Starting phenix.real_space_refine on Wed Mar 5 19:22:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x13_21987/03_2025/6x13_21987.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x13_21987/03_2025/6x13_21987.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6x13_21987/03_2025/6x13_21987.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x13_21987/03_2025/6x13_21987.map" model { file = "/net/cci-nas-00/data/ceres_data/6x13_21987/03_2025/6x13_21987.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x13_21987/03_2025/6x13_21987.cif" } resolution = 3.66 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 18 5.16 5 C 2067 2.51 5 N 501 2.21 5 O 549 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 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: 3136 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3094 Classifications: {'peptide': 417} Link IDs: {'PTRANS': 18, 'TRANS': 398} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'6OU': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Time building chain proxies: 2.84, per 1000 atoms: 0.91 Number of scatterers: 3136 At special positions: 0 Unit cell: (66.5415, 78.3473, 71.9078, 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 549 8.00 N 501 7.00 C 2067 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 413.5 milliseconds 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 748 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 0 sheets defined 85.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 2 through 9 Processing helix chain 'A' and resid 11 through 33 Processing helix chain 'A' and resid 36 through 72 removed outlier: 3.767A pdb=" N TYR A 42 " --> pdb=" O ALA A 38 " (cutoff:3.500A) Proline residue: A 45 - end of helix removed outlier: 4.340A pdb=" N PHE A 50 " --> pdb=" O PHE A 46 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N VAL A 51 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N MET A 59 " --> pdb=" O CYS A 55 " (cutoff:3.500A) Proline residue: A 60 - end of helix removed outlier: 3.929A pdb=" N PHE A 63 " --> pdb=" O MET A 59 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA A 64 " --> pdb=" O PRO A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 78 removed outlier: 3.811A pdb=" N LEU A 78 " --> pdb=" O PRO A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 107 removed outlier: 4.218A pdb=" N LYS A 84 " --> pdb=" O ARG A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 137 Processing helix chain 'A' and resid 141 through 147 Processing helix chain 'A' and resid 150 through 169 Processing helix chain 'A' and resid 174 through 220 removed outlier: 3.850A pdb=" N LYS A 196 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE A 197 " --> pdb=" O ALA A 193 " (cutoff:3.500A) Proline residue: A 206 - end of helix removed outlier: 3.771A pdb=" N TYR A 215 " --> pdb=" O ALA A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 254 removed outlier: 4.362A pdb=" N GLU A 227 " --> pdb=" O HIS A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 276 removed outlier: 3.974A pdb=" N PHE A 261 " --> pdb=" O ASP A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 293 Processing helix chain 'A' and resid 295 through 309 Proline residue: A 304 - end of helix Processing helix chain 'A' and resid 312 through 328 Processing helix chain 'A' and resid 334 through 349 Processing helix chain 'A' and resid 357 through 371 Processing helix chain 'A' and resid 376 through 418 removed outlier: 3.754A pdb=" N ILE A 386 " --> pdb=" O ALA A 382 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ALA A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ILE A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N GLY A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP A 405 " --> pdb=" O ASN A 401 " (cutoff:3.500A) 258 hydrogen bonds defined for protein. 