Starting phenix.real_space_refine on Wed Sep 17 06:57:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mw8_48697/09_2025/9mw8_48697.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mw8_48697/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9mw8_48697/09_2025/9mw8_48697.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mw8_48697/09_2025/9mw8_48697.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mw8_48697/09_2025/9mw8_48697.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mw8_48697/09_2025/9mw8_48697.map" } 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-2.0-5805/lib/python3.9/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: 1.61, per 1000 atoms: 0.25 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: 0.51 Conformation dependent library (CDL) restraints added in 399.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.82 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: 1.29 Time building geometry restraints manager: 0.68 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: 1.960 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.950 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.390 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren 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 covalent geometry : bond 0.00230 ( 6640) covalent geometry : angle 0.63413 ( 9206) hydrogen bonds : bond 0.15121 ( 328) hydrogen bonds : angle 5.58456 ( 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 : 0.174 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: 0.0732 time to fit residues: 6.1903 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 : 0.225 ------------------------------------------------------------------------------- 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: 10.0000 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... 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 = 0.4556 r_free = 0.4556 target = 0.144095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.096062 restraints weight = 28221.396| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 6.40 r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.0958 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= 0.111 Angle : 0.590 10.743 9206 Z= 0.286 Chirality : 0.036 0.145 1078 Planarity : 0.004 0.047 984 Dihedral : 15.889 91.460 1533 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.79 % Favored : 97.05 % Rotamer: Outliers : 2.67 % Allowed : 19.50 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.33), residues: 645 helix: 2.30 (0.28), residues: 316 sheet: 1.03 (0.52), residues: 91 loop : -0.59 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 274 TYR 0.008 0.001 TYR A 538 PHE 0.014 0.001 PHE A 530 TRP 0.008 0.002 TRP A 286 HIS 0.007 0.001 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 6640) covalent geometry : angle 0.58951 ( 9206) hydrogen bonds : bond 0.03708 ( 328) hydrogen bonds : angle 4.07099 ( 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 70 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 320 ILE cc_start: 0.9055 (mm) cc_final: 0.8843 (mm) outliers start: 16 outliers final: 7 residues processed: 68 average time/residue: 0.0819 time to fit residues: 7.5255 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 : 0.224 ------------------------------------------------------------------------------- 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 34 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 25 optimal weight: 0.0070 chunk 3 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 53 optimal weight: 0.0570 chunk 54 optimal weight: 1.9990 overall best weight: 0.7518 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.143878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.095570 restraints weight = 27966.610| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 6.30 r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6640 Z= 0.103 Angle : 0.568 11.475 9206 Z= 0.271 Chirality : 0.036 0.142 1078 Planarity : 0.004 0.047 984 Dihedral : 15.797 88.251 1530 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.95 % Favored : 96.90 % Rotamer: Outliers : 2.67 % Allowed : 20.33 % 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 aren not related in a simple way. whole: 1.64 (0.33), residues: 645 helix: 2.27 (0.28), residues: 316 sheet: 0.97 (0.54), residues: 85 loop : -0.46 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 559 TYR 0.008 0.001 TYR A 538 PHE 0.011 0.001 PHE A 530 TRP 0.008 0.002 TRP A 286 HIS 0.012 0.001 HIS A 159 Details of bonding type rmsd covalent geometry : bond 0.00214 ( 6640) covalent geometry : angle 0.56834 ( 9206) hydrogen bonds : bond 0.03426 ( 328) hydrogen bonds : angle 3.86856 ( 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 71 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 55 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 320 ILE cc_start: 0.9055 (mm) cc_final: 0.8811 (mm) outliers start: 16 outliers final: 9 residues processed: 69 average time/residue: 0.0871 time to fit residues: 8.0609 Evaluate