Starting phenix.real_space_refine on Sat May 10 14:27:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mw8_48697/05_2025/9mw8_48697.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mw8_48697/05_2025/9mw8_48697.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mw8_48697/05_2025/9mw8_48697.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mw8_48697/05_2025/9mw8_48697.map" model { file = "/net/cci-nas-00/data/ceres_data/9mw8_48697/05_2025/9mw8_48697.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mw8_48697/05_2025/9mw8_48697.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 54 5.49 5 Mg 1 5.21 5 S 24 5.16 5 C 3836 2.51 5 N 1128 2.21 5 O 1376 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 6419 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5252 Classifications: {'peptide': 647} Link IDs: {'PTRANS': 26, 'TRANS': 620} 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, 'rna2p_pyr': 1, 'rna3p_pur': 15, 'rna3p_pyr': 11} Link IDs: {'rna2p': 1, 'rna3p': 25} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.00, per 1000 atoms: 0.78 Number of scatterers: 6419 At special positions: 0 Unit cell: (91.56, 93.304, 103.768, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 24 16.00 P 54 15.00 Mg 1 11.99 O 1376 8.00 N 1128 7.00 C 3836 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: 1.83 Conformation dependent library (CDL) restraints added in 817.7 milliseconds 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1252 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 3 sheets defined 56.9% alpha, 10.2% beta 27 base pairs and 34 stacking pairs defined. Time for finding SS restraints: 2.30 Creating SS restraints... Processing helix chain 'A' and resid 12 through 25 removed outlier: 3.562A pdb=" N ARG A 21 " --> pdb=" O GLU A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 48 removed outlier: 3.765A pdb=" N LEU A 48 " --> pdb=" O LEU A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 54 Processing helix chain 'A' and resid 70 through 84 removed outlier: 3.916A pdb=" N ASN A 74 " --> pdb=" O VAL A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 100 removed outlier: 3.762A pdb=" N MET A 95 " --> pdb=" O VAL A 92 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N VAL A 97 " --> pdb=" O ASP A 94 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N ASP A 98 " --> pdb=" O MET A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 112 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 removed outlier: 3.937A pdb=" N ALA A 147 " --> pdb=" O CYS A 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 144 through 147' Processing helix chain 'A' and resid 151 through 162 removed outlier: 4.087A pdb=" N ASN A 162 " --> pdb=" O ARG A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 200 removed outlier: 4.402A pdb=" N LYS A 190 " --> pdb=" O ASN A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 211 removed outlier: 3.653A pdb=" N GLU A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU A 211 " --> pdb=" O SER A 207 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 206 through 211' Processing helix chain 'A' and resid 212 through 218 removed outlier: 4.036A pdb=" N TYR A 217 " --> pdb=" O ALA A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 258 Processing helix chain 'A' and resid 262 through 283 removed outlier: 3.732A 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: 3.738A pdb=" N ASN A 330 " --> pdb=" O ASN A 326 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 331 " --> pdb=" O VAL A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 362 Processing helix chain 'A' and resid 376 through 393 Processing helix chain 'A' and resid 395 through 400 removed outlier: 4.720A pdb=" N PHE A 400 " --> pdb=" O ASP A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 445 through 450 removed outlier: 3.994A pdb=" N GLU A 449 " --> pdb=" O THR A 445 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLU A 450 " --> pdb=" O SER A 446 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 445 through 450' Processing helix chain 'A' and resid 468 through 478 Processing helix chain 'A' and resid 494 through 516 Processing helix chain 'A' and resid 523 through 530 removed outlier: 3.965A pdb=" N PHE A 530 " --> pdb=" O ASP A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 564 removed outlier: 4.603A pdb=" N ILE A 554 " --> pdb=" O MET A 550 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N SER A 555 " --> pdb=" O SER A 551 " (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 90 removed outlier: 3.521A pdb=" N LEU A 115 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL A 67 " --> pdb=" O MET A 117 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ARG A 62 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU A 139 " --> pdb=" O ARG A 62 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N