Starting phenix.real_space_refine on Tue Feb 11 07:42:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uwl_20923/02_2025/6uwl_20923.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uwl_20923/02_2025/6uwl_20923.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6uwl_20923/02_2025/6uwl_20923.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uwl_20923/02_2025/6uwl_20923.map" model { file = "/net/cci-nas-00/data/ceres_data/6uwl_20923/02_2025/6uwl_20923.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uwl_20923/02_2025/6uwl_20923.cif" } resolution = 3.62 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1634 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 18 5.16 5 C 1998 2.51 5 N 479 2.21 5 O 533 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3029 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 2990 Classifications: {'peptide': 402} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 384} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'6OU': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Time building chain proxies: 2.58, per 1000 atoms: 0.85 Number of scatterers: 3029 At special positions: 0 Unit cell: (67.84, 67.84, 77.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 18 16.00 P 1 15.00 O 533 8.00 N 479 7.00 C 1998 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 365.5 milliseconds 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 724 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 0 sheets defined 84.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 2 through 8 removed outlier: 3.820A pdb=" N LYS A 6 " --> pdb=" O GLY A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 11 through 14 removed outlier: 3.518A pdb=" N GLN A 14 " --> pdb=" O PRO A 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 11 through 14' Processing helix chain 'A' and resid 15 through 32 removed outlier: 3.931A pdb=" N VAL A 26 " --> pdb=" O LEU A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 43 Processing helix chain 'A' and resid 43 through 57 removed outlier: 3.971A pdb=" N GLY A 47 " --> pdb=" O VAL A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 70 removed outlier: 3.590A pdb=" N PHE A 63 " --> pdb=" O MET A 59 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER A 65 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 103 removed outlier: 3.755A pdb=" N TYR A 88 " --> pdb=" O LYS A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 136 Processing helix chain 'A' and resid 143 through 148 Processing helix chain 'A' and resid 150 through 169 Processing helix chain 'A' and resid 173 through 220 removed outlier: 3.901A pdb=" N TYR A 195 " --> pdb=" O ALA A 191 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS A 196 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Proline residue: A 206 - end of helix removed outlier: 3.732A pdb=" N GLN A 220 " --> pdb=" O VAL A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 224 removed outlier: 3.826A pdb=" N VAL A 224 " --> pdb=" O GLY A 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 221 through 224' Processing helix chain 'A' and resid 228 through 254 removed outlier: 3.884A pdb=" N THR A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N PHE A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N VAL A 249 " --> pdb=" O LEU A 245 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TYR A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 276 removed outlier: 6.153A pdb=" N ASP A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ALA A 268 " --> pdb=" O HIS A 264 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG A 276 " --> pdb=" O ALA A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 293 Processing helix chain 'A' and resid 295 through 300 Processing helix chain 'A' and resid 301 through 310 removed outlier: 4.050A pdb=" N THR A 308 " --> pdb=" O PRO A 304 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASN A 310 " --> pdb=" O GLY A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 327 removed outlier: 4.012A pdb=" N GLY A 319 " --> pdb=" O ALA A 315 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL A 320 " --> pdb=" O LEU A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 351 removed outlier: 3.678A pdb=" N ILE A 341 " --> pdb=" O