771 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: 0.84 Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 482 1.31 - 1.43: 788 1.43 - 1.56: 1878 1.56 - 1.68: 14 1.68 - 1.81: 34 Bond restraints: 3196 Sorted by residual: bond pdb=" C16 6OU A 501 " pdb=" O18 6OU A 501 " ideal model delta sigma weight residual 1.327 1.413 -0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" C31 6OU A 501 " pdb=" O30 6OU A 501 " ideal model delta sigma weight residual 1.331 1.410 -0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" C39 6OU A 501 " pdb=" C40 6OU A 501 " ideal model delta sigma weight residual 1.497 1.567 -0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C15 6OU A 501 " pdb=" C16 6OU A 501 " ideal model delta sigma weight residual 1.501 1.562 -0.061 2.00e-02 2.50e+03 9.21e+00 bond pdb=" C38 6OU A 501 " pdb=" C39 6OU A 501 " ideal model delta sigma weight residual 1.530 1.580 -0.050 2.00e-02 2.50e+03 6.24e+00 ... (remaining 3191 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.09: 4263 3.09 - 6.17: 67 6.17 - 9.26: 15 9.26 - 12.35: 3 12.35 - 15.43: 1 Bond angle restraints: 4349 Sorted by residual: angle pdb=" O22 6OU A 501 " pdb=" P23 6OU A 501 " pdb=" O26 6OU A 501 " ideal model delta sigma weight residual 93.95 109.38 -15.43 3.00e+00 1.11e-01 2.65e+01 angle pdb=" N ALA A 205 " pdb=" CA ALA A 205 " pdb=" C ALA A 205 " ideal model delta sigma weight residual 109.81 120.46 -10.65 2.21e+00 2.05e-01 2.32e+01 angle pdb=" N GLY A 357 " pdb=" CA GLY A 357 " pdb=" C GLY A 357 " ideal model delta sigma weight residual 113.18 121.87 -8.69 2.37e+00 1.78e-01 1.34e+01 angle pdb=" CA TYR A 299 " pdb=" CB TYR A 299 " pdb=" CG TYR A 299 " ideal model delta sigma weight residual 113.90 120.48 -6.58 1.80e+00 3.09e-01 1.33e+01 angle pdb=" C THR A 275 " pdb=" N ARG A 276 " pdb=" CA ARG A 276 " ideal model delta sigma weight residual 122.08 127.30 -5.22 1.47e+00 4.63e-01 1.26e+01 ... (remaining 4344 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.76: 1768 25.76 - 51.51: 101 51.51 - 77.27: 16 77.27 - 103.03: 2 103.03 - 128.78: 2 Dihedral angle restraints: 1889 sinusoidal: 707 harmonic: 1182 Sorted by residual: dihedral pdb=" CA LEU A 372 " pdb=" C LEU A 372 " pdb=" N PRO A 373 " pdb=" CA PRO A 373 " ideal model delta harmonic sigma weight residual -180.00 -159.13 -20.87 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" C09 6OU A 501 " pdb=" C10 6OU A 501 " pdb=" C11 6OU A 501 " pdb=" C12 6OU A 501 " ideal model delta sinusoidal sigma weight residual 179.71 -51.51 -128.78 1 3.00e+01 1.11e-03 1.73e+01 dihedral pdb=" C20 6OU A 501 " pdb=" C31 6OU A 501 " pdb=" O30 6OU A 501 " pdb=" C33 6OU A 501 " ideal model delta sinusoidal sigma weight residual -177.41 -63.97 -113.44 1 3.00e+01 1.11e-03 1.49e+01 ... (remaining 1886 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 347 0.040 - 0.080: 138 0.080 - 0.119: 43 0.119 - 0.159: 7 0.159 - 0.199: 5 Chirality restraints: 540 Sorted by residual: chirality pdb=" C20 6OU A 501 " pdb=" C19 6OU A 501 " pdb=" C21 6OU A 501 " pdb=" O30 6OU A 501 " both_signs ideal model delta sigma weight residual False 2.35 2.54 -0.20 2.00e-01 2.50e+01 9.91e-01 chirality pdb=" CA LEU A 303 " pdb=" N LEU A 303 " pdb=" C LEU A 303 " pdb=" CB LEU A 303 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.84e-01 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 2.31 0.18 2.00e-01 2.50e+01 7.80e-01 ... (remaining 537 not shown) Planarity restraints: 533 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 44 " 0.043 5.00e-02 4.00e+02 6.45e-02 6.66e+00 pdb=" N PRO A 45 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 45 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 45 " 0.036 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 2.21e-02 4.87e+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 delta sigma weight rms_deltas residual plane pdb=" C LEU A 303 " -0.036 5.00e-02 4.00e+02 5.42e-02 4.70e+00 pdb=" N PRO A 304 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 304 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 304 " -0.031 5.00e-02 4.00e+02 ... (remaining 530 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 1023 2.85 - 3.36: 3072 3.36 - 3.88: 5111 3.88 - 4.39: 5458 4.39 - 