Starting phenix.real_space_refine on Thu Jul 2 03:50:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mx5_48710/07_2026/9mx5_48710.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mx5_48710/07_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_48710/07_2026/9mx5_48710.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mx5_48710/07_2026/9mx5_48710.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mx5_48710/07_2026/9mx5_48710.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mx5_48710/07_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 1.68, per 1000 atoms: 0.26 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: 0.62 Conformation dependent library (CDL) restraints added in 297.8 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: 0.45 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: 0.97 Time building geometry restraints manager: 0.76 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: 9130 1.78 - 3.56: 105 3.56 - 5.35: 18 5.35 - 7.13: 7 7.13 - 8.91: 3 Bond angle restraints: 9263 Sorted by residual: angle pdb=" CB MET A 632 " pdb=" CG MET A 632 " pdb=" SD MET A 632 " ideal model delta sigma weight residual 112.70 121.61 -8.91 3.00e+00 1.11e-01 8.82e+00 angle pdb=" CB MET A 589 " pdb=" CG MET A 589 " pdb=" SD MET A 589 " ideal model delta sigma weight residual 112.70 121.56 -8.86 3.00e+00 1.11e-01 8.73e+00 angle pdb=" CB MET A 157 " pdb=" CG MET A 157 " pdb=" SD MET A 157 " ideal model delta sigma weight residual 112.70 120.91 -8.21 3.00e+00 1.11e-01 7.49e+00 angle pdb=" CA GLN A 581 " pdb=" CB GLN A 581 " pdb=" CG GLN A 581 " ideal model delta sigma weight residual 114.10 118.97 -4.87 2.00e+00 2.50e-01 5.93e+00 angle pdb=" C1' C B 22 " pdb=" N1 C B 22 " pdb=" C2 C B 22 " ideal model delta sigma weight residual 118.80 121.18 -2.38 1.10e+00 8.26e-01 4.69e+00 ... (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: 775 0.032 - 0.063: 210 0.063 - 0.095: 61 0.095 - 0.126: 35 0.126 - 0.158: 3 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=" CB ILE A 454 " pdb=" CA ILE A 454 " pdb=" CG1 ILE A 454 " pdb=" CG2 ILE A 454 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 4.97e-01 chirality pdb=" CA ILE A 28 " pdb=" N ILE A 28 " pdb=" C ILE A 28 " pdb=" CB ILE A 28 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.39e-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: 2.420 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.520 Find NCS groups from input model: 0.030 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.340 ------------------------------------------------------------------------------- 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= 0.167 Angle : 0.556 8.910 9263 Z= 0.323 Chirality : 0.037 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 0.00329 / 0.17 ( 6683) covalent geometry : angle 0.55551 / 0.32 ( 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 : 0.212 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: 0.0800 time to fit residues: 5.8802 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 : 0.160 ------------------------------------------------------------------------------- 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 A 599 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.137020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.090240 restraints weight = 14364.457| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 3.78 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.0767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6683 Z= 0.110 Angle : 0.545 10.125 9263 Z= 0.273 Chirality : 0.036 0.134 1084 Planarity : 0.004 0.044 992 Dihedral : 14.946 73.711 1536 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.69 % Favored : 96.15 % Rotamer: Outliers : 1.65 % Allowed : 20.50 % Favored : 77.85 % 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 (0.32), residues: 650 helix: 3.02 (0.28), residues: 320 sheet: 1.76 (0.56), residues: 82 loop : -1.12 (0.34), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 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 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 ( 6683) covalent geometry : angle 0.54540 / 0.27 ( 9263) hydrogen bonds : bond 0.04737 / 3.15 ( 314) hydrogen bonds : angle 3.76161 / 2.65 ( 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 51 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.134 