GLN A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 371 removed outlier: 3.705A pdb=" N MET A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 415 removed outlier: 4.016A pdb=" N MET A 385 " --> pdb=" O ALA A 381 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE A 386 " --> pdb=" O ALA A 382 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ALA A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ILE A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU A 393 " --> pdb=" O ILE A 389 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N MET A 395 " --> pdb=" O ALA A 391 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLY A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) 221 hydrogen bonds defined for protein. 663 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.83 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 467 1.31 - 1.43: 749 1.43 - 1.56: 1819 1.56 - 1.68: 13 1.68 - 1.81: 35 Bond restraints: 3083 Sorted by residual: bond pdb=" C16 6OU A 502 " pdb=" O18 6OU A 502 " ideal model delta sigma weight residual 1.327 1.413 -0.086 2.00e-02 2.50e+03 1.83e+01 bond pdb=" C31 6OU A 502 " pdb=" O30 6OU A 502 " ideal model delta sigma weight residual 1.331 1.403 -0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" C39 6OU A 502 " pdb=" C40 6OU A 502 " ideal model delta sigma weight residual 1.497 1.565 -0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" C15 6OU A 502 " pdb=" C16 6OU A 502 " ideal model delta sigma weight residual 1.501 1.558 -0.057 2.00e-02 2.50e+03 8.21e+00 bond pdb=" SD FME A 1 " pdb=" CE FME A 1 " ideal model delta sigma weight residual 1.805 1.751 0.054 2.00e-02 2.50e+03 7.33e+00 ... (remaining 3078 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.26: 4095 3.26 - 6.51: 77 6.51 - 9.77: 14 9.77 - 13.02: 2 13.02 - 16.28: 2 Bond angle restraints: 4190 Sorted by residual: angle pdb=" N ALA A 205 " pdb=" CA ALA A 205 " pdb=" C ALA A 205 " ideal model delta sigma weight residual 109.81 120.81 -11.00 2.21e+00 2.05e-01 2.48e+01 angle pdb=" CA LEU A 228 " pdb=" CB LEU A 228 " pdb=" CG LEU A 228 " ideal model delta sigma weight residual 116.30 132.58 -16.28 3.50e+00 8.16e-02 2.16e+01 angle pdb=" O22 6OU A 502 " pdb=" P23 6OU A 502 " pdb=" O26 6OU A 502 " ideal model delta sigma weight residual 93.95 107.46 -13.51 3.00e+00 1.11e-01 2.03e+01 angle pdb=" C ILE A 294 " pdb=" N SER A 295 " pdb=" CA SER A 295 " ideal model delta sigma weight residual 121.54 129.72 -8.18 1.91e+00 2.74e-01 1.83e+01 angle pdb=" CA TYR A 299 " pdb=" CB TYR A 299 " pdb=" CG TYR A 299 " ideal model delta sigma weight residual 113.90 121.13 -7.23 1.80e+00 3.09e-01 1.61e+01 ... (remaining 4185 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.45: 1708 25.45 - 50.91: 100 50.91 - 76.36: 14 76.36 - 101.81: 0 101.81 - 127.26: 3 Dihedral angle restraints: 1825 sinusoidal: 684 harmonic: 1141 Sorted by residual: dihedral pdb=" CA ILE A 294 " pdb=" C ILE A 294 " pdb=" N SER A 295 " pdb=" CA SER A 295 " ideal model delta harmonic sigma weight residual 180.00 143.05 36.95 0 5.00e+00 4.00e-02 5.46e+01 dihedral pdb=" CA PRO A 75 " pdb=" C PRO A 75 " pdb=" N ALA A 76 " pdb=" CA ALA A 76 " ideal model delta harmonic sigma weight residual -180.00 -153.43 -26.57 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA SER A 72 " pdb=" C SER A 72 " pdb=" N ILE A 73 " pdb=" CA ILE A 73 " ideal model delta harmonic sigma weight residual 180.00 159.02 20.98 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 1822 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 357 0.052 - 0.105: 112 0.105 - 0.157: 45 0.157 - 0.209: 9 0.209 - 0.262: 1 Chirality restraints: 524 Sorted by residual: chirality pdb=" CB ILE A 73 " pdb=" CA ILE A 73 " pdb=" CG1 ILE A 73 " pdb=" CG2 ILE A 73 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CB VAL A 62 " pdb=" CA VAL A 62 " pdb=" CG1 VAL A 62 " pdb=" CG2 VAL A 62 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA ALA A 205 " pdb=" N ALA A 205 " pdb=" C ALA A 205 " pdb=" CB ALA A 205 " both_signs ideal model delta sigma weight residual False 2.48 2.29 0.20 2.00e-01 2.50e+01 9.51e-01 ... (remaining 521 not shown) Planarity restraints: 510 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 355 " 0.042 5.00e-02 4.00e+02 6.40e-02 