Starting phenix.real_space_refine on Thu Mar 6 03:40:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hg7_34737/03_2025/8hg7_34737.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hg7_34737/03_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_34737/03_2025/8hg7_34737.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hg7_34737/03_2025/8hg7_34737.map" model { file = "/net/cci-nas-00/data/ceres_data/8hg7_34737/03_2025/8hg7_34737.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hg7_34737/03_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-5624/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: 3.31, per 1000 atoms: 0.69 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: 1.21 Conformation dependent library (CDL) restraints added in 617.6 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: 0.43 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: 1.28 Time building geometry restraints manager: 1.39 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: 0.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.500 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.980 ------------------------------------------------------------------------------- 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 : 0.017 0.092 4934 Z= 1.083 Angle : 2.192 10.711 6728 Z= 1.612 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 *********************** 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 : 0.468 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: 0.2575 time to fit residues: 25.9442 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 : 0.467 ------------------------------------------------------------------------------- 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 4934 Z= 0.190 Angle : 0.639 7.426 6728 Z= 0.335 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 *********************** 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 : 0.514 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: 0.2568 time to fit residues: 25.0948 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 : 0.448 ------------------------------------------------------------------------------- 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: 0.9990 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: 0.8980 chunk 2 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 53 optimal weight: 0.0060 chunk 23 optimal weight: 0.9990 overall best weight: 0.7596 ------------------------------------------------------------------------------- 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 = 0.3276 r_free = 0.3276 target = 0.124116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.103817 restraints weight = 5165.877| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 1.27 r_work: 0.2925 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4934 Z= 0.163 Angle : 0.572 7.204 6728 Z= 0.298 Chirality : 0.040 0.161 782 Planarity : 0.005 0.041 824 Dihedral : 6.316 57.245 728 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.39 % Allowed : 11.53 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.35), residues: 613 helix: 1.49 (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 0.021 0.001 TYR A 256 ARG 0.002 0.000 ARG A 267 *********************** 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 : 0.530 Fit side-chains REVERT: A 191 THR cc_start: 0.8607 (m) cc_final: 0.8358 (m) REVERT: A 216 MET cc_start: 0.8631 (ttp) cc_final: 0.8317 (ttp) REVERT: A 323 THR cc_start: 0.9159 (OUTLIER) cc_final: 0.8915 (p) REVERT: A 352 ARG cc_start: 0.7371 (ttm110) cc_final: 0.7009 (ttm170) REVERT: A 382 MET cc_start: 0.8208 (mmm) cc_final: 0.8000 (mmm) REVERT: A 412 ARG cc_start: 0.7385 (ttt180) cc_final: 0.6953 (ttp80) REVERT: A 553 ARG cc_start: 0.7738 (mtp-110) cc_final: 0.7313 (ttp80) outliers start: 7 outliers final: 2 residues processed: 73 average time/residue: 0.2237 time to fit residues: 20.1818 Evaluate side-chains 68 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 65 time to evaluate : 0.447 ------------------------------------------------------------------------------- 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: 