PHE A 64 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N PHE A 141 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N LEU A 66 " --> pdb=" O PHE A 141 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ARG A 170 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU A 139 " --> pdb=" O ARG A 170 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU A 172 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR A 27 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR A 175 " --> pdb=" O VAL A 29 " (cutoff:3.500A) removed outlier: 6.238A 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: 6.103A pdb=" N LYS A 222 " --> pdb=" O TYR A 486 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ILE A 488 " --> pdb=" O LYS A 222 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE A 224 " --> pdb=" O ILE A 488 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N VAL A 490 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL A 226 " --> pdb=" O VAL A 490 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N MET A 489 " --> pdb=" O ARG A 462 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE A 371 " --> pdb=" O VAL A 461 " (cutoff:3.500A) removed outlier: 6.155A 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 582 263 hydrogen bonds defined for protein. 768 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 65 hydrogen bonds 130 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 34 stacking parallelities Total time for adding SS restraints: 2.43 Time building geometry restraints manager: 2.12 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: 1884 1.34 - 1.46: 1216 1.46 - 1.57: 3397 1.57 - 1.69: 107 1.69 - 1.81: 36 Bond restraints: 6640 Sorted by residual: bond pdb=" CB LYS A 271 " pdb=" CG LYS A 271 " ideal model delta sigma weight residual 1.520 1.482 0.038 3.00e-02 1.11e+03 1.63e+00 bond pdb=" CG ARG A 274 " pdb=" CD ARG A 274 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.63e+00 bond pdb=" CA THR A 549 " pdb=" CB THR A 549 " ideal model delta sigma weight residual 1.532 1.550 -0.018 1.74e-02 3.30e+03 1.04e+00 bond pdb=" CB ASP A 544 " pdb=" CG ASP A 544 " ideal model delta sigma weight residual 1.516 1.541 -0.025 2.50e-02 1.60e+03 9.66e-01 bond pdb=" CG ARG A 559 " pdb=" CD ARG A 559 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.43e-01 ... (remaining 6635 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 9111 2.62 - 5.25: 75 5.25 - 7.87: 16 7.87 - 10.50: 3 10.50 - 13.12: 1 Bond angle restraints: 9206 Sorted by residual: angle pdb=" CA ARG A 274 " pdb=" CB ARG A 274 " pdb=" CG ARG A 274 " ideal model delta sigma weight residual 114.10 127.22 -13.12 2.00e+00 2.50e-01 4.30e+01 angle pdb=" N VAL A 448 " pdb=" CA VAL A 448 " pdb=" C VAL A 448 " ideal model delta sigma weight residual 113.22 108.43 4.79 1.23e+00 6.61e-01 1.52e+01 angle pdb=" C LEU A 273 " pdb=" N ARG A 274 " pdb=" CA ARG A 274 " ideal model delta sigma weight residual 121.14 114.60 6.54 1.75e+00 3.27e-01 1.40e+01 angle pdb=" N ARG A 274 " pdb=" CA ARG A 274 " pdb=" C ARG A 274 " ideal model delta sigma weight residual 112.89 108.81 4.08 1.24e+00 6.50e-01 1.08e+01 angle pdb=" C GLU A 211 " pdb=" N VAL A 212 " pdb=" CA VAL A 212 " ideal model delta sigma weight residual 121.97 127.75 -5.78 1.80e+00 3.09e-01 1.03e+01 ... (remaining 9201 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.65: 3584 18.65 - 37.30: 400 37.30 - 55.95: 115 55.95 - 74.60: 69 74.60 - 93.25: 8 Dihedral angle restraints: 4176 sinusoidal: 2261 harmonic: 1915 Sorted by residual: dihedral pdb=" O2A ADP A 702 " pdb=" O3A ADP A 702 " pdb=" PA ADP A 702 " pdb=" PB ADP A 702 " ideal model delta sinusoidal sigma weight residual -60.00 -153.25 93.25 1 2.00e+01 2.50e-03 2.54e+01 dihedral pdb=" CA GLU A 450 " pdb=" C GLU A 450 " pdb=" N GLY A 451 " pdb=" CA GLY A 451 " ideal model delta harmonic sigma weight residual 180.00 159.51 20.49 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA LYS A 416 " pdb=" C LYS A 416 " pdb=" N GLU A 417 " pdb=" CA GLU A 417 " ideal model delta harmonic sigma weight residual -180.00 -162.27 -17.73 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 4173 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 756 0.030 - 0.059: 216 0.059 - 0.089: 59 0.089 - 0.118: 37 0.118 - 0.148: 10 Chirality restraints: 1078 Sorted by residual: chirality pdb=" CA ILE A 371 " pdb=" N ILE A 371 " pdb=" C ILE A 371 " pdb=" CB ILE A 371 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.44e-01 chirality pdb=" CG LEU A 317 " pdb=" CB LEU A 317 " pdb=" CD1 LEU A 317 " pdb=" CD2 LEU A 317 " both_signs ideal model delta sigma weight residual False -2.59 -2.73 0.14 2.00e-01 2.50e+01 5.07e-01 chirality pdb=" CB VAL A 67 " pdb=" CA VAL A 67 " pdb=" CG1 VAL A 67 " pdb=" CG2 VAL A 67 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.35e-01 ... (remaining 1075 not