6.56e+00 pdb=" N PRO A 356 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 356 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 356 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 44 " -0.041 5.00e-02 4.00e+02 6.14e-02 6.03e+00 pdb=" N PRO A 45 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO A 45 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 45 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 243 " -0.011 2.00e-02 2.50e+03 2.19e-02 4.81e+00 pdb=" C ILE A 243 " 0.038 2.00e-02 2.50e+03 pdb=" O ILE A 243 " -0.014 2.00e-02 2.50e+03 pdb=" N LEU A 244 " -0.013 2.00e-02 2.50e+03 ... (remaining 507 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 926 2.82 - 3.34: 2992 3.34 - 3.86: 5003 3.86 - 4.38: 5617 4.38 - 4.90: 9689 Nonbonded interactions: 24227 Sorted by model distance: nonbonded pdb=" OH TYR A 247 " pdb=" OD2 ASP A 312 " model vdw 2.303 3.040 nonbonded pdb=" OH TYR A 236 " pdb=" O ILE A 392 " model vdw 2.313 3.040 nonbonded pdb=" O THR A 403 " pdb=" OG1 THR A 407 " model vdw 2.326 3.040 nonbonded pdb=" O ILE A 61 " pdb=" OG SER A 65 " model vdw 2.342 3.040 nonbonded pdb=" O MET A 311 " pdb=" OG SER A 349 " model vdw 2.349 3.040 ... (remaining 24222 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 group one per residue 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.010 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 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 : 0.008 0.086 3083 Z= 0.518 Angle : 1.158 16.279 4190 Z= 0.567 Chirality : 0.060 0.262 524 Planarity : 0.009 0.064 510 Dihedral : 16.853 127.264 1101 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.58 % Favored : 92.17 % Rotamer: Outliers : 0.00 % Allowed : 14.01 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.71 (0.31), residues: 396 helix: -2.71 (0.20), residues: 321 sheet: None (None), residues: 0 loop : -3.85 (0.67), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS A 264 PHE 0.017 0.002 PHE A 248 TYR 0.028 0.002 TYR A 299 ARG 0.003 0.000 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: A 42 TYR cc_start: 0.8103 (m-80) cc_final: 0.7888 (m-80) REVERT: A 337 GLN cc_start: 0.7418 (mm-40) cc_final: 0.5815 (tt0) REVERT: A 362 MET cc_start: 0.8500 (mmm) cc_final: 0.8280 (mmp) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.1493 time to fit residues: 16.5855 Evaluate side-chains 70 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 0.0770 chunk 31 optimal weight: 0.0970 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 0.0020 chunk 11 optimal weight: 0.7980 overall best weight: 0.2944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 40 HIS A 173 ASN A 199 ASN ** A 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.132381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.106713 restraints weight = 5815.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.109086 restraints weight = 3286.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.110671 restraints weight = 2353.116| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3083 Z= 0.205 Angle : 0.671 9.835 4190 Z= 0.340 Chirality : 0.042 0.139 524 Planarity : 0.006 0.053 510 Dihedral : 11.405 90.143 463 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.06 % Favored : 93.69 % Rotamer: Outliers : 2.87 % Allowed : 18.79 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.40), residues: 396 helix: -0.74 (0.26), residues: 323 sheet: None (None), residues: 0 loop : -3.42 (0.74), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 37 PHE 0.015 0.001 PHE A 324 TYR 0.024 0.001 TYR A 299 ARG 0.006 0.001 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.355 Fit side-chains REVERT: A 42 TYR cc_start: 0.8064 (m-80) cc_final: 0.7833 (m-80) REVERT: A 102 ILE cc_start: 0.8395 (mt) cc_final: 0.8181 (mt) REVERT: A 227 GLU cc_start: 0.7927 (tm-30) cc_final: 0.7300 (tm-30) REVERT: A 269 MET cc_start: 0.8521 (ttm) cc_final: 0.8113 (mtt) REVERT: A 337 GLN cc_start: 0.7568 (mm-40) cc_final: 0.6218 (tt0) REVERT: A 406 LEU cc_start: 0.8926 (mm) cc_final: 0.8574 (mp) outliers start: 9 outliers final: 6 residues processed: 89 average time/residue: 0.1209 time to fit residues: 13.4132 Evaluate side-chains 81 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 355 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 19 optimal weight: 0.1980 chunk 16 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 10 optimal weight: 0.0770 chunk 35 optimal weight: 0.5980 chunk 5 optimal weight: 0.4980 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS A 318 GLN A 332 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.129506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.101524 restraints weight = 5764.