2.9990 chunk 55 optimal weight: 20.0000 chunk 51 optimal weight: 0.9990 chunk 16 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 44 optimal weight: 0.8980 chunk 56 optimal weight: 8.9990 chunk 21 optimal weight: 0.7980 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.3232 r_free = 0.3232 target = 0.120807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.100492 restraints weight = 5182.723| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 1.28 r_work: 0.2872 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4934 Z= 0.226 Angle : 0.603 7.544 6728 Z= 0.311 Chirality : 0.042 0.166 782 Planarity : 0.005 0.044 824 Dihedral : 6.212 57.019 727 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.39 % Allowed : 12.33 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.35), residues: 613 helix: 1.54 (0.25), residues: 452 sheet: None (None), residues: 0 loop : -0.93 (0.50), residues: 161 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 0.010 0.001 PHE A 534 TYR 0.020 0.002 TYR A 256 ARG 0.003 0.000 ARG A 130 *********************** 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 77 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.522 Fit side-chains REVERT: A 150 TYR cc_start: 0.8435 (m-10) cc_final: 0.7622 (m-10) REVERT: A 191 THR cc_start: 0.8693 (m) cc_final: 0.8448 (m) REVERT: A 216 MET cc_start: 0.8690 (ttp) cc_final: 0.8392 (ttp) REVERT: A 323 THR cc_start: 0.9192 (OUTLIER) cc_final: 0.8970 (p) REVERT: A 328 MET cc_start: 0.8695 (mtt) cc_final: 0.8312 (mtt) REVERT: A 352 ARG cc_start: 0.7423 (ttm110) cc_final: 0.6962 (ttm170) REVERT: A 363 ASN cc_start: 0.8673 (m-40) cc_final: 0.8469 (m110) REVERT: A 382 MET cc_start: 0.8385 (mmm) cc_final: 0.8127 (mmm) REVERT: A 412 ARG cc_start: 0.7437 (ttt180) cc_final: 0.6987 (ttp80) REVERT: A 455 TYR cc_start: 0.8010 (m-10) cc_final: 0.7550 (m-10) REVERT: A 553 ARG cc_start: 0.7787 (mtp-110) cc_final: 0.7384 (ttp80) REVERT: A 554 LYS cc_start: 0.8088 (pttt) cc_final: 0.7846 (pttm) outliers start: 7 outliers final: 5 residues processed: 73 average time/residue: 0.2165 time to fit residues: 19.5300 Evaluate side-chains 72 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.524 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 48 optimal weight: 0.9990 chunk 55 optimal weight: 20.0000 chunk 45 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 35 optimal weight: 0.0040 chunk 60 optimal weight: 0.9990 chunk 27 optimal weight: 0.2980 chunk 1 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- 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 = 0.3282 r_free = 0.3282 target = 0.124903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.104834 restraints weight = 5220.915| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 1.28 r_work: 0.2935 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4934 Z= 0.160 Angle : 0.547 7.048 6728 Z= 0.283 Chirality : 0.040 0.161 782 Planarity : 0.005 0.042 824 Dihedral : 5.996 55.388 727 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.59 % Allowed : 12.72 % 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: 1.66 (0.35), residues: 613 helix: 1.77 (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 0.009 0.001 TRP A 42 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 *********************** 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 78 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.470 Fit side-chains REVERT: A 150 TYR cc_start: 0.8383 (m-10) cc_final: 0.7614 (m-10) REVERT: A 191 THR cc_start: 0.8603 (m) cc_final: 0.8344 (m) REVERT: A 216 MET cc_start: 0.8662 (ttp) cc_final: 0.8381 (ttp) REVERT: A 323 THR cc_start: 0.9163 (OUTLIER) cc_final: 0.8957 (p) REVERT: A 352 ARG cc_start: 0.7389 (ttm110) cc_final: 0.7098 (ttm170) REVERT: A 363 ASN cc_start: 0.8633 (m-40) cc_final: 0.8396 (m110) REVERT: A 382 MET cc_start: 0.8305 (mmm) cc_final: 0.8072 (mmm) REVERT: A 412 ARG cc_start: 0.7477 (ttt180) cc_final: 0.7021 (ttp80) REVERT: A 553 ARG cc_start: 0.7732 (mtp-110) cc_final: 0.7369 (ttp80) REVERT: A 660 MET cc_start: 0.8631 (ttp) cc_final: 0.8390 (ttp) outliers start: 8 outliers final: 4 