Starting phenix.real_space_refine on Tue Aug 4 19:44:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mx5_48710/08_2026/9mx5_48710.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mx5_48710/08_2026/9mx5_48710.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mx5_48710/08_2026/9mx5_48710.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mx5_48710/08_2026/9mx5_48710.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mx5_48710/08_2026/9mx5_48710.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mx5_48710/08_2026/9mx5_48710.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.012 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: 8 Type Number sf(0) Gaussians Al 1 5.89 5 P 54 5.49 5 Mg 1 5.21 5 S 25 5.16 5 C 3858 2.51 5 N 1133 2.21 5 O 1388 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6463 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 652, 5292 Classifications: {'peptide': 652} Link IDs: {'PTRANS': 26, 'TRANS': 625} Chain: "B" Number of atoms: 566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 566 Classifications: {'RNA': 27} Modifications used: {'5*END': 1, 'rna3p_pur': 12, 'rna3p_pyr': 15} Link IDs: {'rna3p': 26} Chain: "C" Number of atoms: 573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 573 Classifications: {'RNA': 27} Modifications used: {'5*END': 1, 'rna3p_pur': 15, 'rna3p_pyr': 12} Link IDs: {'rna3p': 26} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 1.03, per 1000 atoms: 0.16 Number of scatterers: 6463 At special positions: 0 Unit cell: (92.432, 92.432, 112.488, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 25 16.00 P 54 15.00 Al 1 13.00 Mg 1 11.99 F 3 9.00 O 1388 8.00 N 1133 7.00 C 3858 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.34 Conformation dependent library (CDL) restraints added in 189.4 milliseconds 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1262 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 3 sheets defined 53.2% alpha, 10.3% beta 27 base pairs and 39 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 12 through 25 removed outlier: 3.646A pdb=" N LYS A 25 " --> pdb=" O ARG A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 48 removed outlier: 3.504A pdb=" N LEU A 48 " --> pdb=" O LEU A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 52 removed outlier: 3.766A pdb=" N ILE A 52 " --> pdb=" O ALA A 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 49 through 52' Processing helix chain 'A' and resid 69 through 84 Processing helix chain 'A' and resid 101 through 112 removed outlier: 3.546A pdb=" N HIS A 112 " --> pdb=" O GLU A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 128 Processing helix chain 'A' and resid 132 through 134 No H-bonds generated for 'chain 'A' and resid 132 through 134' Processing helix chain 'A' and resid 144 through 147 Processing helix chain 'A' and resid 151 through 162 removed outlier: 3.884A pdb=" N ASN A 162 " --> pdb=" O ARG A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 168 removed outlier: 3.520A pdb=" N ASP A 167 " --> pdb=" O GLU A 164 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARG A 168 " --> pdb=" O GLN A 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 164 through 168' Processing helix chain 'A' and resid 187 through 200 Processing helix chain 'A' and resid 234 through 258 Processing helix chain 'A' and resid 262 through 283 removed outlier: 3.774A pdb=" N LEU A 266 " --> pdb=" O ASP A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 303 Processing helix chain 'A' and resid 307 through 331 removed outlier: 3.646A pdb=" N ASN A 330 " --> pdb=" O ASN A 326 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A 331 " --> pdb=" O VAL A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 344 through 364 removed outlier: 4.491A pdb=" N ASN A 363 " --> pdb=" O SER A 359 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N SER A 364 " --> pdb=" O ASN A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 394 removed outlier: 3.517A pdb=" N ALA A 380 " --> pdb=" O ARG A 376 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 468 through 479 removed outlier: 4.591A pdb=" N ALA A 479 " --> pdb=" O SER A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 516 removed outlier: 3.553A pdb=" N ARG A 514 " --> pdb=" O LYS A 510 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N