shown) Planarity restraints: 984 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 321 " 0.022 2.00e-02 2.50e+03 2.21e-02 8.51e+00 pdb=" CG PHE A 321 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 PHE A 321 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE A 321 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE A 321 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 321 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 321 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 454 " -0.030 5.00e-02 4.00e+02 4.61e-02 3.40e+00 pdb=" N PRO A 455 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 455 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 455 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 151 " 0.029 5.00e-02 4.00e+02 4.35e-02 3.02e+00 pdb=" N PRO A 152 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 152 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 152 " 0.024 5.00e-02 4.00e+02 ... (remaining 981 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 76 2.64 - 3.21: 5990 3.21 - 3.77: 11020 3.77 - 4.34: 13842 4.34 - 4.90: 20341 Nonbonded interactions: 51269 Sorted by model distance: nonbonded pdb=" NH1 ARG A 274 " pdb=" OD1 ASP A 275 " model vdw 2.077 3.120 nonbonded pdb=" O GLU A 211 " pdb=" N ALA A 213 " model vdw 2.174 3.120 nonbonded pdb=" O ILE A 254 " pdb=" OG SER A 258 " model vdw 2.257 3.040 nonbonded pdb=" OH TYR A 91 " pdb=" OE1 GLU A 108 " model vdw 2.270 3.040 nonbonded pdb=" O GLU A 322 " pdb=" ND2 ASN A 326 " model vdw 2.299 3.120 ... (remaining 51264 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: 2.270 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.650 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 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 : 0.002 0.038 6640 Z= 0.114 Angle : 0.634 13.122 9206 Z= 0.313 Chirality : 0.036 0.148 1078 Planarity : 0.004 0.056 984 Dihedral : 18.267 93.248 2924 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.26 % Favored : 96.59 % Rotamer: Outliers : 1.33 % Allowed : 23.33 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.33), residues: 645 helix: 2.06 (0.28), residues: 307 sheet: 1.12 (0.56), residues: 86 loop : -0.37 (0.40), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 105 HIS 0.006 0.001 HIS A 83 PHE 0.051 0.002 PHE A 321 TYR 0.008 0.001 TYR A 538 ARG 0.023 0.001 ARG A 274 Details of bonding type rmsd hydrogen bonds : bond 0.15121 ( 328) hydrogen bonds : angle 5.58456 ( 898) covalent geometry : bond 0.00230 ( 6640) covalent geometry : angle 0.63413 ( 9206) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 MET cc_start: 0.5398 (ttm) cc_final: 0.5150 (ttm) REVERT: A 513 LEU cc_start: 0.8887 (tp) cc_final: 0.8566 (pp) outliers start: 8 outliers final: 6 residues processed: 60 average time/residue: 0.1695 time to fit residues: 14.2924 Evaluate side-chains 59 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 PHE Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 378 TYR Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 594 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 57 optimal weight: 6.9990 chunk 51 optimal weight: 9.9990 chunk 28 optimal weight: 0.8980 chunk 17 optimal weight: 0.0870 chunk 34 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 HIS A 474 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.144108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.096134 restraints weight = 28043.211| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 6.47 r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6640 Z= 0.112 Angle : 0.588 10.904 9206 Z= 0.285 Chirality : 0.036 0.144 1078 Planarity : 0.004 0.047 984 Dihedral : 15.886 91.305 1533 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.79 % Favored : 97.05 % Rotamer: Outliers : 2.67 % Allowed : 19.17 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.33), residues: 645 helix: 2.31 (0.28), residues: 316 sheet: 1.04 (0.52), residues: 91 loop : -0.59 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 286 HIS 0.008 0.001 HIS A 83 PHE 0.013 0.001 PHE A 530 TYR 0.008 0.001 TYR A 538 ARG 0.007 0.001 ARG A 559 Details of bonding type rmsd hydrogen bonds : bond 0.03708 ( 328) hydrogen bonds : angle 4.08380 ( 898) covalent geometry : bond 0.00226 ( 6640) covalent geometry : angle 0.58821 ( 9206) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 320 ILE cc_start: 0.9060 (mm) cc_final: 0.8850 (mm) outliers start: 16 outliers final: 8 residues processed: 69 average time/residue: 0.2121 time to fit residues: 19.8764 Evaluate side-chains 61 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 378 TYR Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 594 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 21 optimal weight: 6.9990 chunk 35 optimal weight: 0.0170 chunk 14 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 16 