ( 8) covalent geometry : bond 0.00249 ( 4934) covalent geometry : angle 0.56512 ( 6728) *********************** 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 76 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.469 Fit side-chains REVERT: A 150 TYR cc_start: 0.8350 (m-10) cc_final: 0.7575 (m-10) REVERT: A 191 THR cc_start: 0.8574 (m) cc_final: 0.8304 (m) REVERT: A 216 MET cc_start: 0.8632 (ttp) cc_final: 0.8333 (ttp) REVERT: A 323 THR cc_start: 0.9158 (OUTLIER) cc_final: 0.8936 (p) REVERT: A 328 MET cc_start: 0.8628 (mtt) cc_final: 0.8231 (mtt) REVERT: A 352 ARG cc_start: 0.7416 (ttm110) cc_final: 0.6998 (ttm170) REVERT: A 382 MET cc_start: 0.8272 (mmm) cc_final: 0.8045 (mmm) REVERT: A 412 ARG cc_start: 0.7424 (ttt180) cc_final: 0.6951 (ttp80) REVERT: A 553 ARG cc_start: 0.7708 (mtp-110) cc_final: 0.7295 (ttp80) outliers start: 7 outliers final: 3 residues processed: 72 average time/residue: 0.2104 time to fit residues: 18.7647 Evaluate side-chains 70 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 475 LEU 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 17 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 55 optimal weight: 8.9990 chunk 45 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 49 optimal weight: 20.0000 chunk 35 optimal weight: 8.9990 chunk 60 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.118674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.098406 restraints weight = 5288.002| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 1.28 r_work: 0.2845 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4938 Z= 0.169 Angle : 0.629 7.030 6736 Z= 0.326 Chirality : 0.044 0.170 782 Planarity : 0.005 0.045 824 Dihedral : 6.187 57.067 727 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.99 % Allowed : 12.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.35), residues: 613 helix: 1.53 (0.25), residues: 453 sheet: None (None), residues: 0 loop : -0.85 (0.51), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 487 HIS 0.003 0.001 HIS A 555 PHE 0.012 0.001 PHE A 666 TYR 0.019 0.002 TYR A 256 ARG 0.004 0.000 ARG A 130 Details of bonding type rmsd hydrogen bonds : bond 0.04709 ( 338) hydrogen bonds : angle 5.28257 ( 1005) SS BOND : bond 0.00581 ( 4) SS BOND : angle 1.84858 ( 8) covalent geometry : bond 0.00404 ( 4934) covalent geometry : angle 0.62640 ( 6728) *********************** 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 79 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.493 Fit side-chains REVERT: A 44 MET cc_start: 0.7650 (mtp) cc_final: 0.7435 (mtp) REVERT: A 150 TYR cc_start: 0.8472 (m-10) cc_final: 0.7651 (m-10) REVERT: A 191 THR cc_start: 0.8545 (m) cc_final: 0.8265 (m) REVERT: A 198 MET cc_start: 0.8293 (mtt) cc_final: 0.7832 (mtt) REVERT: A 216 MET cc_start: 0.8686 (ttp) cc_final: 0.8239 (ttp) REVERT: A 323 THR cc_start: 0.9194 (OUTLIER) cc_final: 0.8987 (p) REVERT: A 382 MET cc_start: 0.8426 (mmm) cc_final: 0.8148 (mmm) REVERT: A 412 ARG cc_start: 0.7503 (ttt180) cc_final: 0.7016 (ttp80) REVERT: A 455 TYR cc_start: 0.8047 (m-10) cc_final: 0.7539 (m-10) REVERT: A 553 ARG cc_start: 0.7805 (mtp-110) cc_final: 0.7389 (ttp80) REVERT: A 554 LYS cc_start: 0.8136 (pttt) cc_final: 0.7867 (pttm) REVERT: A 660 MET cc_start: 0.8615 (ttp) cc_final: 0.8392 (ttp) outliers start: 10 outliers final: 8 residues processed: 74 average time/residue: 0.1965 time to fit residues: 18.3505 Evaluate side-chains 75 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.494 ------------------------------------------------------------------------------- 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 323 THR Chi-restraints excluded: chain A residue 359 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 0 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 39 optimal weight: 0.0070 chunk 7 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 overall best weight: 1.