CYS A 516 " --> pdb=" O LEU A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 530 removed outlier: 3.652A pdb=" N PHE A 527 " --> pdb=" O SER A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 551 No H-bonds generated for 'chain 'A' and resid 549 through 551' Processing helix chain 'A' and resid 552 through 564 removed outlier: 3.503A pdb=" N LEU A 556 " --> pdb=" O SER A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 633 Processing helix chain 'A' and resid 645 through 652 Processing sheet with id=AA1, first strand: chain 'A' and resid 88 through 91 removed outlier: 6.250A pdb=" N GLY A 89 " --> pdb=" O VAL A 116 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N THR A 118 " --> pdb=" O GLY A 89 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N TYR A 91 " --> pdb=" O THR A 118 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR A 63 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N MET A 117 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N PHE A 65 " --> pdb=" O MET A 117 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ARG A 62 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU A 139 " --> pdb=" O ARG A 62 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N PHE A 64 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N PHE A 141 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LEU A 66 " --> pdb=" O PHE A 141 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG A 170 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR A 27 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY A 173 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ILE A 28 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 222 through 228 removed outlier: 5.964A pdb=" N LYS A 222 " --> pdb=" O TYR A 486 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N ILE A 488 " --> pdb=" O LYS A 222 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE A 224 " --> pdb=" O ILE A 488 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N VAL A 490 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL A 226 " --> pdb=" O VAL A 490 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET A 489 " --> pdb=" O ARG A 462 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE A 371 " --> pdb=" O VAL A 461 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ASP A 404 " --> pdb=" O VAL A 443 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 575 through 582 removed outlier: 3.528A pdb=" N GLN A 581 " --> pdb=" O MET A 589 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET A 589 " --> pdb=" O GLN A 581 " (cutoff:3.500A) 249 hydrogen bonds defined for protein. 738 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 65 hydrogen bonds 130 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 39 stacking parallelities Total time for adding SS restraints: 1.09 Time building geometry restraints manager: 0.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1859 1.34 - 1.46: 1266 1.46 - 1.58: 3410 1.58 - 1.70: 110 1.70 - 1.81: 38 Bond restraints: 6683 Sorted by residual: bond pdb=" CG LEU A 299 " pdb=" CD2 LEU A 299 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.81e+00 bond pdb=" N7 A B 24 " pdb=" C5 A B 24 " ideal model delta sigma weight residual 1.388 1.381 0.007 6.00e-03 2.78e+04 1.33e+00 bond pdb=" C4 ADP A 702 " pdb=" C5 ADP A 702 " ideal model delta sigma weight residual 1.490 1.467 0.023 2.00e-02 2.50e+03 1.33e+00 bond pdb=" CB VAL A 73 " pdb=" CG1 VAL A 73 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.03e+00 bond pdb=" N1 C B 23 " pdb=" C6 C B 23 " ideal model delta sigma weight residual 1.367 1.361 0.006 6.00e-03 2.78e+04 9.71e-01 ... (remaining 6678 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 8969 1.78 - 3.56: 266 3.56 - 5.35: 18 5.35 - 7.13: 7 7.13 - 8.91: 3 Bond angle restraints: 9263 Sorted by residual: angle pdb=" O5' C B 26 " pdb=" C5' C B 26 " pdb=" C4' C B 26 " ideal model delta sigma weight residual 109.40 112.54 -3.14 8.00e-01 1.56e+00 1.54e+01 angle pdb=" O5' U B 25 " pdb=" C5' U B 25 " pdb=" C4' U B 25 " ideal model delta sigma weight residual 109.40 112.40 -3.00 8.00e-01 1.56e+00 1.40e+01 angle pdb=" O5' U C 4 " pdb=" C5' U C 4 " pdb=" C4' U C 4 " ideal model delta sigma weight residual 109.40 112.31 -2.91 8.00e-01 1.56e+00 1.32e+01 angle pdb=" O5' U C 11 " pdb=" C5' U C 11 " pdb=" C4' U C 11 " ideal model delta sigma weight residual 109.40 112.21 -2.81 8.00e-01 1.56e+00 1.23e+01 angle pdb=" O5' G B 18 " pdb=" C5' G B 18 " pdb=" C4' G B 18 " ideal model delta sigma weight residual 109.40 112.14 -2.74 8.00e-01 1.56e+00 1.17e+01 ... (remaining 9258 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 3545 17.73 - 35.46: 446 35.46 - 53.19: 133 53.19 - 70.92: 59 70.92 - 88.64: 19 Dihedral angle restraints: 4202 sinusoidal: 2272 harmonic: 1930 Sorted by residual: dihedral pdb=" CA ARG A 603 " pdb=" C ARG A 603 " pdb=" N GLU A 604 " pdb=" CA GLU A 604 " ideal model delta harmonic sigma weight residual -180.00 -163.39 -16.61 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CB GLU A 309 " pdb=" CG GLU A 309 " pdb=" CD GLU A 309 " pdb=" OE1 GLU A 309 " ideal model delta sinusoidal sigma weight residual 0.00 88.64 -88.64 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CG ARG A 170 " pdb=" CD ARG A 170 " pdb=" NE ARG A 170 " pdb=" CZ ARG A 170 " ideal model delta sinusoidal sigma weight residual 90.00 133.83 -43.83 2 1.50e+01 4.44e-03 1.02e+01 ... (remaining 4199 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 710 0.032 - 0.063: 219 0.063 - 0.095: 62 0.095 - 0.126: 37 0.126 - 0.158: 56 Chirality restraints: 1084 Sorted by residual: chirality pdb=" CA LEU A 299 " pdb=" N LEU A 299 " pdb=" C LEU A 299 " pdb=" CB LEU A 299 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.24e-01 chirality pdb=" C2' A B 20 " pdb=" C3' A B 20 " pdb=" O2' A B 20 " pdb=" C1' A B 20 " both_signs ideal model delta sigma weight residual False -2.62 -2.77 0.15 2.00e-01 2.50e+01 5.46e-01 chirality pdb=" C2' U B 25 " pdb=" C3' U B 25 " pdb=" O2' U B 25 " pdb=" C1' U B 25 " both_signs ideal model delta sigma weight residual False -2.62 -2.76 0.14 2.00e-01 2.50e+01 5.19e-01 ... (remaining 1081 not shown) Planarity restraints: 992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 151 " -0.030 5.00e-02 4.00e+02 4.61e-02 3.41e+00 pdb=" N PRO A 152 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 152 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 152 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 184 " 0.021 5.00e-02 4.00e+02 3.20e-02 1.64e+00 pdb=" N PRO A 185 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 185 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 185 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A B 24 " -0.016 2.00e-02 2.50e+03 7.27e-03 1.45e+00 pdb=" N9 A B 24 " 0.017 2.00e-02 2.50e+03 pdb=" C8 A B 24 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A B 24 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A B 24 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A B 24 " -0.001 2.00e-02 2.50e+03 pdb=" N6 A B 24 " -0.004 2.00e-02 2.50e+03 pdb=" N1 A B 24 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A B 24 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A B 24 " 0.003 2.00e-02 2.50e+03 pdb=" C4 A B 24 " 0.001 2.00e-02 2.50e+03 ... (remaining 989 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 291 2.72 - 3.26: 6384 3.26 - 3.81: 10639 3.81 - 4.35: 12579 4.35 - 4.90: 19658 Nonbonded interactions: 49551 Sorted by model distance: nonbonded pdb=" F1 AF3 A 701 " pdb=" O3B ADP A 702 " model vdw 2.169 2.990 nonbonded pdb=" OG SER A 412 " pdb=" OG SER A 414 " model vdw 2.278 3.040 nonbonded pdb=" O SER A 600 " pdb=" NH1 ARG A 603 " model vdw 2.283 3.120 nonbonded pdb=" N ASP A 544 " pdb=" OD1 ASP A 544 " model vdw 2.317 3.120 nonbonded pdb=" OG SER A 252 " pdb=" NZ LYS A 270 " model vdw 2.340 3.120 ... (remaining 49546 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: 1.850 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 5.790 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 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 : 0.003 0.044 6683 Z= 0.174 Angle : 0.643 8.910 9263 Z= 0.405 Chirality : 0.048 0.158 1084 Planarity : 0.004 0.046 992 Dihedral : 18.208 88.644 2940 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.15 % Favored : 95.69 % Rotamer: Outliers : 1.32 % Allowed : 21.16 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.32), residues: 650 helix: 3.26 (0.28), residues: 304 sheet: 1.27 (0.57), residues: 85 loop : -1.02 (0.32), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 547 TYR 0.012 0.001 TYR A 14 PHE 0.014 0.002 PHE A 498 TRP 0.004 0.001 TRP A 286 HIS 