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.8861 (ptt) cc_final: 0.8642 (ptt) REVERT: A 157 MET cc_start: 0.9254 (mmm) cc_final: 0.8990 (mmm) REVERT: A 342 PHE cc_start: 0.6896 (p90) cc_final: 0.6215 (p90) REVERT: A 397 ASP cc_start: 0.8560 (m-30) cc_final: 0.8305 (m-30) REVERT: A 590 PHE cc_start: 0.8978 (m-80) cc_final: 0.8145 (m-80) outliers start: 10 outliers final: 4 residues processed: 48 average time/residue: 0.0848 time to fit residues: 5.3852 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 : 0.222 ------------------------------------------------------------------------------- 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 600 SER 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: 2.9990 chunk 1 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 67 optimal weight: 8.9990 chunk 2 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 = 0.4177 r_free = 0.4177 target = 0.131206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.083184 restraints weight = 14163.423| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 3.70 r_work: 0.3018 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6683 Z= 0.211 Angle : 0.621 8.471 9263 Z= 0.319 Chirality : 0.039 0.152 1084 Planarity : 0.005 0.051 992 Dihedral : 14.845 73.655 1527 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.15 % Favored : 95.69 % Rotamer: Outliers : 2.15 % Allowed : 20.00 % Favored : 77.85 % 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: 1.64 (0.32), residues: 650 helix: 2.84 (0.28), residues: 317 sheet: 1.14 (0.52), residues: 94 loop : -1.50 (0.35), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 547 TYR 0.014 0.001 TYR A 14 PHE 0.022 0.002 PHE A 498 TRP 0.010 0.001 TRP A 286 HIS 0.005 0.001 HIS A 558 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.21 ( 6683) covalent geometry : angle 0.62142 / 0.32 ( 9263) hydrogen bonds : bond 0.06809 / 4.54 ( 314) hydrogen bonds : angle 3.91533 / 2.73 ( 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: 13 poor density : 42 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.8993 (ptt) cc_final: 0.8747 (ptt) REVERT: A 199 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8702 (mp) REVERT: A 282 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7469 (mp0) REVERT: A 342 PHE cc_start: 0.7175 (p90) cc_final: 0.6589 (p90) REVERT: A 396 ASP cc_start: 0.8720 (p0) cc_final: 0.7937 (p0) REVERT: A 397 ASP cc_start: 0.8837 (m-30) cc_final: 0.8264 (m-30) REVERT: A 495 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.7885 (ptmt) REVERT: A 590 PHE cc_start: 0.9006 (m-80) cc_final: 0.8459 (m-80) REVERT: A 604 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7677 (tp30) outliers start: 13 outliers final: 3 residues processed: 54 average time/residue: 0.0970 time to fit residues: 7.0902 Evaluate side-chains 44 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.241 ------------------------------------------------------------------------------- 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 604 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 63 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 66 optimal weight: 10.0000 chunk 32 optimal weight: 0.0980 chunk 25 optimal weight: 20.0000 chunk 44 optimal weight: 0.0030 chunk 41 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 10 optimal weight: 0.1980 chunk 52 optimal weight: 10.0000 overall best weight: 0.3790 ------------------------------------------------------------------------------- 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 = 0.4212 r_free = 0.4212 target = 0.133824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.086618 restraints weight = 14105.965| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 3.68 r_work: 0.3044 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6683 Z= 0.101 Angle : 0.538 10.385 9263 Z= 0.270 Chirality : 0.036 0.155 1084 Planarity : 0.004 0.048 992 Dihedral : 14.809 73.766 1527 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.38 % Favored : 96.46 % Rotamer: Outliers : 1.32 % Allowed : 22.31 % 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: 3.08 (0.28), residues: 315 sheet: 1.18 (0.52), residues: 96 loop : -1.30 (0.36), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 295 TYR 0.010 0.001 TYR A 14 PHE 0.017 0.001 PHE A 400 TRP 0.008 0.001 TRP A 286 HIS 0.002 0.001 HIS A 630 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.10 ( 6683) covalent geometry : angle 0.53782 / 0.27 ( 9263) hydrogen bonds : bond 0.04483 / 2.96 ( 314) hydrogen bonds : angle 3.57218 / 2.50 ( 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 49 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 282 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7480 (mp0) REVERT: A 315 GLU cc_start: 0.9266 (mm-30) cc_final: 0.8889 (mm-30) REVERT: A 323 GLN cc_start: 0.9304 (pp30) cc_final: 0.9098 (pp30) REVERT: A 342 PHE cc_start: 0.7015 (p90) cc_final: 0.6476 (p90) REVERT: A 530 PHE cc_start: 0.6631 (OUTLIER) cc_final: 0.4765 (p90) REVERT: A 590 PHE cc_start: 0.9019 (m-80) cc_final: 0.8529 (m-80) outliers start: 8 outliers final: 4 residues processed: 48 average time/residue: 0.0778 time to fit residues: 5.1371 Evaluate side-chains 45 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.181 ------------------------------------------------------------------------------- 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 403 CYS Chi-restraints excluded: chain A residue 530 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 1.9990 chunk 67 optimal weight: 8.9990 chunk 46 optimal weight: 0.9990 chunk 68 optimal weight: 10.0000 chunk 65 optimal weight: 40.0000 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 8.9990 chunk 58 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 = 0.4155 r_free = 0.4155 target = 0.130025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.082189 restraints weight = 14346.763| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 3.68 r_work: 0.3021 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 6683 Z= 0.211 Angle : 0.636 10.755 9263 Z= 0.321 Chirality : 0.038 0.147 1084 Planarity : 0.005 0.091 992 Dihedral : 14.811 73.713 1527 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.31 % Favored : 95.54 % Rotamer: Outliers : 2.98 % Allowed : 20.99 % 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: 1.63 (0.33), residues: 650 helix: 2.96 (0.28), residues: 314 sheet: 0.92 (0.52), residues: 95 loop : -1.57 (0.36), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 314 TYR 0.015 0.001 TYR A 14 PHE 0.022 0.002 PHE A 498 TRP 0.008 0.001 TRP A 286 HIS 0.006 0.001 HIS A 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.21 ( 6683) covalent geometry : angle 0.63578 / 0.32 ( 9263) hydrogen bonds : bond 0.06678 / 4.44 ( 314) hydrogen bonds : angle 3.87847 / 2.69 ( 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: 18 poor density : 35 time to evaluate : 0.236 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: 0.8611 (mt0) REVERT: A 199 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8721 (mp) REVERT: A 282 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7454 (mp0) REVERT: A 299 LEU cc_start: 0.8585 (mm) cc_final: 0.8176 (tp) REVERT: A 315 GLU cc_start: 0.9270 (mm-30) cc_final: 0.8866 (mm-30) REVERT: A 323 GLN cc_start: 0.9333 (pp30) cc_final: 0.9118 (pp30) REVERT: A 342 PHE cc_start: 0.7171 (p90) cc_final: 0.6692 (p90) REVERT: A 375 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8467 (tp30) REVERT: A 495 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.7772 (ptmt) REVERT: A 530 PHE cc_start: 0.6824 (OUTLIER) cc_final: 0.5041 (p90) REVERT: A 604 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7764 (tp30) outliers start: 18 outliers final: 6 residues processed: 51 average time/residue: 0.0803 time to fit residues: 5.5072 Evaluate side-chains 48 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 35 time to evaluate : 0.233 ------------------------------------------------------------------------------- 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 282 GLU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 375 GLU 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 604 GLU 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: 0.9980 chunk 5 optimal weight: 0.8980 chunk 31 optimal weight: 9.9990 chunk 10 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.4192 r_free = 0.4192 target = 0.132096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.084346 restraints weight = 14227.206| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 3.72 r_work: 0.3058 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2185 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= 0.122 Angle : 0.571 10.905 9263 Z= 0.281 Chirality : 0.036 0.137 1084 