Starting phenix.real_space_refine on Thu Mar 6 03:29:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uwl_20923/03_2025/6uwl_20923.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uwl_20923/03_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_20923/03_2025/6uwl_20923.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uwl_20923/03_2025/6uwl_20923.map" model { file = "/net/cci-nas-00/data/ceres_data/6uwl_20923/03_2025/6uwl_20923.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uwl_20923/03_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-5624/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: 2.85, per 1000 atoms: 0.94 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: 1.01 Conformation dependent library (CDL) restraints added in 393.4 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: 0.30 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: 0.80 Time building geometry restraints manager: 1.02 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: 1.030 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: 0.020 Set scattering table: 0.030 Process input model: 12.950 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.320 ------------------------------------------------------------------------------- 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 : 0.320 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: 0.1502 time to fit residues: 16.6596 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 : 0.329 ------------------------------------------------------------------------------- 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: 0.0270 chunk 11 optimal weight: 0.7980 overall best weight: 0.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.131824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.106073 restraints weight = 5827.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.108411 restraints weight = 3292.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.109986 restraints weight = 2365.526| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3083 Z= 0.205 Angle : 0.671 9.892 4190 Z= 0.340 Chirality : 0.041 0.138 524 Planarity : 0.006 0.054 510 Dihedral : 11.310 88.640 463 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.06 % Favored : 93.69 % Rotamer: Outliers : 2.55 % Allowed : 19.11 % 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: -1.96 (0.40), residues: 396 helix: -0.71 (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 332 PHE 0.015 0.001 PHE A 324 TYR 0.025 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 90 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.321 Fit side-chains REVERT: A 42 TYR cc_start: 0.8068 (m-80) cc_final: 0.7836 (m-80) REVERT: A 102 ILE cc_start: 0.8396 (mt) cc_final: 0.8185 (mt) REVERT: A 227 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7289 (tm-30) REVERT: A 269 MET cc_start: 0.8527 (ttm) cc_final: 0.8103 (mtt) REVERT: A 337 GLN cc_start: 0.7552 (mm-40) cc_final: 0.6211 (tt0) REVERT: A 406 LEU cc_start: 0.8919 (mm) cc_final: 0.8566 (mp) outliers start: 8 outliers final: 5 residues processed: 88 average time/residue: 0.1189 time to fit residues: 13.1074 Evaluate side-chains 80 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 0.0980 chunk 39 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 10 optimal weight: 0.2980 chunk 35 optimal weight: 3.9990 chunk 5 optimal weight: 0.4980 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 A 332 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.129109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.101248 restraints weight = 5806.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.103647 restraints weight = 3254.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.105202 restraints weight = 2316.057| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3083 Z= 0.216 Angle : 0.663 10.038 4190 Z= 0.332 Chirality : 0.042 0.137 524 Planarity : 0.005 0.051 510 Dihedral : 9.795 86.469 463 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.05 % Favored : 94.70 % Rotamer: Outliers : 2.55 % Allowed : 21.66 % Favored : 75.80 % 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: -0.94 (0.42), residues: 396 helix: 0.05 (0.28), residues: 324 sheet: None (None), residues: 0 loop : -3.40 (0.74), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS A 37 PHE 0.019 0.001 PHE A 261 TYR 0.024 0.001 TYR A 299 ARG 0.003 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 95 