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.119842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.099591 restraints weight = 5239.470| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 1.28 r_work: 0.2858 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4938 Z= 0.145 Angle : 0.591 6.940 6736 Z= 0.308 Chirality : 0.042 0.166 782 Planarity : 0.005 0.045 824 Dihedral : 6.092 56.472 727 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.99 % Allowed : 12.33 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.35), residues: 613 helix: 1.58 (0.25), residues: 453 sheet: None (None), residues: 0 loop : -0.81 (0.51), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 487 HIS 0.003 0.001 HIS A 555 PHE 0.011 0.001 PHE A 534 TYR 0.019 0.001 TYR A 256 ARG 0.004 0.000 ARG A 130 Details of bonding type rmsd hydrogen bonds : bond 0.04409 ( 338) hydrogen bonds : angle 5.18889 ( 1005) SS BOND : bond 0.00477 ( 4) SS BOND : angle 1.41735 ( 8) covalent geometry : bond 0.00338 ( 4934) covalent geometry : angle 0.58904 ( 6728) *********************** 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 79 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.466 Fit side-chains REVERT: A 44 MET cc_start: 0.7611 (mtp) cc_final: 0.7334 (mtp) REVERT: A 150 TYR cc_start: 0.8464 (m-10) cc_final: 0.7657 (m-10) REVERT: A 191 THR cc_start: 0.8539 (m) cc_final: 0.8251 (m) REVERT: A 198 MET cc_start: 0.8357 (mtt) cc_final: 0.7902 (mtt) REVERT: A 216 MET cc_start: 0.8686 (ttp) cc_final: 0.8353 (ttp) REVERT: A 323 THR cc_start: 0.9187 (OUTLIER) cc_final: 0.8967 (p) REVERT: A 328 MET cc_start: 0.8667 (mtt) cc_final: 0.8297 (mtt) REVERT: A 342 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8241 (mt-10) REVERT: A 382 MET cc_start: 0.8441 (mmm) cc_final: 0.8198 (mmm) REVERT: A 412 ARG cc_start: 0.7499 (ttt180) cc_final: 0.7006 (ttp80) REVERT: A 455 TYR cc_start: 0.8064 (m-10) cc_final: 0.7574 (m-10) REVERT: A 553 ARG cc_start: 0.7825 (mtp-110) cc_final: 0.7400 (ttp80) outliers start: 10 outliers final: 6 residues processed: 74 average time/residue: 0.1966 time to fit residues: 18.3532 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 : 0.468 ------------------------------------------------------------------------------- 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 323 THR Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 475 LEU 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 2 optimal weight: 8.9990 chunk 47 optimal weight: 6.9990 chunk 19 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 35 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 29 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.122280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.102360 restraints weight = 5173.168| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.24 r_work: 0.2902 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4938 Z= 0.123 Angle : 0.566 6.967 6736 Z= 0.294 Chirality : 0.041 0.164 782 Planarity : 0.005 0.044 824 Dihedral : 5.972 55.437 727 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.19 % Allowed : 12.13 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.35), residues: 613 helix: 1.71 (0.25), residues: 453 sheet: None (None), residues: 0 loop : -0.64 (0.51), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 487 HIS 0.002 0.001 HIS A 555 PHE 0.010 0.001 PHE A 534 TYR 0.019 0.001 TYR A 256 ARG 0.003 0.000 ARG A 130 Details of bonding type rmsd hydrogen bonds : bond 0.03988 ( 338) hydrogen bonds : angle 5.04007 ( 1005) SS BOND : bond 0.00452 ( 4) SS BOND : angle 1.65444 ( 8) covalent geometry : bond 0.00278 ( 4934) covalent geometry : angle 0.56393 ( 6728) *********************** 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 81 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.468 Fit side-chains REVERT: A 44 MET cc_start: 0.7619 (mtp) cc_final: 0.7322 (mtp) REVERT: A 150 TYR cc_start: 0.8431 (m-10) cc_final: 0.7635 (m-10) REVERT: A 191 THR cc_start: 0.8519 (m) cc_final: 0.8245 (m) REVERT: A 216 MET cc_start: 0.8657 (ttp) cc_final: 0.8342 (ttp) REVERT: A 323 THR cc_start: 0.9188 (OUTLIER) cc_final: 0.8973 (p) REVERT: A 382 MET cc_start: 0.8384 (mmm) cc_final: 0.8148 (mmm) REVERT: A 412 ARG cc_start: 0.7473 (ttt180) cc_final: 0.6633 (tmt-80) REVERT: A 455 TYR cc_start: 0.8049 (m-10) cc_final: 0.7637 (m-10) REVERT: A 553 ARG cc_start: 0.7827 (mtp-110) cc_final: 0.7387 (ttp80) REVERT: A 660 MET cc_start: 0.8580 (ttp) cc_final: 0.8366 (ttp) outliers start: 11 outliers final: 6 residues processed: 77 average time/residue: 0.2021 time to fit residues: 19.5960 Evaluate side-chains 72 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.474 ------------------------------------------------------------------------------- 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 242 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 