optimal weight: 0.0980 chunk 58 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 HIS A 245 ASN A 587 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.144682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.098225 restraints weight = 28413.703| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 6.23 r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6640 Z= 0.095 Angle : 0.564 11.320 9206 Z= 0.268 Chirality : 0.035 0.143 1078 Planarity : 0.004 0.046 984 Dihedral : 15.789 88.614 1530 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.95 % Favored : 96.90 % Rotamer: Outliers : 2.33 % Allowed : 20.67 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.33), residues: 645 helix: 2.31 (0.28), residues: 316 sheet: 1.23 (0.54), residues: 83 loop : -0.49 (0.39), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 286 HIS 0.003 0.001 HIS A 83 PHE 0.011 0.001 PHE A 530 TYR 0.007 0.001 TYR A 538 ARG 0.003 0.000 ARG A 547 Details of bonding type rmsd hydrogen bonds : bond 0.03285 ( 328) hydrogen bonds : angle 3.84264 ( 898) covalent geometry : bond 0.00194 ( 6640) covalent geometry : angle 0.56415 ( 9206) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.7493 (tpp) cc_final: 0.7285 (tpp) REVERT: A 320 ILE cc_start: 0.9038 (mm) cc_final: 0.8798 (mm) outliers start: 14 outliers final: 7 residues processed: 68 average time/residue: 0.1803 time to fit residues: 16.5271 Evaluate side-chains 60 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 594 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 44 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 29 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 14 optimal weight: 0.2980 chunk 41 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 chunk 25 optimal weight: 0.0010 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.144451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.097527 restraints weight = 28468.282| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 6.26 r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6640 Z= 0.096 Angle : 0.551 11.401 9206 Z= 0.261 Chirality : 0.036 0.207 1078 Planarity : 0.004 0.046 984 Dihedral : 15.661 82.456 1528 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.10 % Favored : 96.74 % Rotamer: Outliers : 2.17 % Allowed : 21.33 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.33), residues: 645 helix: 2.33 (0.28), residues: 316 sheet: 1.24 (0.55), residues: 81 loop : -0.52 (0.39), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 286 HIS 0.003 0.001 HIS A 83 PHE 0.010 0.001 PHE A 342 TYR 0.007 0.001 TYR A 538 ARG 0.006 0.000 ARG A 559 Details of bonding type rmsd hydrogen bonds : bond 0.03203 ( 328) hydrogen bonds : angle 3.68199 ( 898) covalent geometry : bond 0.00198 ( 6640) covalent geometry : angle 0.55144 ( 9206) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 320 ILE cc_start: 0.9084 (mm) cc_final: 0.8846 (mm) REVERT: A 513 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8368 (tp) outliers start: 13 outliers final: 9 residues processed: 67 average time/residue: 0.1842 time to fit residues: 16.7696 Evaluate side-chains 62 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 378 TYR Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 517 HIS Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 602 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 55 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 53 optimal weight: 0.3980 chunk 57 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.143986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.096348 restraints weight = 28026.148| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 6.33 r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6640 Z= 0.097 Angle : 0.552 11.578 9206 Z= 0.261 Chirality : 0.036 0.187 1078 Planarity : 0.004 0.048 984 Dihedral : 15.597 73.597 1528 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.95 % Favored : 96.90 % Rotamer: Outliers : 2.67 % Allowed : 21.83 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.33), residues: 645 helix: 2.34 (0.28), residues: 316 sheet: 1.27 (0.56), residues: 81 loop : -0.52 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 286 HIS 0.003 0.001 HIS A 83 PHE 0.010 0.001 PHE A 321 TYR 0.008 0.001 TYR A 538 ARG 0.006 0.000 ARG A 559 Details of bonding type rmsd hydrogen bonds : bond 0.03144 ( 328) hydrogen bonds : angle 3.58316 ( 898) covalent geometry : bond 0.00206 ( 6640) covalent geometry : angle 0.55247 ( 9206) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.7579 (tpp) cc_final: 0.7357 (tpp) REVERT: A 320 ILE cc_start: 0.9075 (mm) cc_final: 0.8822 (mm) REVERT: A 513 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8528 (tp) outliers start: 16 outliers final: 10 residues processed: 69 average time/residue: 0.1827 time to fit residues: 17.0600 Evaluate side-chains 63 