Planarity : 0.004 0.051 992 Dihedral : 14.796 73.765 1527 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.00 % Favored : 95.85 % Rotamer: Outliers : 2.48 % Allowed : 21.65 % 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: 1.86 (0.33), residues: 650 helix: 3.13 (0.28), residues: 314 sheet: 1.11 (0.53), residues: 95 loop : -1.46 (0.37), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 514 TYR 0.013 0.001 TYR A 14 PHE 0.012 0.001 PHE A 498 TRP 0.008 0.001 TRP A 286 HIS 0.005 0.001 HIS A 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 6683) covalent geometry : angle 0.57131 / 0.28 ( 9263) hydrogen bonds : bond 0.05064 / 3.35 ( 314) hydrogen bonds : angle 3.58550 / 2.49 ( 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: 15 poor density : 37 time to evaluate : 0.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 GLN cc_start: 0.9346 (OUTLIER) cc_final: 0.8623 (mt0) REVERT: A 282 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7536 (mp0) REVERT: A 299 LEU cc_start: 0.8483 (mm) cc_final: 0.8018 (tp) REVERT: A 315 GLU cc_start: 0.9258 (mm-30) cc_final: 0.8852 (mm-30) REVERT: A 342 PHE cc_start: 0.7032 (p90) cc_final: 0.6587 (p90) REVERT: A 456 LYS cc_start: 0.5716 (OUTLIER) cc_final: 0.4657 (mmtt) REVERT: A 495 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.7782 (ptmt) REVERT: A 530 PHE cc_start: 0.6788 (OUTLIER) cc_final: 0.5090 (p90) REVERT: A 632 MET cc_start: 0.8452 (tmm) cc_final: 0.8224 (ttp) outliers start: 15 outliers final: 5 residues processed: 51 average time/residue: 0.0718 time to fit residues: 5.0119 Evaluate side-chains 46 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.134 ------------------------------------------------------------------------------- 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 282 GLU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 456 LYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 23 optimal weight: 8.9990 chunk 30 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 54 optimal weight: 0.0980 chunk 13 optimal weight: 0.8980 chunk 36 optimal weight: 10.0000 chunk 17 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 25 optimal weight: 20.0000 chunk 0 optimal weight: 8.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 323 GLN ** 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 = 0.4175 r_free = 0.4175 target = 0.130955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.082798 restraints weight = 14334.350| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 3.84 r_work: 0.3063 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6683 Z= 0.138 Angle : 0.579 12.092 9263 Z= 0.286 Chirality : 0.037 0.138 1084 Planarity : 0.004 0.050 992 Dihedral : 14.770 73.743 1527 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.31 % Favored : 95.54 % Rotamer: Outliers : 2.31 % Allowed : 21.65 % 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: 1.80 (0.33), residues: 650 helix: 3.11 (0.28), residues: 314 sheet: 0.86 (0.51), residues: 101 loop : -1.47 (0.37), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 232 TYR 0.012 0.001 TYR A 14 PHE 0.020 0.002 PHE A 358 TRP 0.008 0.001 TRP A 286 HIS 0.005 0.001 HIS A 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 6683) covalent geometry : angle 0.57855 / 0.29 ( 9263) hydrogen bonds : bond 0.05089 / 3.38 ( 314) hydrogen bonds : angle 3.57752 / 2.48 ( 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 51 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 37 time to evaluate : 0.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 GLN cc_start: 0.9343 (OUTLIER) cc_final: 0.8625 (mt0) REVERT: A 282 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7524 (mp0) REVERT: A 299 LEU cc_start: 0.8465 (mm) cc_final: 0.8006 (tp) REVERT: A 315 GLU cc_start: 0.9217 (mm-30) cc_final: 0.8801 (mm-30) REVERT: A 342 PHE cc_start: 0.7025 (p90) cc_final: 0.6631 (p90) REVERT: A 456 LYS cc_start: 0.5718 (OUTLIER) cc_final: 0.4587 (mmtt) REVERT: A 495 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.7772 (ptmt) REVERT: A 530 PHE cc_start: 0.6850 (OUTLIER) cc_final: 0.5117 (p90) outliers start: 14 outliers final: 5 residues processed: 51 average time/residue: 0.0697 time to fit residues: 5.0014 Evaluate side-chains 45 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.236 ------------------------------------------------------------------------------- 