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.103947 restraints weight = 3231.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.105500 restraints weight = 2303.596| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3083 Z= 0.211 Angle : 0.666 10.085 4190 Z= 0.333 Chirality : 0.042 0.138 524 Planarity : 0.005 0.051 510 Dihedral : 9.883 86.656 463 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.80 % Favored : 94.95 % Rotamer: Outliers : 2.87 % Allowed : 20.70 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.42), residues: 396 helix: 0.05 (0.28), residues: 323 sheet: None (None), residues: 0 loop : -3.27 (0.74), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS A 37 PHE 0.009 0.001 PHE A 324 TYR 0.023 0.001 TYR A 299 ARG 0.004 0.001 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.337 Fit side-chains REVERT: A 86 VAL cc_start: 0.9303 (t) cc_final: 0.9067 (m) REVERT: A 136 ASP cc_start: 0.8222 (t0) cc_final: 0.8011 (t0) REVERT: A 286 MET cc_start: 0.8434 (mtp) cc_final: 0.8086 (mtp) REVERT: A 337 GLN cc_start: 0.7689 (mm-40) cc_final: 0.6218 (tt0) REVERT: A 406 LEU cc_start: 0.8868 (mm) cc_final: 0.8532 (mt) outliers start: 9 outliers final: 5 residues processed: 90 average time/residue: 0.1121 time to fit residues: 12.7353 Evaluate side-chains 84 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 79 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 366 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 32 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 12 optimal weight: 0.1980 chunk 29 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 28 optimal weight: 0.0970 chunk 7 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS A 318 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.130075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.102225 restraints weight = 5902.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.104632 restraints weight = 3240.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.106140 restraints weight = 2284.224| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3083 Z= 0.215 Angle : 0.670 10.056 4190 Z= 0.331 Chirality : 0.043 0.136 524 Planarity : 0.005 0.053 510 Dihedral : 8.816 73.069 463 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.56 % Favored : 94.19 % Rotamer: Outliers : 3.18 % Allowed : 23.89 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.43), residues: 396 helix: 0.50 (0.29), residues: 323 sheet: None (None), residues: 0 loop : -3.40 (0.72), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS A 37 PHE 0.008 0.001 PHE A 324 TYR 0.022 0.001 TYR A 299 ARG 0.004 0.001 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.335 Fit side-chains REVERT: A 83 VAL cc_start: 0.8345 (m) cc_final: 0.8036 (m) REVERT: A 86 VAL cc_start: 0.9231 (t) cc_final: 0.8993 (m) REVERT: A 136 ASP cc_start: 0.8226 (t0) cc_final: 0.7976 (t0) REVERT: A 247 TYR cc_start: 0.7879 (m-80) cc_final: 0.7615 (m-80) REVERT: A 269 MET cc_start: 0.8570 (mtt) cc_final: 0.8254 (mtt) REVERT: A 275 THR cc_start: 0.8990 (OUTLIER) cc_final: 0.8739 (t) REVERT: A 337 GLN cc_start: 0.7564 (mm-40) cc_final: 0.6198 (tt0) REVERT: A 390 ASP cc_start: 0.7765 (t0) cc_final: 0.7250 (t0) REVERT: A 397 ARG cc_start: 0.7275 (ttm110) cc_final: 0.7039 (ttm110) REVERT: A 399 MET cc_start: 0.8213 (tpt) cc_final: 0.7491 (tpt) REVERT: A 406 LEU cc_start: 0.8814 (mm) cc_final: 0.8450 (mt) outliers start: 10 outliers final: 8 residues processed: 85 average time/residue: 0.1343 time to fit residues: 14.0198 Evaluate side-chains 81 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 366 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 8 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 15 optimal weight: 0.3980 chunk 34 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 31 optimal weight: 7.9990 chunk 33 optimal weight: 0.5980 chunk 12 optimal weight: 0.0050 chunk 22 optimal weight: 0.5980 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS A 318 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.129563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.101859 restraints weight = 5951.