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 594 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 55 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 52 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.143407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.097099 restraints weight = 27889.989| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 6.07 r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 6640 Z= 0.105 Angle : 0.587 11.323 9206 Z= 0.276 Chirality : 0.036 0.162 1078 Planarity : 0.004 0.048 984 Dihedral : 15.549 73.608 1528 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.10 % Favored : 96.74 % Rotamer: Outliers : 2.83 % Allowed : 22.50 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.33), residues: 645 helix: 2.34 (0.28), residues: 316 sheet: 1.22 (0.56), residues: 81 loop : -0.54 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 286 HIS 0.008 0.001 HIS A 159 PHE 0.010 0.001 PHE A 342 TYR 0.008 0.001 TYR A 538 ARG 0.004 0.000 ARG A 559 Details of bonding type rmsd hydrogen bonds : bond 0.03150 ( 328) hydrogen bonds : angle 3.61144 ( 898) covalent geometry : bond 0.00229 ( 6640) covalent geometry : angle 0.58666 ( 9206) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 51 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 11 residues processed: 65 average time/residue: 0.1740 time to fit residues: 15.5194 Evaluate side-chains 61 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 378 TYR Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 594 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 67 optimal weight: 10.0000 chunk 63 optimal weight: 0.0020 chunk 38 optimal weight: 0.9980 chunk 66 optimal weight: 7.9990 chunk 48 optimal weight: 0.7980 chunk 30 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 8 optimal weight: 0.6980 overall best weight: 0.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 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 = 0.4541 r_free = 0.4541 target = 0.142801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.095228 restraints weight = 27866.887| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 5.99 r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6640 Z= 0.110 Angle : 0.592 12.620 9206 Z= 0.279 Chirality : 0.036 0.162 1078 Planarity : 0.004 0.048 984 Dihedral : 15.540 73.637 1528 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.10 % Favored : 96.74 % Rotamer: Outliers : 2.33 % Allowed : 23.67 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.33), residues: 645 helix: 2.36 (0.28), residues: 316 sheet: 1.04 (0.56), residues: 83 loop : -0.54 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 286 HIS 0.005 0.001 HIS A 159 PHE 0.010 0.001 PHE A 342 TYR 0.009 0.001 TYR A 538 ARG 0.008 0.000 ARG A 559 Details of bonding type rmsd hydrogen bonds : bond 0.03222 ( 328) hydrogen bonds : angle 3.59481 ( 898) covalent geometry : bond 0.00237 ( 6640) covalent geometry : angle 0.59195 ( 9206) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 11 residues processed: 64 average time/residue: 0.1771 time to fit residues: 15.6508 Evaluate side-chains 63 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 378 TYR Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 594 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 40 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 63 optimal weight: 0.0770 chunk 66 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 47 optimal weight: 7.9990 overall best weight: 1.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 159 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.141261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.093160 restraints weight = 27950.878| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 6.19 r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 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 : 0.003 0.029 6640 Z= 0.129 Angle : 0.613 11.876 9206 Z= 0.291 Chirality : 0.037 0.158 1078 Planarity : 0.004 0.048 984 Dihedral : 15.552 73.706 1528 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.31 % Allowed : 2.79 % Favored : 96.90 % Rotamer: Outliers : 2.83 % Allowed : 23.50 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.33), residues: 645 helix: 2.17 (0.28), residues: 316 sheet: 0.84 (0.55), residues: 85 loop : -0.54 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 286 HIS 0.008 0.001 HIS A 159 PHE 0.050 0.002 PHE A 321 TYR 0.011 0.001 TYR A 538 ARG 0.006 0.000 ARG A 559 Details of bonding type rmsd hydrogen bonds : bond 0.03538 ( 328) hydrogen bonds : angle 3.68476 ( 898) covalent geometry : bond 0.00282 ( 6640) covalent geometry : angle 0.61320 ( 9206) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 56 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 GLU cc_start: 0.6618 (OUTLIER) cc_final: 0.6029 (tm-30) outliers start: 17 outliers final: 12 