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.283 Fit side-chains REVERT: A 86 VAL cc_start: 0.9318 (t) cc_final: 0.9070 (m) REVERT: A 136 ASP cc_start: 0.8239 (t0) cc_final: 0.8023 (t0) REVERT: A 286 MET cc_start: 0.8459 (mtp) cc_final: 0.8111 (mtp) REVERT: A 337 GLN cc_start: 0.7689 (mm-40) cc_final: 0.6183 (tt0) REVERT: A 390 ASP cc_start: 0.8095 (t0) cc_final: 0.7844 (t0) REVERT: A 406 LEU cc_start: 0.8874 (mm) cc_final: 0.8537 (mt) outliers start: 8 outliers final: 5 residues processed: 91 average time/residue: 0.1148 time to fit residues: 13.0940 Evaluate side-chains 77 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.291 ------------------------------------------------------------------------------- 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 341 ILE Chi-restraints excluded: chain A residue 355 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 32 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3635 r_free = 0.3635 target = 0.128931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.102672 restraints weight = 5896.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.104993 restraints weight = 3390.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.106459 restraints weight = 2466.940| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3083 Z= 0.297 Angle : 0.716 10.326 4190 Z= 0.355 Chirality : 0.044 0.155 524 Planarity : 0.005 0.054 510 Dihedral : 9.747 87.987 463 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.31 % Favored : 93.43 % 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: -0.53 (0.43), residues: 396 helix: 0.37 (0.29), residues: 323 sheet: None (None), residues: 0 loop : -3.36 (0.73), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 37 PHE 0.013 0.001 PHE A 261 TYR 0.023 0.001 TYR A 299 ARG 0.003 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 85 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 VAL cc_start: 0.8449 (m) cc_final: 0.8138 (m) REVERT: A 136 ASP cc_start: 0.8224 (t0) cc_final: 0.7975 (t0) REVERT: A 275 THR cc_start: 0.9040 (OUTLIER) cc_final: 0.8829 (t) REVERT: A 337 GLN cc_start: 0.7537 (mm-40) cc_final: 0.6061 (tt0) REVERT: A 390 ASP cc_start: 0.8238 (t0) cc_final: 0.7954 (t0) REVERT: A 406 LEU cc_start: 0.8967 (mm) cc_final: 0.8573 (mt) outliers start: 11 outliers final: 8 residues processed: 80 average time/residue: 0.1277 time to fit residues: 12.8137 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 : 0.293 ------------------------------------------------------------------------------- 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 398 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 8 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 15 optimal weight: 0.0980 chunk 34 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3663 r_free = 0.3663 target = 0.130861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.105204 restraints weight = 5889.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.107547 restraints weight = 3313.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.108988 restraints weight = 2378.476| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3083 Z= 0.239 Angle : 0.698 10.162 4190 Z= 0.341 Chirality : 0.043 0.142 524 Planarity : 0.005 0.053 510 Dihedral : 9.037 81.787 463 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.81 % Favored : 93.94 % Rotamer: Outliers : 3.18 % Allowed : 25.16 % Favored : 71.66 % 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: -0.21 (0.43), residues: 396 helix: 0.61 (0.29), residues: 323 sheet: None (None), residues: 0 loop : -3.41 (0.71), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS A 37 PHE 0.012 0.001 PHE A 261 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 84 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.317 Fit side-chains REVERT: A 136 ASP cc_start: 0.8170 (t0) cc_final: 0.7926 (t0) REVERT: A 247 TYR cc_start: 0.7710 (m-80) cc_final: 0.7475 (m-80) REVERT: A 269 MET cc_start: 0.8524 (mtt) cc_final: 0.7908 (ttt) REVERT: A 286 MET cc_start: 0.8721 (mtp) cc_final: 0.8403 (mtp) REVERT: A 337 GLN cc_start: 0.7584 (mm-40) cc_final: 0.6368 (tt0) REVERT: A 397 ARG cc_start: 0.7180 (ttm110) cc_final: 0.6784 (ttm110) REVERT: A 399 MET cc_start: 0.8205 (tpt) cc_final: 0.7549 (tpt) REVERT: A 406 LEU cc_start: 0.8921 (mm) cc_final: 0.8549 (mt) outliers start: 10 outliers final: 8 residues processed: 81 average time/residue: 0.1362 time to fit residues: 13.6864 Evaluate side-chains 80 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.331 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 5 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 10 optimal weight: 0.4980 chunk 39 optimal weight: 2.9990 chunk 27 optimal weight: 0.4980 chunk 7 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 33 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.129040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.103271 restraints weight = 5981.