475 LEU 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 8 optimal weight: 0.7980 chunk 32 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 chunk 56 optimal weight: 0.0020 chunk 3 optimal weight: 10.0000 chunk 39 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 overall best weight: 1.1192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.122447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.102476 restraints weight = 5216.794| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 1.25 r_work: 0.2905 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2873 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= 0.123 Angle : 0.563 6.940 6736 Z= 0.294 Chirality : 0.041 0.170 782 Planarity : 0.005 0.043 824 Dihedral : 5.915 54.938 727 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.79 % Allowed : 13.32 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.35), residues: 613 helix: 1.76 (0.25), residues: 453 sheet: None (None), residues: 0 loop : -0.57 (0.51), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 487 HIS 0.002 0.001 HIS A 555 PHE 0.010 0.001 PHE A 534 TYR 0.018 0.001 TYR A 256 ARG 0.003 0.000 ARG A 267 Details of bonding type rmsd hydrogen bonds : bond 0.03977 ( 338) hydrogen bonds : angle 5.01447 ( 1005) SS BOND : bond 0.00396 ( 4) SS BOND : angle 1.39078 ( 8) covalent geometry : bond 0.00278 ( 4934) covalent geometry : angle 0.56095 ( 6728) *********************** 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 79 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.479 Fit side-chains REVERT: A 44 MET cc_start: 0.7717 (mtp) cc_final: 0.7397 (mtp) REVERT: A 150 TYR cc_start: 0.8432 (m-10) cc_final: 0.7631 (m-10) REVERT: A 191 THR cc_start: 0.8507 (m) cc_final: 0.8224 (m) REVERT: A 216 MET cc_start: 0.8655 (ttp) cc_final: 0.8320 (ttp) REVERT: A 323 THR cc_start: 0.9191 (OUTLIER) cc_final: 0.8971 (p) REVERT: A 382 MET cc_start: 0.8369 (mmm) cc_final: 0.8152 (mmm) REVERT: A 412 ARG cc_start: 0.7478 (ttt180) cc_final: 0.6634 (tmt-80) REVERT: A 455 TYR cc_start: 0.8044 (m-10) cc_final: 0.7672 (m-10) REVERT: A 553 ARG cc_start: 0.7808 (mtp-110) cc_final: 0.7392 (ttp80) outliers start: 9 outliers final: 7 residues processed: 74 average time/residue: 0.2125 time to fit residues: 19.5864 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 : 0.498 ------------------------------------------------------------------------------- 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 323 THR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 475 LEU 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 34 optimal weight: 4.9990 chunk 55 optimal weight: 9.9990 chunk 48 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 27 optimal weight: 0.4980 chunk 5 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.122633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.102731 restraints weight = 5183.416| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 1.25 r_work: 0.2909 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 4938 Z= 0.123 Angle : 0.563 6.949 6736 Z= 0.294 Chirality : 0.041 0.174 782 Planarity : 0.005 0.043 824 Dihedral : 5.877 54.597 727 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.79 % Allowed : 13.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.35), residues: 613 helix: 1.79 (0.25), residues: 453 sheet: None (None), residues: 0 loop : -0.53 (0.51), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 487 HIS 0.002 0.001 HIS A 555 PHE 0.009 0.001 PHE A 534 TYR 0.017 0.001 TYR A 256 ARG 0.003 0.000 ARG A 267 Details of bonding type rmsd hydrogen bonds : bond 0.03952 ( 338) hydrogen bonds : angle 4.99118 ( 1005) SS BOND : bond 0.00381 ( 4) SS BOND : angle 1.29134 ( 8) covalent geometry : bond 0.00277 ( 4934) covalent geometry : angle 0.56153 ( 6728) *********************** 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 78 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.533 Fit side-chains REVERT: A 44 MET cc_start: 0.7838 (mtp) cc_final: 0.7533 (mtp) REVERT: A 150 TYR cc_start: 0.8435 (m-10) cc_final: 0.7636 (m-10) REVERT: A 191 THR cc_start: 0.8530 (m) cc_final: 0.8267 (m) REVERT: A 216 MET cc_start: 0.8647 (ttp) cc_final: 0.8337 (ttp) REVERT: A 323 THR cc_start: 0.9193 (OUTLIER) cc_final: 0.8975 (p) REVERT: A 352 ARG cc_start: 0.7199 (ttm110) cc_final: 0.6904 (ttm170) REVERT: A 382 