Starting phenix.real_space_refine on Thu Jun 5 15:27:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mw8_48697/06_2025/9mw8_48697.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mw8_48697/06_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_48697/06_2025/9mw8_48697.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mw8_48697/06_2025/9mw8_48697.map" model { file = "/net/cci-nas-00/data/ceres_data/9mw8_48697/06_2025/9mw8_48697.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mw8_48697/06_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-5710/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: 4.47, per 1000 atoms: 0.70 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: 1.58 Conformation dependent library (CDL) restraints added in 747.5 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: 2.13 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: 2.39 Time building geometry restraints manager: 1.88 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: 1.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.390 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.560 ------------------------------------------------------------------------------- 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 : 0.703 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: 0.1750 time to fit residues: 14.6586 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 : 0.693 ------------------------------------------------------------------------------- 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 = 54)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.095953 restraints weight = 28043.228| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 6.14 r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 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 0.58822 ( 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 : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 320 ILE cc_start: 0.9051 (mm) cc_final: 0.8834 (mm) outliers start: 16 outliers final: 8 residues processed: 69 average time/residue: 0.2166 time to fit residues: 20.4327 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 : 1.128 ------------------------------------------------------------------------------- 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: 5.9990 chunk 35 optimal weight: 0.0040 chunk 14 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.4555 r_free = 0.4555 target = 0.143941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.095733 restraints weight = 28131.393| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 6.30 r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6640 Z= 0.102 Angle : 0.568 11.454 9206 Z= 0.271 Chirality : 0.036 0.141 1078 Planarity : 0.004 0.047 984 Dihedral : 15.801 88.466 1530 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.26 % Favored : 96.59 % Rotamer: Outliers : 2.50 % Allowed : 20.67 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.33), residues: 645 helix: 2.30 (0.28), residues: 316 sheet: 0.99 (0.54), residues: 85 loop : -0.48 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 286 HIS 0.005 0.001 HIS A 159 PHE 0.012 0.001 PHE A 530 TYR 0.008 0.001 TYR A 538 ARG 0.005 0.000 ARG A 559 Details of bonding type rmsd hydrogen bonds : bond 0.03418 ( 328) hydrogen bonds : angle 3.87994 ( 898) covalent geometry : bond 0.00211 ( 6640) covalent geometry : angle 0.56847 ( 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 70 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.7508 (tpp) cc_final: 0.7304 (tpp) REVERT: A 320 ILE cc_start: 0.9056 (mm) cc_final: 0.8810 (mm) outliers start: 15 outliers final: 9 residues processed: 68 average time/residue: 0.2194 time to fit residues: 20.1459 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 : 0.678 ------------------------------------------------------------------------------- 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 44 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 29 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 30 optimal weight: 8.9990 chunk 25 optimal weight: 0.0980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4552 r_free = 0.4552 target = 0.143499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.095897 restraints weight = 28480.994| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 6.59 r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6640 Z= 0.101 Angle : 0.553 11.475 9206 Z= 0.264 Chirality : 0.036 0.248 1078 Planarity : 0.004 0.047 984 Dihedral : 15.727 82.107 1530 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.10 % Favored : 96.74 % Rotamer: Outliers : 2.67 % Allowed : 21.67 % Favored : 75.67 % 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: 1.64 (0.33), residues: 645 helix: 2.31 (0.28), residues: 316 sheet: 0.92 (0.54), residues: 85 loop : -0.49 (0.40), residues: 244 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 0.025 0.001 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 0.03293 ( 328) hydrogen bonds : angle 3.72595 ( 898) covalent geometry : bond 0.00213 ( 6640) covalent geometry : angle 0.55314 ( 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 67 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.969 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: 0.8808 (mm) REVERT: A 513 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8445 (tp) outliers start: 16 outliers final: 11 residues processed: 66 average time/residue: 0.3347 time to fit residues: 33.2770 Evaluate side-chains 63 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.757 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 26 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 52 optimal weight: 7.9990 chunk 53 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4551 r_free = 0.4551 target = 0.143315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.095844 restraints weight = 28178.236| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 6.12 r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.1744 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= 0.101 Angle : 0.560 12.580 9206 Z= 0.266 Chirality : 0.036 0.217 1078 Planarity : 0.004 0.049 984 Dihedral : 15.685 74.081 1530 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.10 % Favored : 96.74 % 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: 1.59 (0.33), residues: 645 helix: 2.30 (0.28), residues: 316 sheet: 0.94 (0.54), residues: 83 loop : -0.56 (0.40), residues: 246 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 0.008 0.001 TYR A 538 ARG 0.006 0.000 ARG A 559 Details of bonding type rmsd hydrogen bonds : bond 0.03230 ( 328) hydrogen bonds : angle 3.67390 ( 898) covalent geometry : bond 0.00213 ( 6640) covalent geometry : angle 0.56044 ( 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 73 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 2.