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.104172 restraints weight = 3231.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.105704 restraints weight = 2292.545| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3083 Z= 0.223 Angle : 0.676 9.862 4190 Z= 0.332 Chirality : 0.042 0.137 524 Planarity : 0.005 0.052 510 Dihedral : 8.309 71.423 463 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.81 % Favored : 93.94 % Rotamer: Outliers : 3.50 % Allowed : 24.20 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.43), residues: 396 helix: 0.71 (0.29), residues: 324 sheet: None (None), residues: 0 loop : -3.37 (0.71), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS A 37 PHE 0.007 0.001 PHE A 324 TYR 0.022 0.001 TYR A 299 ARG 0.004 0.001 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: A 10 TYR cc_start: 0.7666 (OUTLIER) cc_final: 0.7090 (t80) REVERT: A 83 VAL cc_start: 0.8359 (m) cc_final: 0.8050 (m) REVERT: A 86 VAL cc_start: 0.9227 (t) cc_final: 0.8988 (m) REVERT: A 136 ASP cc_start: 0.8253 (t0) cc_final: 0.7989 (t0) REVERT: A 247 TYR cc_start: 0.7872 (m-80) cc_final: 0.7611 (m-80) REVERT: A 286 MET cc_start: 0.8607 (mtp) cc_final: 0.8266 (mtp) REVERT: A 337 GLN cc_start: 0.7508 (mm-40) cc_final: 0.6232 (tt0) REVERT: A 390 ASP cc_start: 0.7877 (t0) cc_final: 0.7560 (t0) REVERT: A 397 ARG cc_start: 0.7291 (ttm110) cc_final: 0.7046 (ttm110) REVERT: A 406 LEU cc_start: 0.8837 (mm) cc_final: 0.8482 (mt) outliers start: 11 outliers final: 7 residues processed: 84 average time/residue: 0.1232 time to fit residues: 12.9875 Evaluate side-chains 81 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 366 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 5 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 10 optimal weight: 0.0970 chunk 39 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.128898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.101381 restraints weight = 5969.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.103766 restraints weight = 3196.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.105280 restraints weight = 2239.355| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3083 Z= 0.262 Angle : 0.703 9.849 4190 Z= 0.346 Chirality : 0.044 0.153 524 Planarity : 0.005 0.054 510 Dihedral : 8.387 76.357 463 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.06 % Favored : 93.69 % Rotamer: Outliers : 3.18 % Allowed : 26.11 % Favored : 70.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.43), residues: 396 helix: 0.62 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -3.30 (0.72), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS A 37 PHE 0.006 0.001 PHE A 324 TYR 0.021 0.001 TYR A 299 ARG 0.002 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.344 Fit side-chains REVERT: A 10 TYR cc_start: 0.7630 (OUTLIER) cc_final: 0.7039 (t80) REVERT: A 83 VAL cc_start: 0.8408 (m) cc_final: 0.8094 (m) REVERT: A 86 VAL cc_start: 0.9256 (t) cc_final: 0.9017 (m) REVERT: A 136 ASP cc_start: 0.8247 (t0) cc_final: 0.8011 (t0) REVERT: A 247 TYR cc_start: 0.7884 (m-80) cc_final: 0.7650 (m-80) REVERT: A 269 MET cc_start: 0.8507 (mtt) cc_final: 0.7838 (ttt) REVERT: A 286 MET cc_start: 0.8618 (mtp) cc_final: 0.8240 (mtp) REVERT: A 337 GLN cc_start: 0.7573 (mm-40) cc_final: 0.6337 (tt0) REVERT: A 390 ASP cc_start: 0.8046 (t0) cc_final: 0.7759 (t0) REVERT: A 397 ARG cc_start: 0.7225 (ttm110) cc_final: 0.6792 (ttm110) REVERT: A 399 MET cc_start: 0.8082 (tpt) cc_final: 0.7255 (tpt) REVERT: A 406 LEU cc_start: 0.8873 (mm) cc_final: 0.8473 (mt) outliers start: 10 outliers final: 8 residues processed: 81 average time/residue: 0.1283 time to fit residues: 13.0360 Evaluate side-chains 80 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 355 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 18 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 6 optimal weight: 0.3980 chunk 20 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.127683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.099888 restraints weight = 5947.