MET cc_start: 0.8428 (mmm) cc_final: 0.8198 (mmm) REVERT: A 412 ARG cc_start: 0.7458 (ttt180) cc_final: 0.6633 (tmt-80) REVERT: A 455 TYR cc_start: 0.7969 (m-10) cc_final: 0.7599 (m-10) REVERT: A 553 ARG cc_start: 0.7796 (mtp-110) cc_final: 0.7403 (ttp80) outliers start: 9 outliers final: 7 residues processed: 74 average time/residue: 0.2066 time to fit residues: 19.1872 Evaluate side-chains 77 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.508 ------------------------------------------------------------------------------- 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 323 THR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 642 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 6 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 9 optimal weight: 0.5980 chunk 21 optimal weight: 7.9990 chunk 43 optimal weight: 0.6980 chunk 3 optimal weight: 9.9990 chunk 39 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.119805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.099857 restraints weight = 5269.270| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 1.26 r_work: 0.2866 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 4938 Z= 0.148 Angle : 0.597 7.017 6736 Z= 0.311 Chirality : 0.042 0.171 782 Planarity : 0.005 0.044 824 Dihedral : 5.965 55.130 727 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.99 % Allowed : 12.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.35), residues: 613 helix: 1.68 (0.25), residues: 453 sheet: None (None), residues: 0 loop : -0.55 (0.52), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 487 HIS 0.003 0.001 HIS A 555 PHE 0.011 0.001 PHE A 534 TYR 0.016 0.001 TYR A 256 ARG 0.003 0.000 ARG A 130 Details of bonding type rmsd hydrogen bonds : bond 0.04416 ( 338) hydrogen bonds : angle 5.13112 ( 1005) SS BOND : bond 0.00500 ( 4) SS BOND : angle 1.54775 ( 8) covalent geometry : bond 0.00348 ( 4934) covalent geometry : angle 0.59492 ( 6728) ********************** 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: 10 poor density : 69 time to evaluate : 0.458 Fit side-chains REVERT: A 44 MET cc_start: 0.7856 (mtp) cc_final: 0.7546 (mtp) REVERT: A 150 TYR cc_start: 0.8474 (m-10) cc_final: 0.7669 (m-10) REVERT: A 191 THR cc_start: 0.8664 (m) cc_final: 0.8379 (m) REVERT: A 216 MET cc_start: 0.8672 (ttp) cc_final: 0.8312 (ttp) REVERT: A 323 THR cc_start: 0.9195 (OUTLIER) cc_final: 0.8970 (p) REVERT: A 352 ARG cc_start: 0.7194 (ttm110) cc_final: 0.6858 (ttm170) REVERT: A 412 ARG cc_start: 0.7473 (ttt180) cc_final: 0.6979 (ttp80) REVERT: A 455 TYR cc_start: 0.7963 (m-10) cc_final: 0.7592 (m-10) REVERT: A 553 ARG cc_start: 0.7836 (mtp-110) cc_final: 0.7415 (ttp80) outliers start: 10 outliers final: 9 residues processed: 75 average time/residue: 0.2683 time to fit residues: 25.3737 Evaluate side-chains 79 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.881 ------------------------------------------------------------------------------- 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 281 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 359 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 22 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 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 = 0.119590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.099555 restraints weight = 5270.178| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 1.27 r_work: 0.2864 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 4938 Z= 0.151 Angle : 0.611 6.961 6736 Z= 0.317 Chirality : 0.042 0.170 782 Planarity : 0.005 0.044 824 Dihedral : 5.987 55.234 727 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.99 % Allowed : 13.12 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.35), residues: 613 helix: 1.64 (0.25), residues: 453 sheet: None (None), residues: 0 loop : -0.60 (0.52), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 487 HIS 0.003 0.001 HIS A 555 PHE 0.011 0.001 PHE A 534 TYR 0.017 0.001 TYR A 256 ARG 0.003 0.000 ARG A 130 Details of bonding type rmsd hydrogen bonds : bond 0.04456 ( 338) hydrogen bonds : angle 5.13869 ( 1005) SS BOND : bond 0.00541 ( 4) SS BOND : angle 2.05884 ( 8) covalent geometry : bond 0.00356 ( 4934) covalent geometry : angle 0.60770 ( 6728) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2794.42 seconds wall clock time: 49 minutes 40.49 seconds (2980.49 seconds total)