0.003 0.001 HIS A 558 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.17 ( 6683) covalent geometry : angle 0.64302 / 0.41 ( 9263) hydrogen bonds : bond 0.12757 / 8.36 ( 314) hydrogen bonds : angle 4.50461 / 3.12 ( 868) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.138 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 GLN cc_start: 0.9428 (OUTLIER) cc_final: 0.8429 (mp10) REVERT: A 117 MET cc_start: 0.9033 (ptt) cc_final: 0.8785 (ptt) REVERT: A 342 PHE cc_start: 0.6990 (p90) cc_final: 0.6195 (p90) REVERT: A 600 SER cc_start: 0.9047 (t) cc_final: 0.8460 (p) outliers start: 8 outliers final: 3 residues processed: 54 average time/residue: 0.0612 time to fit residues: 4.5357 Evaluate side-chains 43 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 599 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.0670 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 50.0000 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.0020 chunk 27 optimal weight: 0.8980 overall best weight: 0.5126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 289 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.137149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.090827 restraints weight = 14191.295| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 3.72 r_work: 0.3226 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.0742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6683 Z= 0.109 Angle : 0.547 10.293 9263 Z= 0.275 Chirality : 0.036 0.136 1084 Planarity : 0.004 0.044 992 Dihedral : 15.028 73.630 1536 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.69 % Favored : 96.15 % Rotamer: Outliers : 1.82 % Allowed : 20.99 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.33), residues: 650 helix: 3.04 (0.28), residues: 320 sheet: 1.77 (0.56), residues: 82 loop : -1.11 (0.34), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 547 TYR 0.009 0.001 TYR A 14 PHE 0.009 0.001 PHE A 9 TRP 0.005 0.001 TRP A 286 HIS 0.003 0.001 HIS A 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.11 ( 6683) covalent geometry : angle 0.54706 / 0.27 ( 9263) hydrogen bonds : bond 0.04916 / 3.27 ( 314) hydrogen bonds : angle 3.80868 / 2.68 ( 868) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.8960 (ptt) cc_final: 0.8741 (ptt) REVERT: A 157 MET cc_start: 0.9340 (mmm) cc_final: 0.9089 (mmm) REVERT: A 342 PHE cc_start: 0.6869 (p90) cc_final: 0.6149 (p90) REVERT: A 397 ASP cc_start: 0.8674 (m-30) cc_final: 0.8434 (m-30) REVERT: A 590 PHE cc_start: 0.8948 (m-80) cc_final: 0.8041 (m-80) REVERT: A 600 SER cc_start: 0.9073 (t) cc_final: 0.8546 (p) REVERT: A 604 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7597 (tp30) outliers start: 11 outliers final: 3 residues processed: 50 average time/residue: 0.0596 time to fit residues: 4.0660 Evaluate side-chains 44 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 526 ASP Chi-restraints excluded: chain A residue 604 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 31 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 67 optimal weight: 10.0000 chunk 2 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.134749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.087822 restraints weight = 14160.484| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 3.67 r_work: 0.3108 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6683 Z= 0.130 Angle : 0.541 9.590 9263 Z= 0.272 Chirality : 0.036 0.137 1084 Planarity : 0.004 0.046 992 Dihedral : 14.786 73.770 1527 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.00 % Favored : 95.85 % Rotamer: Outliers : 1.98 % Allowed : 19.67 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.10 (0.33), residues: 650 helix: 3.19 (0.28), residues: 314 sheet: 1.57 (0.53), residues: 92 loop : -1.26 (0.35), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 514 TYR 0.010 0.001 TYR A 160 PHE 0.013 0.002 PHE A 498 TRP 0.007 0.001 TRP A 286 HIS 0.003 0.001 HIS A 558 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 6683) covalent geometry : angle 0.54073 / 0.27 ( 9263) hydrogen bonds : bond 0.04890 / 3.25 ( 314) hydrogen bonds : angle 3.56785 / 2.49 ( 868) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.8938 (ptt) cc_final: 0.8712 (ptt) REVERT: A 282 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7620 (mp0) REVERT: A 342 PHE cc_start: 0.7006 (p90) cc_final: 