residues processed: 74 average time/residue: 0.1873 time to fit residues: 17.5428 Evaluate side-chains 73 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.464 ------------------------------------------------------------------------------- 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 359 VAL 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 0 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.3271 r_free = 0.3271 target = 0.123884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.103707 restraints weight = 5180.647| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 1.28 r_work: 0.2919 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4934 Z= 0.179 Angle : 0.551 7.044 6728 Z= 0.286 Chirality : 0.040 0.161 782 Planarity : 0.004 0.042 824 Dihedral : 5.918 55.067 727 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.82 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: 1.72 (0.35), residues: 613 helix: 1.81 (0.25), residues: 454 sheet: None (None), residues: 0 loop : -0.82 (0.51), residues: 159 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 0.018 0.001 TYR A 256 ARG 0.003 0.000 ARG A 267 *********************** 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 80 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.464 Fit side-chains REVERT: A 150 TYR cc_start: 0.8397 (m-10) cc_final: 0.7620 (m-10) REVERT: A 191 THR cc_start: 0.8647 (m) cc_final: 0.8376 (m) REVERT: A 198 MET cc_start: 0.8118 (mtt) cc_final: 0.7733 (mtt) REVERT: A 216 MET cc_start: 0.8669 (ttp) cc_final: 0.8398 (ttp) REVERT: A 323 THR cc_start: 0.9191 (OUTLIER) cc_final: 0.8984 (p) REVERT: A 352 ARG cc_start: 0.7407 (ttm110) cc_final: 0.7094 (ttm170) REVERT: A 363 ASN cc_start: 0.8646 (m-40) cc_final: 0.8314 (m110) REVERT: A 382 MET cc_start: 0.8403 (mmm) cc_final: 0.8182 (mmm) REVERT: A 412 ARG cc_start: 0.7487 (ttt180) cc_final: 0.7041 (ttp80) REVERT: A 455 TYR cc_start: 0.8057 (m-10) cc_final: 0.7608 (m-10) REVERT: A 553 ARG cc_start: 0.7759 (mtp-110) cc_final: 0.7370 (ttp80) REVERT: A 554 LYS cc_start: 0.8085 (pttt) cc_final: 0.7838 (pttm) REVERT: A 660 MET cc_start: 0.8631 (ttp) cc_final: 0.8423 (ttp) outliers start: 9 outliers final: 6 residues processed: 77 average time/residue: 0.2065 time to fit residues: 20.0976 Evaluate side-chains 75 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.517 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 2 optimal weight: 3.9990 chunk 47 optimal weight: 8.9990 chunk 19 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 35 optimal weight: 0.0070 chunk 17 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 29 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 376 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.123019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.102972 restraints weight = 5150.387| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 1.26 r_work: 0.2914 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 4934 Z= 0.190 Angle : 0.562 7.021 6728 Z= 0.292 Chirality : 0.041 0.164 782 Planarity : 0.005 0.042 824 Dihedral : 5.904 55.106 727 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.39 % Allowed : 13.12 % 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 (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: 1.85 (0.35), residues: 613 helix: 1.85 (0.25), residues: 453 sheet: None (None), residues: 0 loop : -0.56 (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 0.002 0.000 ARG A 267 *********************** 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 84 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.504 Fit side-chains REVERT: A 150 TYR cc_start: 0.8422 (m-10) cc_final: 0.7626 (m-10) REVERT: A 191 THR cc_start: 0.8659 (m) cc_final: 0.8380 (m) REVERT: A 198 MET cc_start: 0.8227 (mtt) cc_final: 0.7872 (mtt) REVERT: A 216 MET cc_start: 0.8625 (ttp) cc_final: 0.8330 (ttp) REVERT: A 323 THR cc_start: 0.9189 (OUTLIER) cc_final: 0.8976 (p) REVERT: A 352 ARG cc_start: 0.7275 (ttm110) cc_final: 0.7022 (ttm170) REVERT: A 363 ASN cc_start: 0.8484 (m-40) cc_final: 0.8110 (m110) REVERT: A 382 MET cc_start: 0.8367 (mmm) cc_final: 0.8131 (mmm) REVERT: A 412 ARG cc_start: 0.7469 (ttt180) cc_final: 0.7018 (ttp80) REVERT: A 455 TYR cc_start: 0.8043 (m-10) cc_final: 0.7674 (m-10) REVERT: A 553 ARG cc_start: 0.7791 (mtp-110) cc_final: 0.7407 (ttp80) REVERT: A 554 LYS cc_start: 0.8103 (pttt) cc_final: 0.7837 (pttm) outliers start: 12 outliers final: 7 residues processed: 81 average time/residue: 0.1862 time to fit residues: 19.1421 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 242 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 364 ILE 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: 0.9980 chunk 24 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 14 optimal weight: 7.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- 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 = 0.3215 r_free = 0.3215 target = 0.119256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.099034 restraints weight = 5248.113| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 1.27 r_work: 0.2850 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 4934 Z= 0.258 Angle : 0.611 7.010 6728 Z= 0.319 Chirality : 0.043 0.170 782 Planarity : 0.005 0.044 824 Dihedral : 6.064 56.245 727 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.19 % Allowed : 13.32 % 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 (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: 1.56 (0.35), residues: 613 helix: 1.62 (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 0.011 0.001 TRP A 487 HIS 0.003 0.001 HIS A 555 PHE 0.011 0.001 PHE A 534 TYR 0.017 0.002 TYR A 256 ARG 0.002 0.000 ARG A 267 *********************** 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 80 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.470 Fit side-chains REVERT: A 150 TYR cc_start: 0.8478 (m-10) cc_final: 0.7666 (m-10) REVERT: A 191 THR cc_start: 0.8604 (m) cc_final: 0.8285 (m) REVERT: A 198 MET cc_start: 0.8410 (mtt) cc_final: 0.8020 (mtt) REVERT: A 216 MET cc_start: 0.8687 (ttp) cc_final: 0.8347 (ttp) REVERT: A 323 THR cc_start: 0.9198 (OUTLIER) cc_final: 0.8971 (p) REVERT: A 328 MET cc_start: 0.8679 (mtt) cc_final: 0.8288 (mtt) REVERT: A 382 MET cc_start: 0.8477 (mmm) cc_final: 0.8239 (mmm) REVERT: A 412 ARG cc_start: 0.7486 (ttt180) cc_final: 0.6640 (tmt-80) REVERT: A 455 TYR cc_start: 0.8063 (m-10) cc_final: 0.7644 (m-10) REVERT: A 553 ARG cc_start: 0.7844 (mtp-110) cc_final: 0.7432 (ttp80) outliers start: 11 outliers final: 10 residues processed: 75 average time/residue: 0.1966 time to fit residues: 18.6601 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 : 0.491 ------------------------------------------------------------------------------- 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 202 THR 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 346 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 364 ILE 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: 1.9990 chunk 55 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- 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 = 0.121870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.101295 restraints weight = 5198.065| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 1.31 r_work: 0.2891 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 4934 Z= 0.199 Angle : 0.566 6.960 6728 Z= 0.296 Chirality : 0.041 0.170 782 Planarity : 0.005 0.042 824 Dihedral : 5.960 55.462 727 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.19 % Allowed : 13.12 % Favored : 84.69 % 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: 1.73 (0.35), residues: 613 helix: 1.73 (0.25), residues: 452 sheet: None (None), residues: 0 loop : -0.46 (0.52), residues: 161 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 0.002 0.000 ARG A 267 *********************** 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 80 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.510 Fit side-chains REVERT: A 150 TYR cc_start: 0.8406 (m-10) cc_final: 0.7611 (m-10) REVERT: A 191 THR cc_start: 0.8503 (m) cc_final: 0.8194 (m) REVERT: A 198 MET cc_start: 0.8366 (mtt) cc_final: 0.7912 (mtt) REVERT: A 216 MET cc_start: 0.8646 (ttp) cc_final: 0.8321 (ttp) REVERT: A 323 