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 282 GLU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 456 LYS 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: 0.9990 chunk 55 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 5 optimal weight: 0.0040 chunk 21 optimal weight: 4.9990 chunk 58 optimal weight: 0.0770 chunk 57 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 53 optimal weight: 0.0970 overall best weight: 0.4150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.132621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.085280 restraints weight = 14213.580| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 3.70 r_work: 0.3047 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2377 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= 0.098 Angle : 0.609 20.809 9263 Z= 0.288 Chirality : 0.036 0.139 1084 Planarity : 0.004 0.049 992 Dihedral : 14.749 73.763 1527 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.54 % Favored : 96.31 % Rotamer: Outliers : 1.16 % Allowed : 22.98 % 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: 1.81 (0.33), residues: 650 helix: 3.00 (0.29), residues: 320 sheet: 0.83 (0.52), residues: 100 loop : -1.38 (0.36), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 314 TYR 0.009 0.001 TYR A 14 PHE 0.022 0.001 PHE A 358 TRP 0.008 0.001 TRP A 286 HIS 0.005 0.001 HIS A 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.10 ( 6683) covalent geometry : angle 0.60855 / 0.29 ( 9263) hydrogen bonds : bond 0.03960 / 2.62 ( 314) hydrogen bonds : angle 3.44099 / 2.39 ( 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 43 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 GLN cc_start: 0.9213 (OUTLIER) cc_final: 0.8527 (mt0) REVERT: A 299 LEU cc_start: 0.8480 (mm) cc_final: 0.8024 (tp) REVERT: A 315 GLU cc_start: 0.9118 (mm-30) cc_final: 0.8699 (mm-30) REVERT: A 342 PHE cc_start: 0.6935 (p90) cc_final: 0.6559 (p90) REVERT: A 530 PHE cc_start: 0.6645 (OUTLIER) cc_final: 0.4985 (p90) outliers start: 7 outliers final: 3 residues processed: 43 average time/residue: 0.0612 time to fit residues: 3.8351 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 : 0.191 ------------------------------------------------------------------------------- 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 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: 9.9990 chunk 47 optimal weight: 0.9980 chunk 25 optimal weight: 20.0000 chunk 64 optimal weight: 0.8980 chunk 53 optimal weight: 0.3980 chunk 48 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 33 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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 = 0.4187 r_free = 0.4187 target = 0.131763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.084812 restraints weight = 14381.658| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 3.64 r_work: 0.3005 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6683 Z= 0.144 Angle : 0.618 16.935 9263 Z= 0.299 Chirality : 0.036 0.140 1084 Planarity : 0.004 0.050 992 Dihedral : 14.725 73.741 1527 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.31 % Favored : 95.54 % Rotamer: Outliers : 1.82 % Allowed : 22.48 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.34), residues: 650 helix: 3.22 (0.28), residues: 314 sheet: 0.93 (0.51), residues: 101 loop : -1.45 (0.37), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 314 TYR 0.010 0.001 TYR A 14 PHE 0.013 0.001 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 0.00342 / 0.14 ( 6683) covalent geometry : angle 0.61797 / 0.30 ( 9263) hydrogen bonds : bond 0.04815 / 3.20 ( 314) hydrogen bonds : angle 3.54451 / 2.46 ( 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 48 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 GLN cc_start: 0.9259 (OUTLIER) cc_final: 0.8538 (mt0) REVERT: A 299 LEU cc_start: 0.8430 (mm) cc_final: 0.7972 (tp) REVERT: A 315 GLU cc_start: 0.9097 (mm-30) cc_final: 0.8697 (mm-30) REVERT: A 342 PHE cc_start: 0.7030 (p90) cc_final: 0.6704 (p90) REVERT: A 456 LYS cc_start: 0.5702 (OUTLIER) cc_final: 0.4613 (mmtt) REVERT: A 495 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7771 (ptmt) REVERT: A 530 PHE cc_start: 0.6761 (OUTLIER) cc_final: 0.5104 (p90) REVERT: A 600 SER cc_start: 0.9040 (OUTLIER) cc_final: 0.8743 (t) outliers start: 11 outliers final: 3 residues processed: 47 average time/residue: 