0.6373 (p90) REVERT: A 396 ASP cc_start: 0.8668 (p0) cc_final: 0.7896 (p0) REVERT: A 397 ASP cc_start: 0.8780 (m-30) cc_final: 0.8294 (m-30) REVERT: A 495 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.7827 (ptmt) REVERT: A 590 PHE cc_start: 0.9018 (m-80) cc_final: 0.8524 (m-80) REVERT: A 600 SER cc_start: 0.9130 (OUTLIER) cc_final: 0.8573 (p) outliers start: 12 outliers final: 4 residues processed: 54 average time/residue: 0.0712 time to fit residues: 5.1178 Evaluate side-chains 47 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 495 LYS Chi-restraints excluded: chain A residue 526 ASP Chi-restraints excluded: chain A residue 600 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 63 optimal weight: 3.9990 chunk 17 optimal weight: 0.0670 chunk 9 optimal weight: 2.9990 chunk 66 optimal weight: 20.0000 chunk 32 optimal weight: 0.2980 chunk 25 optimal weight: 20.0000 chunk 44 optimal weight: 0.0170 chunk 41 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 52 optimal weight: 20.0000 overall best weight: 0.8158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.134676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.087418 restraints weight = 14243.291| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 3.72 r_work: 0.3058 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6683 Z= 0.111 Angle : 0.530 9.705 9263 Z= 0.266 Chirality : 0.036 0.160 1084 Planarity : 0.004 0.047 992 Dihedral : 14.778 73.828 1527 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.85 % Favored : 96.00 % Rotamer: Outliers : 1.98 % Allowed : 21.16 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.33), residues: 650 helix: 3.24 (0.28), residues: 314 sheet: 1.47 (0.53), residues: 94 loop : -1.28 (0.36), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 547 TYR 0.009 0.001 TYR A 14 PHE 0.010 0.001 PHE A 498 TRP 0.006 0.001 TRP A 286 HIS 0.006 0.001 HIS A 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 6683) covalent geometry : angle 0.52953 / 0.27 ( 9263) hydrogen bonds : bond 0.04419 / 2.93 ( 314) hydrogen bonds : angle 3.51895 / 2.46 ( 868) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.8926 (ptt) cc_final: 0.8710 (ptt) REVERT: A 315 GLU cc_start: 0.9232 (mm-30) cc_final: 0.8849 (mm-30) REVERT: A 342 PHE cc_start: 0.6992 (p90) cc_final: 0.6429 (p90) REVERT: A 397 ASP cc_start: 0.8763 (m-30) cc_final: 0.8540 (m-30) REVERT: A 495 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.7709 (ptmt) REVERT: A 530 PHE cc_start: 0.6589 (OUTLIER) cc_final: 0.4730 (p90) REVERT: A 590 PHE cc_start: 0.9023 (m-80) cc_final: 0.8584 (m-80) REVERT: A 600 SER cc_start: 0.9071 (OUTLIER) cc_final: 0.8521 (p) outliers start: 12 outliers final: 4 residues processed: 52 average time/residue: 0.0681 time to fit residues: 4.7256 Evaluate side-chains 47 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 495 LYS Chi-restraints excluded: chain A residue 530 PHE Chi-restraints excluded: chain A residue 600 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 65 optimal weight: 50.0000 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 53 optimal weight: 0.2980 chunk 64 optimal weight: 0.0970 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.131400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.083799 restraints weight = 14354.992| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 3.67 r_work: 0.3057 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6683 Z= 0.182 Angle : 0.608 10.539 9263 Z= 0.303 Chirality : 0.038 0.143 1084 Planarity : 0.005 0.092 992 Dihedral : 14.800 73.815 1527 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.31 % Favored : 95.54 % Rotamer: Outliers : 2.31 % Allowed : 21.16 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.33), residues: 650 helix: 3.07 (0.28), residues: 314 sheet: 1.35 (0.52), residues: 94 loop : -1.43 (0.36), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 314 TYR 0.013 0.001 TYR A 14 PHE 0.018 0.002 PHE A 498 TRP 0.006 0.001 TRP A 286 HIS 0.005 0.001 HIS A 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 ( 6683) covalent geometry : angle 0.60793 / 0.30 ( 9263) hydrogen bonds : bond 0.05802 / 3.87 ( 314) hydrogen bonds : angle 3.72910 / 2.58 ( 868) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 39 time to evaluate : 0.