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.105668 restraints weight = 3364.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.107129 restraints weight = 2407.572| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3083 Z= 0.270 Angle : 0.704 10.307 4190 Z= 0.347 Chirality : 0.044 0.153 524 Planarity : 0.005 0.054 510 Dihedral : 8.948 84.079 463 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.06 % Favored : 93.69 % Rotamer: Outliers : 4.78 % Allowed : 26.11 % Favored : 69.11 % 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: -0.22 (0.43), residues: 396 helix: 0.60 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -3.51 (0.70), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS A 37 PHE 0.009 0.001 PHE A 261 TYR 0.021 0.001 TYR A 299 ARG 0.004 0.001 ARG A 105 *********************** 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 87 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.297 Fit side-chains REVERT: A 83 VAL cc_start: 0.8491 (m) cc_final: 0.8207 (m) REVERT: A 86 VAL cc_start: 0.9268 (t) cc_final: 0.9068 (m) REVERT: A 136 ASP cc_start: 0.8241 (t0) cc_final: 0.8028 (t0) REVERT: A 247 TYR cc_start: 0.7792 (m-80) cc_final: 0.7535 (m-80) REVERT: A 269 MET cc_start: 0.8544 (mtt) cc_final: 0.7912 (ttt) REVERT: A 286 MET cc_start: 0.8700 (mtp) cc_final: 0.8338 (mtp) REVERT: A 337 GLN cc_start: 0.7628 (mm-40) cc_final: 0.6375 (tt0) REVERT: A 399 MET cc_start: 0.8222 (tpt) cc_final: 0.7502 (tpt) REVERT: A 406 LEU cc_start: 0.8958 (mm) cc_final: 0.8539 (mt) outliers start: 15 outliers final: 11 residues processed: 82 average time/residue: 0.1178 time to fit residues: 12.1800 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 : 0.287 ------------------------------------------------------------------------------- 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 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 321 CYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 18 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 6 optimal weight: 0.4980 chunk 20 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 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 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 = 0.3631 r_free = 0.3631 target = 0.127786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.100045 restraints weight = 5966.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.102447 restraints weight = 3270.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.104010 restraints weight = 2309.366| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3083 Z= 0.256 Angle : 0.720 10.627 4190 Z= 0.348 Chirality : 0.043 0.142 524 Planarity : 0.005 0.057 510 Dihedral : 8.671 82.802 463 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.06 % Favored : 93.69 % Rotamer: Outliers : 4.46 % Allowed : 26.43 % Favored : 69.11 % 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: -0.01 (0.43), residues: 396 helix: 0.72 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -3.32 (0.71), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS A 37 PHE 0.010 0.001 PHE A 261 TYR 0.022 0.001 TYR A 299 ARG 0.006 0.001 ARG A 397 *********************** 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 93 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 VAL cc_start: 0.8379 (m) cc_final: 0.8099 (m) REVERT: A 86 VAL cc_start: 0.9283 (t) cc_final: 0.9071 (m) REVERT: A 136 ASP cc_start: 0.8272 (t0) cc_final: 0.8067 (t0) REVERT: A 247 TYR cc_start: 0.7865 (m-80) cc_final: 0.7624 (m-80) REVERT: A 286 MET cc_start: 0.8604 (mtp) cc_final: 0.8208 (mtp) REVERT: A 337 GLN cc_start: 0.7594 (mm-40) cc_final: 0.6308 (tt0) REVERT: A 387 LEU cc_start: 0.8265 (tp) cc_final: 0.7938 (mp) REVERT: A 406 LEU cc_start: 0.8934 (mm) cc_final: 0.8516 (mt) outliers start: 14 outliers final: 12 residues processed: 89 average time/residue: 0.1175 time to fit residues: 13.1538 Evaluate side-chains 86 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.324 ------------------------------------------------------------------------------- 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 131 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 321 CYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 0.4980 chunk 39 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 31 optimal weight: 0.0980 chunk 22 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3580 r_free = 0.3580 target = 0.124608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.096130 restraints weight = 5958.