0.0697 time to fit residues: 4.5755 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 : 0.209 ------------------------------------------------------------------------------- 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 353 ILE Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 456 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 65 optimal weight: 40.0000 chunk 27 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 29 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 41 optimal weight: 8.9990 chunk 57 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 44 optimal weight: 0.0670 chunk 4 optimal weight: 0.9990 overall best weight: 0.8122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 323 GLN ** 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 = 0.4185 r_free = 0.4185 target = 0.131631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.083990 restraints weight = 14297.355| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 3.74 r_work: 0.3095 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6683 Z= 0.118 Angle : 0.653 18.645 9263 Z= 0.313 Chirality : 0.036 0.171 1084 Planarity : 0.004 0.049 992 Dihedral : 14.727 73.762 1527 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.31 % Favored : 95.54 % Rotamer: Outliers : 1.49 % Allowed : 22.98 % Favored : 75.54 % 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: 3.15 (0.28), residues: 314 sheet: 0.99 (0.51), residues: 101 loop : -1.40 (0.37), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 232 TYR 0.011 0.001 TYR A 14 PHE 0.047 0.002 PHE A 400 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 0.00271 / 0.12 ( 6683) covalent geometry : angle 0.65311 / 0.31 ( 9263) hydrogen bonds : bond 0.04453 / 2.95 ( 314) hydrogen bonds : angle 3.58295 / 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 45 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 GLN cc_start: 0.9243 (OUTLIER) cc_final: 0.8555 (mt0) REVERT: A 299 LEU cc_start: 0.8414 (mm) cc_final: 0.7944 (tp) REVERT: A 315 GLU cc_start: 0.9049 (mm-30) cc_final: 0.8646 (mm-30) REVERT: A 342 PHE cc_start: 0.6909 (p90) cc_final: 0.6594 (p90) REVERT: A 456 LYS cc_start: 0.5627 (OUTLIER) cc_final: 0.4486 (mmtt) REVERT: A 495 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7794 (ptmt) REVERT: A 530 PHE cc_start: 0.6778 (OUTLIER) cc_final: 0.5128 (p90) REVERT: A 600 SER cc_start: 0.9028 (OUTLIER) cc_final: 0.8724 (t) outliers start: 9 outliers final: 3 residues processed: 45 average time/residue: 0.0617 time to fit residues: 3.9881 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 : 0.228 ------------------------------------------------------------------------------- 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 343 VAL Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 456 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 18 optimal weight: 0.4980 chunk 55 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 66 optimal weight: 20.0000 chunk 7 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 41 optimal weight: 0.0050 chunk 43 optimal weight: 0.8980 chunk 36 optimal weight: 7.9990 chunk 32 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 323 GLN ** 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 = 0.4221 r_free = 0.4221 target = 0.133515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.086696 restraints weight = 14261.629| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 3.70 r_work: 0.3127 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 6683 Z= 0.104 Angle : 0.621 17.252 9263 Z= 0.298 Chirality : 0.036 0.236 1084 Planarity : 0.004 0.049 992 Dihedral : 14.702 73.758 1527 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.69 % Favored : 96.15 % Rotamer: Outliers : 0.99 % Allowed : 23.47 % Favored : 75.54 % 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: 3.04 (0.29), residues: 321 sheet: 0.99 (0.52), residues: 99 loop : -1.31 (0.36), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 314 TYR 0.008 0.001 TYR A 14 PHE 0.034 0.002 PHE A 400 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 0.00232 / 0.10 ( 6683) covalent geometry : angle 0.62074 / 0.30 ( 9263) hydrogen bonds : bond 0.03811 / 2.50 ( 314) hydrogen bonds : angle 3.51098 / 2.43 ( 868) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1924.65 seconds wall clock time: 33 minutes 34.85 seconds (2014.85 seconds total)