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 GLN cc_start: 0.9363 (OUTLIER) cc_final: 0.8597 (mt0) REVERT: A 117 MET cc_start: 0.9008 (ptt) cc_final: 0.8768 (ptt) REVERT: A 199 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8592 (mp) REVERT: A 299 LEU cc_start: 0.8609 (mm) cc_final: 0.8198 (tp) REVERT: A 315 GLU cc_start: 0.9232 (mm-30) cc_final: 0.8848 (mm-30) REVERT: A 323 GLN cc_start: 0.9401 (pp30) cc_final: 0.9169 (pp30) REVERT: A 342 PHE cc_start: 0.7152 (p90) cc_final: 0.6643 (p90) REVERT: A 397 ASP cc_start: 0.8808 (m-30) cc_final: 0.8501 (m-30) REVERT: A 495 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.7766 (ptmt) REVERT: A 530 PHE cc_start: 0.6706 (OUTLIER) cc_final: 0.4814 (p90) REVERT: A 590 PHE cc_start: 0.9062 (m-80) cc_final: 0.8667 (m-80) REVERT: A 600 SER cc_start: 0.9112 (OUTLIER) cc_final: 0.8595 (p) outliers start: 14 outliers final: 5 residues processed: 52 average time/residue: 0.0618 time to fit residues: 4.4661 Evaluate side-chains 47 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 495 LYS Chi-restraints excluded: chain A residue 526 ASP Chi-restraints excluded: chain A residue 530 PHE Chi-restraints excluded: chain A residue 600 SER Chi-restraints excluded: chain A residue 615 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 8 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 53 optimal weight: 0.1980 chunk 35 optimal weight: 2.9990 chunk 60 optimal weight: 0.0070 chunk 45 optimal weight: 0.0670 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.134096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.086585 restraints weight = 14073.947| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 3.70 r_work: 0.3132 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6683 Z= 0.096 Angle : 0.545 11.188 9263 Z= 0.266 Chirality : 0.035 0.132 1084 Planarity : 0.004 0.048 992 Dihedral : 14.784 73.858 1527 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.08 % Favored : 96.77 % Rotamer: Outliers : 1.98 % Allowed : 22.15 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.33), residues: 650 helix: 3.06 (0.28), residues: 321 sheet: 1.26 (0.52), residues: 101 loop : -1.18 (0.36), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 232 TYR 0.010 0.001 TYR A 14 PHE 0.022 0.001 PHE A 400 TRP 0.007 0.001 TRP A 286 HIS 0.005 0.001 HIS A 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00199 / 0.10 ( 6683) covalent geometry : angle 0.54540 / 0.27 ( 9263) hydrogen bonds : bond 0.03938 / 2.61 ( 314) hydrogen bonds : angle 3.36669 / 2.35 ( 868) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 GLN cc_start: 0.9256 (OUTLIER) cc_final: 0.8536 (mt0) REVERT: A 299 LEU cc_start: 0.8475 (mm) cc_final: 0.8003 (tp) REVERT: A 315 GLU cc_start: 0.9235 (mm-30) cc_final: 0.8817 (mm-30) REVERT: A 323 GLN cc_start: 0.9352 (pp30) cc_final: 0.9124 (pp30) REVERT: A 342 PHE cc_start: 0.6961 (p90) cc_final: 0.6484 (p90) REVERT: A 530 PHE cc_start: 0.6714 (OUTLIER) cc_final: 0.4912 (p90) REVERT: A 590 PHE cc_start: 0.9068 (m-80) cc_final: 0.8671 (m-80) REVERT: A 600 SER cc_start: 0.9088 (OUTLIER) cc_final: 0.8541 (p) outliers start: 12 outliers final: 5 residues processed: 50 average time/residue: 0.0579 time to fit residues: 4.1691 Evaluate side-chains 46 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 530 PHE Chi-restraints excluded: chain A residue 600 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 23 optimal weight: 7.9990 chunk 30 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 25 optimal weight: 20.0000 chunk 0 optimal weight: 9.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.130973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.083377 restraints weight = 14254.557| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 3.68 r_work: 0.3010 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 6683 Z= 0.226 Angle : 0.661 13.335 9263 Z= 0.326 Chirality : 0.040 0.139 1084 Planarity : 0.005 0.049 992 Dihedral : 14.799 73.819 1527 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.62 % Favored : 95.23 % Rotamer: Outliers : 1.98 % Allowed : 21.98 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.33), residues: 650 helix: 3.16 (0.28), residues: 314 sheet: 1.13 (0.52), residues: 94 loop : -1.54 (0.36), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 62 TYR 0.014 0.002 TYR A 14 PHE 0.021 0.003 PHE A 498 TRP 0.006 0.001 TRP A 286 HIS 0.005 0.001 HIS A 630 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.23 ( 6683) covalent geometry : angle 0.66075 / 0.33 ( 9263) hydrogen bonds : bond 0.06563 / 4.39 ( 314) hydrogen bonds : angle 3.79271 / 2.63 ( 868) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 36 time to evaluate : 0.