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.102201 restraints weight = 3283.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.103642 restraints weight = 2345.271| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3083 Z= 0.266 Angle : 0.708 9.937 4190 Z= 0.347 Chirality : 0.043 0.139 524 Planarity : 0.005 0.057 510 Dihedral : 8.341 78.542 463 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.81 % Favored : 93.94 % Rotamer: Outliers : 4.14 % Allowed : 26.43 % Favored : 69.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.43), residues: 396 helix: 0.63 (0.29), residues: 334 sheet: None (None), residues: 0 loop : -3.73 (0.73), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS A 37 PHE 0.007 0.001 PHE A 324 TYR 0.023 0.001 TYR A 299 ARG 0.003 0.000 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.319 Fit side-chains REVERT: A 10 TYR cc_start: 0.7635 (OUTLIER) cc_final: 0.7047 (t80) REVERT: A 83 VAL cc_start: 0.8407 (m) cc_final: 0.8095 (m) REVERT: A 86 VAL cc_start: 0.9244 (t) cc_final: 0.8995 (m) REVERT: A 247 TYR cc_start: 0.7860 (m-80) cc_final: 0.7622 (m-80) REVERT: A 269 MET cc_start: 0.8570 (mtt) cc_final: 0.7912 (ttt) REVERT: A 286 MET cc_start: 0.8650 (mtp) cc_final: 0.8257 (mtp) REVERT: A 337 GLN cc_start: 0.7549 (mm-40) cc_final: 0.6319 (tt0) REVERT: A 387 LEU cc_start: 0.7983 (tp) cc_final: 0.7551 (mp) REVERT: A 390 ASP cc_start: 0.8086 (t0) cc_final: 0.7813 (t0) REVERT: A 397 ARG cc_start: 0.7168 (ttm110) cc_final: 0.6681 (ttm110) REVERT: A 399 MET cc_start: 0.8033 (tpt) cc_final: 0.7171 (tpt) REVERT: A 406 LEU cc_start: 0.8941 (mm) cc_final: 0.8542 (mt) outliers start: 13 outliers final: 10 residues processed: 82 average time/residue: 0.1279 time to fit residues: 13.0615 Evaluate side-chains 85 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 355 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS A 264 HIS A 318 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.126567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.098311 restraints weight = 5916.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.100577 restraints weight = 3231.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.101871 restraints weight = 2300.306| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3083 Z= 0.285 Angle : 0.732 11.065 4190 Z= 0.358 Chirality : 0.043 0.141 524 Planarity : 0.005 0.053 510 Dihedral : 8.469 82.819 463 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.81 % Favored : 93.94 % Rotamer: Outliers : 4.14 % Allowed : 26.43 % Favored : 69.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.43), residues: 396 helix: 0.67 (0.29), residues: 329 sheet: None (None), residues: 0 loop : -3.49 (0.71), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS A 37 PHE 0.006 0.001 PHE A 324 TYR 0.023 0.001 TYR A 299 ARG 0.003 0.000 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 VAL cc_start: 0.8256 (m) cc_final: 0.7935 (m) REVERT: A 86 VAL cc_start: 0.9234 (t) cc_final: 0.9029 (m) REVERT: A 337 GLN cc_start: 0.7626 (mm-40) cc_final: 0.6329 (tt0) REVERT: A 387 LEU cc_start: 0.7904 (tp) cc_final: 0.7482 (mp) REVERT: A 390 ASP cc_start: 0.8198 (t0) cc_final: 0.7904 (t0) REVERT: A 406 LEU cc_start: 0.8962 (mm) cc_final: 0.8539 (mt) outliers start: 13 outliers final: 9 residues processed: 81 average time/residue: 0.1082 time to fit residues: 11.1633 Evaluate side-chains 78 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 355 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 24 optimal weight: 0.4980 chunk 11 optimal weight: 2.9990 chunk 15 optimal weight: 0.3980 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS A 264 HIS A 318 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.127820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.100063 restraints weight = 5932.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.102332 restraints weight = 3307.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.103641 restraints weight = 2374.306| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3083 Z= 0.277 Angle : 0.750 12.403 4190 Z= 0.365 Chirality : 0.044 0.151 524 Planarity : 0.005 0.053 510 Dihedral : 8.477 83.506 463 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.81 % Favored : 93.94 % Rotamer: Outliers : 3.50 % Allowed : 26.75 % Favored : 69.