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.098379 restraints weight = 3376.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.099708 restraints weight = 2438.182| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3083 Z= 0.241 Angle : 0.717 11.612 4190 Z= 0.346 Chirality : 0.043 0.141 524 Planarity : 0.005 0.053 510 Dihedral : 8.398 80.131 463 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.56 % Favored : 94.19 % Rotamer: Outliers : 5.41 % Allowed : 26.75 % Favored : 67.83 % 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: 0.01 (0.43), residues: 396 helix: 0.69 (0.29), residues: 332 sheet: None (None), residues: 0 loop : -3.42 (0.73), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS A 37 PHE 0.009 0.001 PHE A 261 TYR 0.022 0.001 TYR A 299 ARG 0.006 0.001 ARG A 397 *********************** 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 91 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: A 83 VAL cc_start: 0.8392 (m) cc_final: 0.8092 (m) REVERT: A 86 VAL cc_start: 0.9258 (t) cc_final: 0.9029 (m) REVERT: A 247 TYR cc_start: 0.7804 (m-80) cc_final: 0.7561 (m-80) REVERT: A 269 MET cc_start: 0.8570 (mtt) cc_final: 0.7970 (ttt) REVERT: A 286 MET cc_start: 0.8659 (mtp) cc_final: 0.8297 (mtp) REVERT: A 337 GLN cc_start: 0.7504 (mm-40) cc_final: 0.6306 (tt0) REVERT: A 387 LEU cc_start: 0.8250 (tp) cc_final: 0.7891 (mp) REVERT: A 399 MET cc_start: 0.8077 (tpt) cc_final: 0.7298 (tpt) REVERT: A 406 LEU cc_start: 0.8905 (mm) cc_final: 0.8478 (mt) outliers start: 17 outliers final: 14 residues processed: 86 average time/residue: 0.1186 time to fit residues: 12.9219 Evaluate side-chains 84 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.295 ------------------------------------------------------------------------------- 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 85 ILE Chi-restraints excluded: chain A residue 131 VAL 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 321 CYS 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 Chi-restraints excluded: chain A residue 386 ILE 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: 1.9990 chunk 24 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 15 optimal weight: 0.1980 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 13 optimal weight: 0.0570 chunk 39 optimal weight: 0.7980 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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** A 318 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.127903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.100063 restraints weight = 5922.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.102405 restraints weight = 3249.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.103857 restraints weight = 2310.474| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3083 Z= 0.243 Angle : 0.735 12.457 4190 Z= 0.354 Chirality : 0.043 0.148 524 Planarity : 0.005 0.057 510 Dihedral : 8.290 79.563 463 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.81 % Favored : 93.94 % Rotamer: Outliers : 5.41 % Allowed : 26.75 % Favored : 67.83 % 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: 0.75 (0.29), residues: 325 sheet: None (None), residues: 0 loop : -3.13 (0.73), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS A 37 PHE 0.009 0.001 PHE A 261 TYR 0.023 0.001 TYR A 299 ARG 0.006 0.001 ARG A 397 *********************** 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 92 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: A 10 TYR cc_start: 0.7670 (OUTLIER) cc_final: 0.7084 (t80) REVERT: A 83 VAL cc_start: 0.8401 (m) cc_final: 0.8110 (m) REVERT: A 86 VAL cc_start: 0.9258 (t) cc_final: 0.9021 (m) REVERT: A 247 TYR cc_start: 0.7841 (m-80) cc_final: 0.7578 (m-80) REVERT: A 269 MET cc_start: 0.8555 (mtt) cc_final: 0.7953 (ttt) REVERT: A 286 MET cc_start: 0.8628 (mtp) cc_final: 0.8265 (mtp) REVERT: A 337 GLN cc_start: 0.7511 (mm-40) cc_final: 0.6314 (tt0) REVERT: A 387 LEU cc_start: 0.8249 (tp) cc_final: 0.7879 (mp) REVERT: A 399 MET cc_start: 0.8084 (tpt) cc_final: 0.7318 (tpt) REVERT: A 406 LEU cc_start: 0.8885 (mm) cc_final: 0.8458 (mt) outliers start: 17 outliers final: 11 residues processed: 87 average time/residue: 0.1250 time to fit residues: 13.6844 Evaluate side-chains 85 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.324 ------------------------------------------------------------------------------- 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 131 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 321 CYS 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 Chi-restraints excluded: chain A residue 386 ILE 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: 0.8980 chunk 10 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 5 optimal weight: 0.4980 chunk 6 optimal weight: 0.0670 chunk 35 optimal weight: 8.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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 = 0.3622 r_free = 0.3622 target = 0.127530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.099569 restraints weight = 5945.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.101869 restraints weight = 3280.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.103315 restraints weight = 2341.683| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3083 Z= 0.257 Angle : 0.745 12.290 4190 Z= 0.358 Chirality : 0.044 0.142 524 Planarity : 0.006 0.059 510 Dihedral : 8.361 81.935 463 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.31 % Favored : 93.43 % Rotamer: Outliers : 4.14 % Allowed : 28.66 % Favored : 67.20 % 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: 0.66 (0.29), residues: 331 sheet: None (None), residues: 0 loop : -3.47 (0.73), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS A 37 PHE 0.009 0.001 PHE A 261 TYR 0.023 0.001 TYR A 299 ARG 0.006 0.001 ARG A 397 ********************** 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 86 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: A 10 TYR cc_start: 0.7659 (OUTLIER) cc_final: 0.7121 (t80) REVERT: A 83 VAL cc_start: 0.8369 (m) cc_final: 0.8080 (m) REVERT: A 86 VAL cc_start: 0.9262 (t) cc_final: 0.9045 (m) REVERT: A 247 TYR cc_start: 0.7860 (m-80) cc_final: 0.7644 (m-80) REVERT: A 269 MET cc_start: 0.8560 (mtt) cc_final: 0.7955 (ttt) REVERT: A 286 MET cc_start: 0.8589 (mtp) cc_final: 0.8229 (mtp) REVERT: A 337 GLN cc_start: 0.7456 (mm-40) cc_final: 0.6249 (tt0) REVERT: A 387 LEU cc_start: 0.8184 (tp) cc_final: 0.7814 (mp) REVERT: A 399 MET cc_start: 0.8009 (tpt) cc_final: 0.7287 (tpt) REVERT: A 406 LEU cc_start: 0.8905 (mm) cc_final: 0.8467 (mt) outliers start: 13 outliers final: 10 residues processed: 81 average time/residue: 0.1258 time to fit residues: 12.8835 Evaluate side-chains 83 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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 131 VAL Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 321 CYS 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 Chi-restraints excluded: chain A residue 386 ILE 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: 2.9990 chunk 30 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 19 optimal weight: 0.3980 chunk 4 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 6 optimal weight: 0.1980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3620 r_free = 0.3620 target = 0.127343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.099284 restraints weight = 5903.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.101555 restraints weight = 3279.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.103028 restraints weight = 2346.268| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3083 Z= 0.240 Angle : 0.734 12.107 4190 Z= 0.353 Chirality : 0.043 0.140 524 Planarity : 0.005 0.058 510 Dihedral : 8.269 80.012 463 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.56 % Favored : 94.19 % Rotamer: Outliers : 4.46 % Allowed : 28.66 % Favored : 66.88 % 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: 0.12 (0.43), residues: 396 helix: 0.79 (0.29), residues: 324 sheet: None (None), residues: 0 loop : -3.06 (0.74), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS A 37 PHE 0.009 0.001 PHE A 261 TYR 0.023 0.001 TYR A 299 ARG 0.006 0.001 ARG A 397 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1368.00 seconds wall clock time: 24 minutes 19.97 seconds (1459.97 seconds total)