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 GLN cc_start: 0.9393 (OUTLIER) cc_final: 0.8633 (mt0) REVERT: A 199 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8739 (mp) REVERT: A 299 LEU cc_start: 0.8474 (mm) cc_final: 0.8005 (tp) REVERT: A 315 GLU cc_start: 0.9212 (mm-30) cc_final: 0.8815 (mm-30) REVERT: A 323 GLN cc_start: 0.9399 (pp30) cc_final: 0.9183 (pp30) REVERT: A 342 PHE cc_start: 0.7108 (p90) cc_final: 0.6709 (p90) REVERT: A 495 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.7784 (ptmt) REVERT: A 530 PHE cc_start: 0.6778 (OUTLIER) cc_final: 0.5064 (p90) REVERT: A 600 SER cc_start: 0.9093 (OUTLIER) cc_final: 0.8566 (p) outliers start: 12 outliers final: 3 residues processed: 47 average time/residue: 0.0666 time to fit residues: 4.4379 Evaluate side-chains 44 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 495 LYS Chi-restraints excluded: chain A residue 530 PHE Chi-restraints excluded: chain A residue 600 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 2 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 56 optimal weight: 0.0570 chunk 5 optimal weight: 0.4980 chunk 21 optimal weight: 4.9990 chunk 58 optimal weight: 0.0970 chunk 57 optimal weight: 1.9990 chunk 16 optimal weight: 0.1980 chunk 54 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.3496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.134340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.087485 restraints weight = 14216.830| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 3.66 r_work: 0.3117 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6683 Z= 0.100 Angle : 0.568 13.149 9263 Z= 0.275 Chirality : 0.035 0.133 1084 Planarity : 0.004 0.048 992 Dihedral : 14.789 73.867 1527 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.77 % Favored : 97.08 % Rotamer: Outliers : 1.49 % Allowed : 22.15 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.33), residues: 650 helix: 3.13 (0.28), residues: 320 sheet: 1.03 (0.51), residues: 102 loop : -1.30 (0.36), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 232 TYR 0.011 0.001 TYR A 14 PHE 0.007 0.001 PHE A 469 TRP 0.009 0.001 TRP A 286 HIS 0.005 0.001 HIS A 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 ( 6683) covalent geometry : angle 0.56837 / 0.28 ( 9263) hydrogen bonds : bond 0.03961 / 2.63 ( 314) hydrogen bonds : angle 3.35404 / 2.33 ( 868) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.9058 (OUTLIER) cc_final: 0.8844 (ttm) REVERT: A 113 GLN cc_start: 0.9261 (OUTLIER) cc_final: 0.8568 (mt0) REVERT: A 299 LEU cc_start: 0.8427 (mm) cc_final: 0.7975 (tp) REVERT: A 315 GLU cc_start: 0.9189 (mm-30) cc_final: 0.8767 (mm-30) REVERT: A 323 GLN cc_start: 0.9403 (pp30) cc_final: 0.9201 (pp30) REVERT: A 342 PHE cc_start: 0.6900 (p90) cc_final: 0.6488 (p90) REVERT: A 530 PHE cc_start: 0.6719 (OUTLIER) cc_final: 0.4999 (p90) outliers start: 9 outliers final: 5 residues processed: 43 average time/residue: 0.0543 time to fit residues: 3.4020 Evaluate side-chains 45 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 MET Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 530 PHE Chi-restraints excluded: chain A residue 600 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 23 optimal weight: 10.0000 chunk 47 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 648 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.131261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.084181 restraints weight = 14562.025| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 3.70 r_work: 0.3049 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 6683 Z= 0.201 Angle : 0.661 18.075 9263 Z= 0.321 Chirality : 0.039 0.143 1084 Planarity : 0.004 0.050 992 Dihedral : 14.786 73.828 1527 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.15 % Favored : 95.69 % Rotamer: Outliers : 1.32 % Allowed : 22.48 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.33), residues: 650 helix: 3.25 (0.28), residues: 314 sheet: 1.13 (0.52), residues: 94 loop : -1.55 (0.36), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 