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.7976 (mtm) cc_final: 0.7747 (mtp) REVERT: A 320 ILE cc_start: 0.9073 (mm) cc_final: 0.8819 (mm) outliers start: 16 outliers final: 9 residues processed: 71 average time/residue: 0.2465 time to fit residues: 23.9631 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 : 1.562 ------------------------------------------------------------------------------- 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 292 ILE Chi-restraints excluded: chain A residue 374 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 55 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 14 optimal weight: 0.2980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4546 r_free = 0.4546 target = 0.142983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.095222 restraints weight = 27799.622| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 6.17 r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6640 Z= 0.104 Angle : 0.577 11.966 9206 Z= 0.273 Chirality : 0.036 0.187 1078 Planarity : 0.004 0.049 984 Dihedral : 15.611 73.613 1528 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.10 % Favored : 96.74 % Rotamer: Outliers : 2.67 % Allowed : 22.83 % Favored : 74.50 % 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: 1.61 (0.33), residues: 645 helix: 2.29 (0.28), residues: 316 sheet: 1.15 (0.55), residues: 81 loop : -0.61 (0.39), 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 0.007 0.000 ARG A 559 Details of bonding type rmsd hydrogen bonds : bond 0.03262 ( 328) hydrogen bonds : angle 3.63664 ( 898) covalent geometry : bond 0.00224 ( 6640) covalent geometry : angle 0.57686 ( 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: 16 poor density : 52 time to evaluate : 1.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.7974 (mtm) cc_final: 0.7752 (mtp) REVERT: A 320 ILE cc_start: 0.9084 (mm) cc_final: 0.8829 (mm) outliers start: 16 outliers final: 12 residues processed: 65 average time/residue: 0.2681 time to fit residues: 24.4159 Evaluate side-chains 63 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 1.711 ------------------------------------------------------------------------------- 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 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 512 LEU 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: 5.9990 chunk 38 optimal weight: 0.8980 chunk 66 optimal weight: 8.9990 chunk 48 optimal weight: 0.9990 chunk 30 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 8 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.4521 r_free = 0.4521 target = 0.141107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.093467 restraints weight = 27941.988| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 6.02 r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6640 Z= 0.123 Angle : 0.593 13.006 9206 Z= 0.284 Chirality : 0.036 0.193 1078 Planarity : 0.004 0.048 984 Dihedral : 15.590 73.682 1528 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.95 % Favored : 96.90 % Rotamer: Outliers : 2.83 % Allowed : 23.00 % Favored : 74.17 % 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: 2.26 (0.28), residues: 316 sheet: 0.92 (0.55), residues: 83 loop : -0.63 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 286 HIS 0.004 0.001 HIS A 159 PHE 0.012 0.001 PHE A 342 TYR 0.011 0.001 TYR A 538 ARG 0.009 0.000 ARG A 559 Details of bonding type rmsd hydrogen bonds : bond 0.03621 ( 328) hydrogen bonds : angle 3.68260 ( 898) covalent geometry : bond 0.00265 ( 6640) covalent geometry : angle 0.59347 ( 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 67 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 50 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 320 ILE cc_start: 0.9119 (mm) cc_final: 0.8864 (mm) REVERT: A 375 GLU cc_start: 0.6590 (OUTLIER) cc_final: 0.6014 (tm-30) outliers start: 17 outliers final: 13 residues processed: 64 average time/residue: 0.1566 time to fit residues: 13.9422 Evaluate side-chains 64 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 50 time to evaluate : 0.646 ------------------------------------------------------------------------------- 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 97 VAL 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 40 optimal weight: 1.9990 chunk 33 optimal weight: 8.9990 chunk 22 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 52 optimal weight: 0.2980 chunk 63 optimal weight: 0.0270 chunk 66 optimal weight: 7.9990 chunk 54 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.8240 ------------------------------------------------------------------------------- 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 = 0.4530 r_free = 0.4530 target = 0.141982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.094034 restraints weight = 27815.374| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 6.15 r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6640 Z= 0.107 Angle : 0.604 12.560 9206 Z= 0.281 Chirality : 0.037 0.201 1078 Planarity : 0.004 0.049 984 Dihedral : 15.560 73.722 1528 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.10 % Favored : 96.74 % Rotamer: Outliers : 2.50 % Allowed : 23.67 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.33), residues: 