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.43), residues: 396 helix: 0.62 (0.29), residues: 333 sheet: None (None), residues: 0 loop : -3.61 (0.73), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS A 37 PHE 0.006 0.001 PHE A 324 TYR 0.022 0.001 TYR A 299 ARG 0.003 0.000 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: A 83 VAL cc_start: 0.8300 (m) cc_final: 0.7973 (m) REVERT: A 86 VAL cc_start: 0.9216 (t) cc_final: 0.8999 (m) REVERT: A 269 MET cc_start: 0.8521 (mtt) cc_final: 0.7909 (ttt) REVERT: A 286 MET cc_start: 0.8680 (mtp) cc_final: 0.8416 (mtp) REVERT: A 337 GLN cc_start: 0.7620 (mm-40) cc_final: 0.6358 (tt0) REVERT: A 399 MET cc_start: 0.8108 (tpt) cc_final: 0.7358 (tpt) outliers start: 11 outliers final: 9 residues processed: 77 average time/residue: 0.1193 time to fit residues: 11.7259 Evaluate side-chains 76 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 355 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 11 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 15 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS ** A 203 GLN ** 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 = 0.3641 r_free = 0.3641 target = 0.128670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.100872 restraints weight = 5934.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.103150 restraints weight = 3304.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.104576 restraints weight = 2370.649| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 3083 Z= 0.264 Angle : 0.738 12.419 4190 Z= 0.357 Chirality : 0.043 0.145 524 Planarity : 0.005 0.056 510 Dihedral : 8.405 82.617 463 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.06 % Favored : 93.69 % Rotamer: Outliers : 3.18 % Allowed : 27.39 % Favored : 69.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.43), residues: 396 helix: 0.64 (0.29), residues: 334 sheet: None (None), residues: 0 loop : -3.48 (0.74), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS A 37 PHE 0.006 0.001 PHE A 324 TYR 0.023 0.001 TYR A 299 ARG 0.003 0.000 ARG A 105 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: A 10 TYR cc_start: 0.7628 (OUTLIER) cc_final: 0.7041 (t80) REVERT: A 83 VAL cc_start: 0.8369 (m) cc_final: 0.8052 (m) REVERT: A 86 VAL cc_start: 0.9213 (t) cc_final: 0.9000 (m) REVERT: A 269 MET cc_start: 0.8571 (mtt) cc_final: 0.7942 (ttt) REVERT: A 286 MET cc_start: 0.8677 (mtp) cc_final: 0.8398 (mtp) REVERT: A 337 GLN cc_start: 0.7585 (mm-40) cc_final: 0.6337 (tt0) REVERT: A 399 MET cc_start: 0.8101 (tpt) cc_final: 0.7368 (tpt) REVERT: A 406 LEU cc_start: 0.8930 (mm) cc_final: 0.8543 (mt) outliers start: 10 outliers final: 8 residues processed: 76 average time/residue: 0.1261 time to fit residues: 12.2895 Evaluate side-chains 78 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 355 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 5 optimal weight: 0.8980 chunk 37 optimal weight: 0.0980 chunk 30 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 6 optimal weight: 0.1980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS A 318 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.128899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.100755 restraints weight = 5916.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.103064 restraints weight = 3282.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.104512 restraints weight = 2359.600| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 3083 Z= 0.233 Angle : 0.736 12.871 4190 Z= 0.354 Chirality : 0.043 0.151 524 Planarity : 0.005 0.059 510 Dihedral : 8.198 77.016 463 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.06 % Favored : 93.69 % Rotamer: Outliers : 3.18 % Allowed : 27.07 % Favored : 69.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.43), residues: 396 helix: 0.72 (0.29), residues: 334 sheet: None (None), residues: 0 loop : -3.48 (0.74), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS A 37 PHE 0.006 0.001 PHE A 324 TYR 0.019 0.001 TYR A 299 ARG 0.003 0.000 ARG A 105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1334.37 seconds wall clock time: 24 minutes 27.81 seconds (1467.81 seconds total)