314 TYR 0.013 0.001 TYR A 14 PHE 0.019 0.002 PHE A 498 TRP 0.006 0.001 TRP A 286 HIS 0.004 0.001 HIS A 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.20 ( 6683) covalent geometry : angle 0.66150 / 0.32 ( 9263) hydrogen bonds : bond 0.06068 / 4.06 ( 314) hydrogen bonds : angle 3.70455 / 2.57 ( 868) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 GLN cc_start: 0.9386 (OUTLIER) cc_final: 0.8639 (mt0) REVERT: A 199 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8759 (mp) REVERT: A 299 LEU cc_start: 0.8447 (mm) cc_final: 0.7962 (tp) REVERT: A 315 GLU cc_start: 0.9060 (mm-30) cc_final: 0.8654 (mm-30) REVERT: A 323 GLN cc_start: 0.9394 (pp30) cc_final: 0.9184 (pp30) REVERT: A 342 PHE cc_start: 0.7062 (p90) cc_final: 0.6735 (p90) REVERT: A 530 PHE cc_start: 0.6815 (OUTLIER) cc_final: 0.5208 (p90) outliers start: 8 outliers final: 2 residues processed: 42 average time/residue: 0.0584 time to fit residues: 3.5515 Evaluate side-chains 41 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 530 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 65 optimal weight: 50.0000 chunk 27 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 44 optimal weight: 0.0980 chunk 4 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 648 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.132320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.085335 restraints weight = 14211.610| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 3.63 r_work: 0.3073 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6683 Z= 0.137 Angle : 0.628 16.573 9263 Z= 0.300 Chirality : 0.037 0.139 1084 Planarity : 0.004 0.050 992 Dihedral : 14.789 73.861 1527 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.00 % Favored : 95.85 % Rotamer: Outliers : 0.66 % Allowed : 22.98 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.33), residues: 650 helix: 3.26 (0.28), residues: 314 sheet: 1.09 (0.52), residues: 95 loop : -1.51 (0.36), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 274 TYR 0.013 0.001 TYR A 14 PHE 0.019 0.002 PHE A 358 TRP 0.008 0.001 TRP A 286 HIS 0.004 0.001 HIS A 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 6683) covalent geometry : angle 0.62807 / 0.30 ( 9263) hydrogen bonds : bond 0.05058 / 3.38 ( 314) hydrogen bonds : angle 3.55654 / 2.48 ( 868) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 GLN cc_start: 0.9332 (OUTLIER) cc_final: 0.8630 (mt0) REVERT: A 299 LEU cc_start: 0.8418 (mm) cc_final: 0.7951 (tp) REVERT: A 315 GLU cc_start: 0.9081 (mm-30) cc_final: 0.8687 (mm-30) REVERT: A 323 GLN cc_start: 0.9406 (pp30) cc_final: 0.9197 (pp30) REVERT: A 342 PHE cc_start: 0.6979 (p90) cc_final: 0.6671 (p90) REVERT: A 530 PHE cc_start: 0.6810 (OUTLIER) cc_final: 0.5204 (p90) outliers start: 4 outliers final: 1 residues processed: 41 average time/residue: 0.0699 time to fit residues: 4.0882 Evaluate side-chains 40 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 530 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 18 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 66 optimal weight: 20.0000 chunk 7 optimal weight: 0.8980 chunk 16 optimal weight: 0.1980 chunk 41 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.133309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.086700 restraints weight = 14263.045| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 3.65 r_work: 0.3087 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6683 Z= 0.125 Angle : 0.614 16.276 9263 Z= 0.292 Chirality : 0.036 0.136 1084 Planarity : 0.004 0.049 992 Dihedral : 14.769 73.847 1527 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.15 % Favored : 95.69 % Rotamer: Outliers : 0.99 % Allowed : 22.98 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.33), residues: 650 helix: 3.22 (0.28), residues: 315 sheet: 0.85 (0.50), residues: 102 loop : -1.44 (0.36), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 314 TYR 0.011 0.001 TYR A 14 PHE 0.042 0.002 PHE A 400 TRP 0.008 0.001 TRP A 286 HIS 0.004 0.001 HIS A 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 ( 6683) covalent geometry : angle 0.61444 / 0.29 ( 9263) hydrogen bonds : bond 0.04638 / 3.10 ( 314) hydrogen bonds : angle 3.48902 / 2.44 ( 868) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1743.65 seconds wall clock time: 30 minutes 23.18 seconds (1823.18 seconds total)