Starting phenix.real_space_refine on Thu Jul 2 03:46:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mw8_48697/07_2026/9mw8_48697.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mw8_48697/07_2026/9mw8_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_48697/07_2026/9mw8_48697.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mw8_48697/07_2026/9mw8_48697.map" model { file = "/net/cci-nas-00/data/ceres_data/9mw8_48697/07_2026/9mw8_48697.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mw8_48697/07_2026/9mw8_48697.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 1.69, per 1000 atoms: 0.26 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: 0.47 Conformation dependent library (CDL) restraints added in 392.9 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: 0.71 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: 1.23 Time building geometry restraints manager: 0.65 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: 3.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.280 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 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= 0.128 Angle : 0.634 13.122 9206 Z= 0.355 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (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 ARG 0.023 0.001 ARG A 274 TYR 0.008 0.001 TYR A 538 PHE 0.051 0.002 PHE A 321 TRP 0.008 0.002 TRP A 105 HIS 0.006 0.001 HIS A 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.13 ( 6640) covalent geometry : angle 0.63416 / 0.35 ( 9206) hydrogen bonds : bond 0.15121 / 9.14 ( 328) hydrogen bonds : angle 5.58456 / 3.94 ( 898) *********************** 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 : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 MET cc_start: 0.5397 (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: 0.0579 time to fit residues: 4.9445 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 : 0.248 ------------------------------------------------------------------------------- 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 49 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.4980 chunk 65 optimal weight: 30.0000 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 9.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4558 r_free = 0.4558 target = 0.144126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.096708 restraints weight = 28264.726| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 6.49 r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.0700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6640 Z= 0.120 Angle : 0.599 9.732 9206 Z= 0.298 Chirality : 0.036 0.153 1078 Planarity : 0.004 0.047 984 Dihedral : 15.978 93.931 1533 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.79 % Favored : 97.05 % Rotamer: Outliers : 2.33 % Allowed : 20.17 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.32), residues: 645 helix: 2.22 (0.28), residues: 316 sheet: 1.15 (0.52), residues: 91 loop : -0.68 (0.39), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 559 TYR 0.008 0.001 TYR A 160 PHE 0.012 0.001 PHE A 530 TRP 0.009 0.002 TRP A 105 HIS 0.006 0.001 HIS A 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.12 ( 6640) covalent geometry : angle 0.59909 / 0.30 ( 9206) hydrogen bonds : bond 0.04471 / 2.89 ( 328) hydrogen bonds : angle 4.32849 / 3.00 ( 898) *********************** 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 68 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 66 average time/residue: 0.0678 time to fit residues: 6.2239 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 : 0.185 ------------------------------------------------------------------------------- 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 452 ILE 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 34 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 25 optimal weight: 0.0270 chunk 3 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 overall best weight: 0.9240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4552 r_free = 0.4552 target = 0.143822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.096091 restraints weight = 27903.771| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 6.57 r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.0981 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= 0.115 Angle : 0.562 7.656 9206 Z= 0.279 Chirality : 0.036 0.146 1078 Planarity : 0.004 0.047 984 Dihedral : 15.852 91.333 1528 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.26 % Favored : 96.59 % Rotamer: Outliers : 2.50 % Allowed : 20.50 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.33), residues: 645 helix: 2.21 (0.28), residues: 316 sheet: 1.25 (0.56), residues: 83 loop : -0.58 (0.39), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 158 TYR 0.010 0.001 TYR A 357 PHE 0.012 0.001 PHE A 530 TRP 0.008 0.002 TRP A 286 HIS 0.017 0.002 HIS A 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.12 ( 6640) covalent geometry : angle 0.56196 / 0.28 ( 9206) hydrogen bonds : bond 0.04083 / 2.64 ( 328) hydrogen bonds : angle 4.10303 / 2.83 ( 898) *********************** 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 67 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 52 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 65 average time/residue: 0.0766 time to fit residues: 6.7496 Evaluate side-chains 59 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.216 ------------------------------------------------------------------------------- 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 594 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 16 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 33 optimal weight: 0.0370 chunk 67 optimal weight: 20.0000 chunk 60 optimal weight: 0.0870 chunk 24 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.5236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 159 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.144493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.096446 restraints weight = 28434.797| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 6.36 r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.1158 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= 0.098 Angle : 0.540 8.193 9206 Z= 0.266 Chirality : 0.036 0.193 1078 Planarity : 0.004 0.046 984 Dihedral : 15.812 90.192 1528 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.26 % Favored : 96.59 % Rotamer: Outliers : 1.83 % Allowed : 21.67 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.33), residues: 645 helix: 2.30 (0.28), residues: 316 sheet: 1.32 (0.56), residues: 81 loop : -0.62 (0.39), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 158 TYR 0.007 0.001 TYR A 538 PHE 0.010 0.001 PHE A 530 TRP 0.007 0.001 TRP A 286 HIS 0.006 0.001 HIS A 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00196 / 0.10 ( 6640) covalent geometry : angle 0.54029 / 0.27 ( 9206) hydrogen bonds : bond 0.03712 / 2.42 ( 328) hydrogen bonds : angle 3.93904 / 2.73 ( 898) *********************** 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 64 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 63 average time/residue: 0.0665 time to fit residues: 5.8260 Evaluate side-chains 58 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 66 LEU 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 378 TYR Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 594 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 23 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 11 optimal weight: 0.2980 chunk 7 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.144038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.096227 restraints weight = 28416.380| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 5.99 r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.1275 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= 0.103 Angle : 0.542 8.433 9206 Z= 0.267 Chirality : 0.036 0.175 1078 Planarity : 0.004 0.046 984 Dihedral : 15.773 87.947 1528 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.10 % Favored : 96.74 % Rotamer: Outliers : 2.17 % Allowed : 22.33 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.33), residues: 645 helix: 2.30 (0.28), residues: 316 sheet: 1.28 (0.57), residues: 81 loop : -0.64 (0.39), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 559 TYR 0.008 0.001 TYR A 538 PHE 0.012 0.001 PHE A 321 TRP 0.008 0.001 TRP A 286 HIS 0.005 0.001 HIS A 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 ( 6640) covalent geometry : angle 0.54151 / 0.27 ( 9206) hydrogen bonds : bond 0.03678 / 2.37 ( 328) hydrogen bonds : angle 3.88476 / 2.67 ( 898) *********************** 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 64 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 62 average time/residue: 0.0818 time to fit residues: 6.8166 Evaluate side-chains 57 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 292 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 17 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 64 optimal weight: 70.0000 chunk 48 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 159 HIS A 278 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.142508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.094037 restraints weight = 28466.754| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 6.79 r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6640 Z= 0.137 Angle : 0.578 8.379 9206 Z= 0.284 Chirality : 0.039 0.394 1078 Planarity : 0.004 0.047 984 Dihedral : 15.760 85.135 1528 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.10 % Favored : 96.74 % Rotamer: Outliers : 3.50 % Allowed : 21.50 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.33), residues: 645 helix: 2.21 (0.28), residues: 316 sheet: 0.82 (0.56), residues: 83 loop : -0.64 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 559 TYR 0.011 0.001 TYR A 538 PHE 0.013 0.002 PHE A 321 TRP 0.010 0.002 TRP A 286 HIS 0.007 0.001 HIS A 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 ( 6640) covalent geometry : angle 0.57804 / 0.28 ( 9206) hydrogen bonds : bond 0.03883 / 2.52 ( 328) hydrogen bonds : angle 3.96803 / 2.73 ( 898) *********************** 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 72 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 51 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8909 (tp) outliers start: 21 outliers final: 12 residues processed: 68 average time/residue: 0.0563 time to fit residues: 5.4435 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 : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 PHE Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 69 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 126 LEU Chi-restraints excluded: chain A residue 273 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 58 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 5 optimal weight: 0.0980 chunk 17 optimal weight: 0.0870 chunk 2 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 64 optimal weight: 70.0000 chunk 21 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4554 r_free = 0.4554 target = 0.143542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.098359 restraints weight = 28218.217| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 6.40 r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.1572 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 : 0.570 9.900 9206 Z= 0.276 Chirality : 0.037 0.243 1078 Planarity : 0.004 0.047 984 Dihedral : 15.757 83.226 1528 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.79 % Favored : 97.05 % Rotamer: Outliers : 2.17 % Allowed : 23.33 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.33), residues: 645 helix: 2.25 (0.28), residues: 316 sheet: 1.12 (0.56), residues: 81 loop : -0.63 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 559 TYR 0.008 0.001 TYR A 160 PHE 0.011 0.001 PHE A 530 TRP 0.008 0.001 TRP A 286 HIS 0.003 0.001 HIS A 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.10 ( 6640) covalent geometry : angle 0.57011 / 0.28 ( 9206) hydrogen bonds : bond 0.03660 / 2.37 ( 328) hydrogen bonds : angle 3.82601 / 2.64 ( 898) *********************** 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 65 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 62 average time/residue: 0.0531 time to fit residues: 4.6627 Evaluate side-chains 58 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.134 ------------------------------------------------------------------------------- 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 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 594 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 18 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4547 r_free = 0.4547 target = 0.142987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.095312 restraints weight = 28093.024| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 6.18 r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.1689 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= 0.110 Angle : 0.569 9.059 9206 Z= 0.277 Chirality : 0.036 0.163 1078 Planarity : 0.004 0.049 984 Dihedral : 15.719 79.281 1528 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.95 % Favored : 96.90 % Rotamer: Outliers : 2.00 % Allowed : 24.