side-chains 62 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.224 ------------------------------------------------------------------------------- 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 16 optimal weight: 3.9990 chunk 14 optimal weight: 0.0270 chunk 31 optimal weight: 0.9990 chunk 50 optimal weight: 0.4980 chunk 33 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 overall best weight: 0.5638 ------------------------------------------------------------------------------- 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 587 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.144370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.097711 restraints weight = 28225.532| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 6.26 r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.1546 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= 0.097 Angle : 0.558 11.869 9206 Z= 0.264 Chirality : 0.036 0.211 1078 Planarity : 0.004 0.046 984 Dihedral : 15.725 83.274 1530 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.95 % Favored : 96.90 % Rotamer: Outliers : 1.83 % Allowed : 22.00 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.33), residues: 645 helix: 2.30 (0.28), residues: 316 sheet: 0.91 (0.53), residues: 85 loop : -0.46 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 559 TYR 0.007 0.001 TYR A 538 PHE 0.009 0.001 PHE A 342 TRP 0.007 0.001 TRP A 286 HIS 0.003 0.001 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00203 ( 6640) covalent geometry : angle 0.55780 ( 9206) hydrogen bonds : bond 0.03166 ( 328) hydrogen bonds : angle 3.69749 ( 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 67 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 320 ILE cc_start: 0.9072 (mm) cc_final: 0.8828 (mm) REVERT: A 513 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8432 (tp) outliers start: 11 outliers final: 7 residues processed: 66 average time/residue: 0.0966 time to fit residues: 8.4770 Evaluate side-chains 59 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 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 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 23 optimal weight: 0.9980 chunk 18 optimal weight: 0.0970 chunk 24 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 48 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 11 optimal weight: 5.9990 chunk 7 optimal weight: 0.0000 overall best weight: 0.4982 ------------------------------------------------------------------------------- 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 = 0.4568 r_free = 0.4568 target = 0.144523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.097437 restraints weight = 28315.550| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 7.28 r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 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 : 0.002 0.028 6640 Z= 0.093 Angle : 0.552 11.743 9206 Z= 0.261 Chirality : 0.036 0.200 1078 Planarity : 0.004 0.048 984 Dihedral : 15.642 73.755 1530 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.95 % Favored : 96.90 % Rotamer: Outliers : 2.00 % Allowed : 22.50 % 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 aren not related in a simple way. whole: 1.71 (0.33), residues: 645 helix: 2.33 (0.28), residues: 316 sheet: 1.28 (0.55), residues: 81 loop : -0.52 (0.39), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 559 TYR 0.007 0.001 TYR A 538 PHE 0.010 0.001 PHE A 9 TRP 0.007 0.001 TRP A 286 HIS 0.002 0.001 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00194 ( 6640) covalent geometry : angle 0.55205 ( 9206) hydrogen bonds : bond 0.03063 ( 328) hydrogen bonds : angle 3.57008 ( 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 69 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.7544 (tpp) cc_final: 0.7316 (tpp) REVERT: A 320 ILE cc_start: 0.9098 (mm) cc_final: 0.8858 (mm) REVERT: A 513 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8465 (tp) outliers start: 12 outliers final: 6 residues processed: 67 average time/residue: 0.0878 time to fit residues: 8.0423 Evaluate side-chains 58 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 594 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 17 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 0.0670 chunk 57 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 45 optimal weight: 0.7980 chunk 64 optimal weight: 50.0000 chunk 48 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- 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 = 0.4553 r_free = 0.4553 target = 0.143621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.095629 restraints weight = 28254.209| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 6.36 r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 6640 Z= 0.101 Angle : 0.585 11.670 9206 Z= 0.275 Chirality : 0.036 0.185 1078 Planarity : 0.004 0.048 984 Dihedral : 15.550 73.598 1528 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.10 % Favored : 96.74 % Rotamer: Outliers : 2.67 % Allowed : 22.67 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.73 (0.33), residues: 645 helix: 2.35 (0.28), residues: 317 sheet: 1.30 (0.57), residues: 81 loop : -0.52 (0.39), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 559 TYR 0.008 0.001 TYR A 538 PHE 0.012 0.001 PHE A 9 TRP 0.008 0.001 TRP A 286 HIS 0.003 0.001 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 6640) covalent geometry : angle 0.58465 ( 9206) hydrogen bonds : bond 0.03133 ( 328) hydrogen bonds : angle 3.58470 ( 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 68 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 52 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 320 ILE cc_start: 0.9086 (mm) cc_final: 0.8885 (mt) outliers start: 16 outliers final: 10 residues processed: 67 average time/residue: 0.0813 time to fit residues: 7.5877 Evaluate side-chains 61 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 92 VAL 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 431 LEU 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: 4.9990 chunk 9 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 17 optimal weight: 0.0980 chunk 2 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 64 optimal weight: 50.0000 chunk 21 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.4510 r_free = 0.4510 target = 0.140350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.092583 restraints weight = 28116.474| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 6.25 r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6640 Z= 0.139 Angle : 0.624 12.493 9206 Z= 0.299 Chirality : 0.037 0.212 1078 Planarity : 0.004 0.047 984 Dihedral : 15.593 73.736 1528 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.31 % Allowed : 2.79 % Favored : 96.90 % Rotamer: Outliers : 3.00 % Allowed : 23.33 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.33), residues: 645 helix: 2.23 (0.28), residues: 317 sheet: 0.76 (0.55), residues: 85 loop : -0.58 (0.40), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 559 TYR 0.013 0.001 TYR A 538 PHE 0.015 0.002 PHE A 398 TRP 0.011 0.002 TRP A 286 HIS 0.004 0.001 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 6640) covalent geometry : angle 0.62416 ( 9206) hydrogen bonds : bond 0.03885 ( 328) hydrogen bonds : angle 3.75133 ( 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 71 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 53 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 320 ILE cc_start: 0.9089 (mm) cc_final: 0.8853 (mm) REVERT: A 375 GLU cc_start: 0.6641 (OUTLIER) cc_final: 0.6024 (tm-30) REVERT: A 512 LEU cc_start: 0.6901 (OUTLIER) cc_final: 0.6565 (tp) outliers start: 18 outliers final: 10 residues processed: 66 average time/residue: 0.0656 time to fit residues: 6.1158 Evaluate side-chains 64 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.251 ------------------------------------------------------------------------------- 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 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 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 18 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.4525 r_free = 0.4525 target = 0.141649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.093628 restraints weight = 27954.678| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 6.21 r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.2391 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= 0.110 Angle : 0.621 12.303 9206 Z= 0.288 Chirality : 0.037 0.174 1078 Planarity : 0.004 0.048 984 Dihedral : 15.551 73.753 1528 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.31 % Allowed : 2.64 % Favored : 97.05 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.55 (0.33), residues: 645 helix: 2.22 (0.28), residues: 316 sheet: 0.99 (0.56), residues: 83 loop : -0.55 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 559 TYR 0.009 0.001 TYR A 538 PHE 0.045 0.002 PHE A 321 TRP 0.010 0.002 TRP A 286 HIS 0.003 0.001 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 6640) covalent geometry : angle 0.62126 ( 9206) hydrogen bonds : bond 0.03402 ( 328) hydrogen bonds : angle 3.62847 ( 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 65 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 320 ILE cc_start: 0.8980 (mm) cc_final: 0.8734 (mm) outliers start: 11 outliers final: 10 residues processed: 62 average time/residue: 0.0734 time to fit residues: 6.3553 Evaluate side-chains 62 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 16 optimal weight: 2.9990 chunk 43 optimal weight: 0.0770 chunk 31 optimal weight: 0.7980 chunk 59 optimal weight: 0.0870 chunk 48 optimal weight: 0.9990 chunk 5 optimal weight: 0.1980 chunk 20 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 8 optimal weight: 0.0170 chunk 30 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.2354 ------------------------------------------------------------------------------- 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 = 0.4557 r_free = 0.4557 target = 0.144221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.097195 restraints weight = 