residues processed: 68 average time/residue: 0.1728 time to fit residues: 16.2078 Evaluate side-chains 68 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 PHE Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 378 TYR Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 594 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 45 optimal weight: 0.1980 chunk 52 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 53 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 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 = 0.4535 r_free = 0.4535 target = 0.142417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.094449 restraints weight = 28318.300| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 6.39 r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6640 Z= 0.106 Angle : 0.603 13.138 9206 Z= 0.283 Chirality : 0.036 0.172 1078 Planarity : 0.004 0.048 984 Dihedral : 15.519 73.718 1528 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.31 % Allowed : 2.79 % Favored : 96.90 % Rotamer: Outliers : 1.83 % Allowed : 25.00 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.33), residues: 645 helix: 2.16 (0.28), residues: 316 sheet: 1.01 (0.57), residues: 83 loop : -0.51 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 286 HIS 0.005 0.001 HIS A 159 PHE 0.053 0.002 PHE A 321 TYR 0.008 0.001 TYR A 538 ARG 0.006 0.000 ARG A 559 Details of bonding type rmsd hydrogen bonds : bond 0.03349 ( 328) hydrogen bonds : angle 3.57010 ( 898) covalent geometry : bond 0.00227 ( 6640) covalent geometry : angle 0.60279 ( 9206) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 MET cc_start: 0.5284 (ttm) cc_final: 0.5078 (ttm) outliers start: 11 outliers final: 9 residues processed: 62 average time/residue: 0.1739 time to fit residues: 14.9054 Evaluate side-chains 61 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 594 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 29 optimal weight: 0.3980 chunk 60 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 50 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 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 = 0.4531 r_free = 0.4531 target = 0.142126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.094630 restraints weight = 28276.683| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 6.20 r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6640 Z= 0.107 Angle : 0.622 12.963 9206 Z= 0.288 Chirality : 0.036 0.148 1078 Planarity : 0.004 0.048 984 Dihedral : 15.507 73.712 1528 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.31 % Allowed : 2.95 % Favored : 96.74 % Rotamer: Outliers : 1.50 % Allowed : 25.50 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.33), residues: 645 helix: 2.25 (0.28), residues: 310 sheet: 0.88 (0.56), residues: 85 loop : -0.32 (0.40), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 286 HIS 0.003 0.001 HIS A 83 PHE 0.056 0.002 PHE A 321 TYR 0.009 0.001 TYR A 538 ARG 0.005 0.000 ARG A 559 Details of bonding type rmsd hydrogen bonds : bond 0.03381 ( 328) hydrogen bonds : angle 3.58649 ( 898) covalent geometry : bond 0.00232 ( 6640) covalent geometry : angle 0.62150 ( 9206) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 MET cc_start: 0.5285 (ttm) cc_final: 0.5077 (ttm) outliers start: 9 outliers final: 9 residues processed: 62 average time/residue: 0.2039 time to fit residues: 16.8752 Evaluate side-chains 63 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 594 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 59 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 2 optimal weight: 0.0370 chunk 38 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 64 optimal weight: 50.0000 chunk 0 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.139070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.091000 restraints weight = 29058.267| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 6.37 r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6640 Z= 0.155 Angle : 0.668 13.020 9206 Z= 0.319 Chirality : 0.038 0.179 1078 Planarity : 0.004 0.047 984 Dihedral : 15.588 73.812 1528 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.31 % Allowed : 3.41 % Favored : 96.28 % Rotamer: Outliers : 1.83 % Allowed : 24.83 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.33), residues: 645 helix: 2.20 (0.28), residues: 310 sheet: 0.67 (0.56), residues: 85 loop : -0.47 (0.40), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 286 HIS 0.004 0.001 HIS A 83 PHE 0.037 0.002 PHE A 321 TYR 0.013 0.001 TYR A 538 ARG 0.004 0.000 ARG A 559 Details of bonding type rmsd hydrogen bonds : bond 0.04297 ( 328) hydrogen bonds : angle 3.81777 ( 898) covalent geometry : bond 0.00338 ( 6640) covalent geometry : angle 0.66843 ( 9206) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4543.70 seconds wall clock time: 79 minutes 6.20 seconds (4746.20 seconds total)