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.33), residues: 645 helix: 2.30 (0.28), residues: 316 sheet: 1.16 (0.56), residues: 81 loop : -0.67 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 559 TYR 0.009 0.001 TYR A 538 PHE 0.044 0.002 PHE A 321 TRP 0.009 0.002 TRP A 286 HIS 0.002 0.001 HIS A 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 ( 6640) covalent geometry : angle 0.56890 / 0.28 ( 9206) hydrogen bonds : bond 0.03600 / 2.33 ( 328) hydrogen bonds : angle 3.80755 / 2.63 ( 898) *********************** 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 61 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 10 residues processed: 59 average time/residue: 0.0670 time to fit residues: 5.5266 Evaluate side-chains 58 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.261 ------------------------------------------------------------------------------- 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 125 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 378 TYR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 548 VAL 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 16 optimal weight: 2.9990 chunk 43 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 20 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4543 r_free = 0.4543 target = 0.142646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.094681 restraints weight = 28625.100| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 6.33 r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6640 Z= 0.119 Angle : 0.591 13.922 9206 Z= 0.285 Chirality : 0.037 0.233 1078 Planarity : 0.004 0.053 984 Dihedral : 15.698 75.150 1528 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.95 % Favored : 96.90 % Rotamer: Outliers : 2.50 % Allowed : 23.50 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.33), residues: 645 helix: 2.19 (0.28), residues: 316 sheet: 0.95 (0.56), residues: 83 loop : -0.65 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 559 TYR 0.010 0.001 TYR A 538 PHE 0.028 0.002 PHE A 321 TRP 0.013 0.002 TRP A 286 HIS 0.002 0.001 HIS A 638 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 ( 6640) covalent geometry : angle 0.59065 / 0.28 ( 9206) hydrogen bonds : bond 0.03676 / 2.37 ( 328) hydrogen bonds : angle 3.84418 / 2.66 ( 898) *********************** 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 67 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 52 time to evaluate : 0.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 LYS cc_start: 0.9120 (mmtt) cc_final: 0.8914 (mmtt) outliers start: 15 outliers final: 14 residues processed: 65 average time/residue: 0.0580 time to fit residues: 5.3064 Evaluate side-chains 65 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 PHE Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 69 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 368 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 378 TYR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 452 ILE 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: 4.9990 chunk 0 optimal weight: 4.9990 chunk 20 optimal weight: 8.9990 chunk 9 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 67 optimal weight: 30.0000 chunk 16 optimal weight: 3.9990 chunk 47 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4518 r_free = 0.4518 target = 0.140820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.093171 restraints weight = 27870.542| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 6.91 r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6640 Z= 0.164 Angle : 0.621 8.463 9206 Z= 0.307 Chirality : 0.040 0.405 1078 Planarity : 0.004 0.056 984 Dihedral : 15.699 73.586 1528 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.26 % Favored : 96.59 % Rotamer: Outliers : 2.67 % Allowed : 23.83 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.33), residues: 645 helix: 2.10 (0.28), residues: 316 sheet: 0.81 (0.56), residues: 83 loop : -0.71 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 559 TYR 0.013 0.001 TYR A 538 PHE 0.022 0.002 PHE A 321 TRP 0.015 0.002 TRP A 286 HIS 0.003 0.001 HIS A 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 ( 6640) covalent geometry : angle 0.62091 / 0.31 ( 9206) hydrogen bonds : bond 0.04201 / 2.72 ( 328) hydrogen bonds : angle 3.96925 / 2.76 ( 898) ********************** 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 69 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 53 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 PHE cc_start: 0.8381 (m-80) cc_final: 0.7962 (m-80) outliers start: 16 outliers final: 15 residues processed: 67 average time/residue: 0.0554 time to fit residues: 5.2380 Evaluate side-chains 67 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 52 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 PHE Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 69 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 368 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 378 TYR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 452 ILE 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 23 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 42 optimal weight: 0.0570 chunk 46 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 63 optimal weight: 40.0000 chunk 36 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.142174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.096306 restraints weight = 28117.517| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 6.00 r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6640 Z= 0.108 Angle : 0.593 10.032 9206 Z= 0.286 Chirality : 0.038 0.347 1078 Planarity : 0.004 0.051 984 Dihedral : 15.681 73.697 1528 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.95 % Favored : 96.90 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.33), residues: 645 helix: 2.15 (0.28), residues: 316 sheet: 0.89 (0.57), residues: 82 loop : -0.55 (0.40), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 559 TYR 0.008 0.001 TYR A 538 PHE 0.031 0.002 PHE A 321 TRP 0.009 0.002 TRP A 286 HIS 0.002 0.001 HIS A 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 ( 6640) covalent geometry : angle 0.59303 / 0.29 ( 9206) hydrogen bonds : bond 0.03733 / 2.43 ( 328) hydrogen bonds : angle 3.79952 / 2.66 ( 898) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1856.51 seconds wall clock time: 32 minutes 28.81 seconds (1948.81 seconds total)