28500.924| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 6.66 r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.2618 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= 0.095 Angle : 0.601 13.804 9206 Z= 0.281 Chirality : 0.036 0.160 1078 Planarity : 0.004 0.048 984 Dihedral : 15.486 73.700 1528 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.31 % Allowed : 2.64 % Favored : 97.05 % Rotamer: Outliers : 1.50 % Allowed : 25.83 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.84 (0.33), residues: 645 helix: 2.43 (0.28), residues: 310 sheet: 1.18 (0.56), residues: 81 loop : -0.31 (0.41), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 559 TYR 0.005 0.001 TYR A 14 PHE 0.017 0.001 PHE A 321 TRP 0.008 0.001 TRP A 286 HIS 0.002 0.001 HIS A 151 Details of bonding type rmsd covalent geometry : bond 0.00190 ( 6640) covalent geometry : angle 0.60085 ( 9206) hydrogen bonds : bond 0.03094 ( 328) hydrogen bonds : angle 3.47075 ( 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 65 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 ARG cc_start: 0.9145 (tpp80) cc_final: 0.8899 (mmm160) outliers start: 9 outliers final: 7 residues processed: 63 average time/residue: 0.0976 time to fit residues: 8.1448 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 : 0.245 ------------------------------------------------------------------------------- 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 125 ILE Chi-restraints excluded: chain A residue 273 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 29 optimal weight: 8.9990 chunk 0 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 67 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 47 optimal weight: 0.0370 chunk 1 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 overall best weight: 1.1664 ------------------------------------------------------------------------------- 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 ** A 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.141162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.093707 restraints weight = 27712.203| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 6.45 r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6640 Z= 0.127 Angle : 0.634 13.212 9206 Z= 0.301 Chirality : 0.037 0.177 1078 Planarity : 0.004 0.049 984 Dihedral : 15.501 73.712 1528 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.31 % Allowed : 3.10 % Favored : 96.59 % Rotamer: Outliers : 1.83 % Allowed : 25.83 % Favored : 72.33 % 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 aren not related in a simple way. whole: 1.67 (0.33), residues: 645 helix: 2.35 (0.28), residues: 310 sheet: 0.94 (0.57), residues: 83 loop : -0.41 (0.40), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 559 TYR 0.010 0.001 TYR A 538 PHE 0.054 0.002 PHE A 321 TRP 0.009 0.002 TRP A 286 HIS 0.004 0.001 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 6640) covalent geometry : angle 0.63367 ( 9206) hydrogen bonds : bond 0.03590 ( 328) hydrogen bonds : angle 3.66994 ( 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 63 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 9 residues processed: 60 average time/residue: 0.0942 time to fit residues: 7.5640 Evaluate side-chains 59 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 PHE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 452 ILE 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: 0.9980 chunk 62 optimal weight: 0.0970 chunk 42 optimal weight: 0.6980 chunk 46 optimal weight: 0.0670 chunk 41 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 63 optimal weight: 0.4980 chunk 36 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.4316 ------------------------------------------------------------------------------- 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 = 0.4540 r_free = 0.4540 target = 0.142718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.095055 restraints weight = 28036.068| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 6.17 r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6640 Z= 0.100 Angle : 0.617 13.211 9206 Z= 0.290 Chirality : 0.037 0.146 1078 Planarity : 0.004 0.048 984 Dihedral : 15.493 73.768 1528 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.31 % Allowed : 2.79 % Favored : 96.90 % Rotamer: Outliers : 1.50 % Allowed : 26.17 % Favored : 72.33 % 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 aren not related in a simple way. whole: 1.73 (0.33), residues: 645 helix: 2.36 (0.28), residues: 310 sheet: 1.23 (0.57), residues: 81 loop : -0.42 (0.40), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 559 TYR 0.006 0.001 TYR A 538 PHE 0.013 0.001 PHE A 321 TRP 0.009 0.001 TRP A 286 HIS 0.017 0.001 HIS A 159 Details of bonding type rmsd covalent geometry : bond 0.00212 ( 6640) covalent geometry : angle 0.61708 ( 9206) hydrogen bonds : bond 0.03314 ( 328) hydrogen bonds : angle 3.55934 ( 898) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2412.29 seconds wall clock time: 41 minutes 58.47 seconds (2518.47 seconds total)