645 helix: 2.23 (0.28), residues: 316 sheet: 0.86 (0.56), residues: 85 loop : -0.46 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 286 HIS 0.003 0.001 HIS A 83 PHE 0.042 0.002 PHE A 321 TYR 0.009 0.001 TYR A 538 ARG 0.007 0.000 ARG A 559 Details of bonding type rmsd hydrogen bonds : bond 0.03314 ( 328) hydrogen bonds : angle 3.61848 ( 898) covalent geometry : bond 0.00228 ( 6640) covalent geometry : angle 0.60446 ( 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 72 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 320 ILE cc_start: 0.9025 (mm) cc_final: 0.8808 (mm) REVERT: A 375 GLU cc_start: 0.6459 (OUTLIER) cc_final: 0.5850 (tm-30) outliers start: 15 outliers final: 12 residues processed: 69 average time/residue: 0.1702 time to fit residues: 16.4501 Evaluate side-chains 67 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.733 ------------------------------------------------------------------------------- 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 97 VAL 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 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: 0.0970 chunk 52 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 38 optimal weight: 0.4980 chunk 41 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 29 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4538 r_free = 0.4538 target = 0.142502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.095474 restraints weight = 28466.587| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 6.54 r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6640 Z= 0.102 Angle : 0.589 13.418 9206 Z= 0.278 Chirality : 0.037 0.166 1078 Planarity : 0.004 0.049 984 Dihedral : 15.522 73.705 1528 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.10 % Favored : 96.74 % Rotamer: Outliers : 2.50 % Allowed : 24.17 % 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: 1.74 (0.33), residues: 645 helix: 2.38 (0.28), residues: 310 sheet: 0.93 (0.56), residues: 83 loop : -0.32 (0.41), residues: 252 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 0.026 0.001 PHE A 321 TYR 0.008 0.001 TYR A 538 ARG 0.011 0.000 ARG A 559 Details of bonding type rmsd hydrogen bonds : bond 0.03269 ( 328) hydrogen bonds : angle 3.56509 ( 898) covalent geometry : bond 0.00215 ( 6640) covalent geometry : angle 0.58909 ( 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 71 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 GLU cc_start: 0.6501 (OUTLIER) cc_final: 0.5886 (tm-30) outliers start: 15 outliers final: 12 residues processed: 67 average time/residue: 0.1999 time to fit residues: 18.0901 Evaluate side-chains 63 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 97 VAL 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 365 SER Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 375 GLU 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: 0.0470 chunk 60 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 45 optimal weight: 0.0070 chunk 6 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 overall best weight: 0.5296 ------------------------------------------------------------------------------- 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 = 0.4539 r_free = 0.4539 target = 0.142824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.094980 restraints weight = 28177.371| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 6.32 r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 6640 Z= 0.104 Angle : 0.633 12.917 9206 Z= 0.299 Chirality : 0.036 0.151 1078 Planarity : 0.004 0.049 984 Dihedral : 15.509 73.720 1528 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.26 % Favored : 96.59 % 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: 1.74 (0.33), residues: 645 helix: 2.38 (0.28), residues: 310 sheet: 0.85 (0.56), residues: 85 loop : -0.30 (0.40), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 286 HIS 0.002 0.001 HIS A 83 PHE 0.015 0.001 PHE A 321 TYR 0.007 0.001 TYR A 538 ARG 0.011 0.000 ARG A 559 Details of bonding type rmsd hydrogen bonds : bond 0.03177 ( 328) hydrogen bonds : angle 3.50597 ( 898) covalent geometry : bond 0.00224 ( 6640) covalent geometry : angle 0.63342 ( 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 65 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 GLU cc_start: 0.6407 (OUTLIER) cc_final: 0.5798 (tm-30) outliers start: 11 outliers final: 10 residues processed: 62 average time/residue: 0.1993 time to fit residues: 16.5812 Evaluate side-chains 62 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 97 VAL 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 374 VAL Chi-restraints excluded: chain A residue 375 GLU 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 594 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 59 optimal weight: 0.5980 chunk 18 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 64 optimal weight: 50.0000 chunk 0 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 29 optimal weight: 0.0980 chunk 36 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.142239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.094543 restraints weight = 28819.804| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 6.21 r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 6640 Z= 0.106 Angle : 0.619 13.112 9206 Z= 0.292 Chirality : 0.036 0.151 1078 Planarity : 0.004 0.049 984 Dihedral : 15.444 73.733 1528 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.78 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: 1.69 (0.33), residues: 645 helix: 2.40 (0.28), residues: 311 sheet: 0.55 (0.64), residues: 67 loop : -0.25 (0.39), residues: 267 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 0.010 0.000 ARG A 559 Details of bonding type rmsd hydrogen bonds : bond 0.03257 ( 328) hydrogen bonds : angle 3.49248 ( 898) covalent geometry : bond 0.00230 ( 6640) covalent geometry : angle 0.61942 ( 9206) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5212.13 seconds wall clock time: 94 minutes 53.81 seconds (5693.81 seconds total)