THR cc_start: 0.9138 (OUTLIER) cc_final: 0.8879 (p) REVERT: A 328 MET cc_start: 0.8593 (mtt) cc_final: 0.8198 (mtt) REVERT: A 352 ARG cc_start: 0.7258 (ttm110) cc_final: 0.6901 (ttm170) REVERT: A 382 MET cc_start: 0.8380 (mmm) cc_final: 0.8155 (mmm) REVERT: A 412 ARG cc_start: 0.7452 (ttt180) cc_final: 0.6544 (tmt-80) REVERT: A 455 TYR cc_start: 0.7915 (m-10) cc_final: 0.7567 (m-10) REVERT: A 553 ARG cc_start: 0.7782 (mtp-110) cc_final: 0.7335 (ttp80) outliers start: 11 outliers final: 8 residues processed: 75 average time/residue: 0.1889 time to fit residues: 17.8711 Evaluate side-chains 77 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.505 ------------------------------------------------------------------------------- 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 202 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 346 VAL 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: 2.9990 chunk 51 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 43 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 overall best weight: 2.9986 ------------------------------------------------------------------------------- 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 = 0.3190 r_free = 0.3190 target = 0.117372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.097153 restraints weight = 5291.897| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 1.27 r_work: 0.2829 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 4934 Z= 0.323 Angle : 0.648 7.061 6728 Z= 0.339 Chirality : 0.045 0.181 782 Planarity : 0.005 0.044 824 Dihedral : 6.141 56.081 727 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.99 % Allowed : 13.32 % Favored : 84.69 % 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: 1.35 (0.35), residues: 613 helix: 1.47 (0.25), residues: 453 sheet: None (None), residues: 0 loop : -0.69 (0.51), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 429 HIS 0.003 0.001 HIS A 555 PHE 0.014 0.002 PHE A 666 TYR 0.018 0.002 TYR A 128 ARG 0.003 0.001 ARG A 130 ********************** 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 80 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.463 Fit side-chains REVERT: A 150 TYR cc_start: 0.8492 (m-10) cc_final: 0.7691 (m-10) REVERT: A 191 THR cc_start: 0.8703 (m) cc_final: 0.8376 (m) REVERT: A 198 MET cc_start: 0.8519 (mtt) cc_final: 0.8166 (mtt) REVERT: A 216 MET cc_start: 0.8701 (ttp) cc_final: 0.8287 (ttp) REVERT: A 328 MET cc_start: 0.8707 (mtt) cc_final: 0.8324 (mtt) REVERT: A 412 ARG cc_start: 0.7480 (ttt180) cc_final: 0.6642 (tmt-80) REVERT: A 455 TYR cc_start: 0.8047 (m-10) cc_final: 0.7571 (m-10) REVERT: A 553 ARG cc_start: 0.7849 (mtp-110) cc_final: 0.7435 (ttp80) outliers start: 10 outliers final: 9 residues processed: 76 average time/residue: 0.1846 time to fit residues: 17.7311 Evaluate side-chains 77 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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 202 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 364 ILE 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 11 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 1 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 = 0.3245 r_free = 0.3245 target = 0.121531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.101424 restraints weight = 5244.370| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 1.28 r_work: 0.2890 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 4934 Z= 0.199 Angle : 0.581 6.914 6728 Z= 0.302 Chirality : 0.041 0.172 782 Planarity : 0.005 0.043 824 Dihedral : 5.717 55.214 726 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.59 % Allowed : 13.72 % Favored : 84.69 % 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: 1.69 (0.35), residues: 613 helix: 1.70 (0.25), residues: 452 sheet: None (None), residues: 0 loop : -0.47 (0.52), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 487 HIS 0.003 0.001 HIS A 555 PHE 0.010 0.001 PHE A 534 TYR 0.018 0.001 TYR A 256 ARG 0.002 0.000 ARG A 267 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2468.32 seconds wall clock time: 43 minutes 11.55 seconds (2591.55 seconds total)