4.90: 9825 Nonbonded interactions: 24489 Sorted by model distance: nonbonded pdb=" O LYS A 414 " pdb=" OG1 THR A 418 " model vdw 2.340 3.040 nonbonded pdb=" OD1 ASP A 390 " pdb=" NH1 ARG A 397 " model vdw 2.402 3.120 nonbonded pdb=" O GLU A 296 " pdb=" OG SER A 300 " model vdw 2.438 3.040 nonbonded pdb=" NZ LYS A 196 " pdb=" O24 6OU A 501 " model vdw 2.439 3.120 nonbonded pdb=" O SER A 171 " pdb=" NH2 ARG A 177 " model vdw 2.454 3.120 ... (remaining 24484 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: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.210 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 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 : 0.007 0.086 3196 Z= 0.439 Angle : 1.044 15.434 4349 Z= 0.516 Chirality : 0.048 0.199 540 Planarity : 0.008 0.065 533 Dihedral : 16.899 128.781 1141 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 0.31 % Allowed : 9.23 % Favored : 90.46 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.73 (0.31), residues: 415 helix: -2.04 (0.20), residues: 351 sheet: None (None), residues: 0 loop : -3.62 (0.61), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 264 PHE 0.009 0.001 PHE A 210 TYR 0.017 0.002 TYR A 299 ARG 0.001 0.000 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 0.321 Fit side-chains REVERT: A 35 TYR cc_start: 0.7029 (m-80) cc_final: 0.6827 (m-10) REVERT: A 59 MET cc_start: 0.9460 (tpp) cc_final: 0.9200 (mmm) REVERT: A 202 MET cc_start: 0.8192 (mmm) cc_final: 0.7863 (mmm) REVERT: A 362 MET cc_start: 0.7455 (ttm) cc_final: 0.7149 (ttm) outliers start: 1 outliers final: 0 residues processed: 61 average time/residue: 0.1608 time to fit residues: 11.9310 Evaluate side-chains 50 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN A 378 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.125099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.098736 restraints weight = 4238.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.101132 restraints weight = 2898.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.102757 restraints weight = 2256.016| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3196 Z= 0.257 Angle : 0.651 6.860 4349 Z= 0.338 Chirality : 0.040 0.153 540 Planarity : 0.006 0.069 533 Dihedral : 11.573 96.425 481 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.92 % Allowed : 14.46 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.39), residues: 415 helix: 0.11 (0.26), residues: 350 sheet: None (None), residues: 0 loop : -3.92 (0.56), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 332 PHE 0.007 0.001 PHE A 273 TYR 0.035 0.002 TYR A 299 ARG 0.003 0.000 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.272 Fit side-chains REVERT: A 169 MET cc_start: 0.8584 (tpp) cc_final: 0.7887 (ttm) REVERT: A 202 MET cc_start: 0.8314 (mmm) cc_final: 0.7922 (mmm) REVERT: A 362 MET cc_start: 0.7413 (ttm) cc_final: 0.6978 (ttm) outliers start: 3 outliers final: 1 residues processed: 56 average time/residue: 0.1495 time to fit residues: 10.3994 Evaluate side-chains 52 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 4 optimal weight: 0.6980 chunk 5 optimal weight: 0.4980 chunk 9 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 35 optimal weight: 0.0050 chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.127333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.101663 restraints weight = 4181.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.103772 restraints weight = 2944.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.105340 restraints weight = 2335.740| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3196 Z= 0.216 Angle : 0.612 6.473 4349 Z= 0.317 Chirality : 0.039 0.141 540 Planarity : 0.005 0.073 533 Dihedral : 9.655 91.857 481 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.23 % Allowed : 15.08 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.42), residues: 415 helix: 0.89 (0.28), residues: 352 sheet: None (None), residues: 0 loop : -3.42 (0.62), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 114 PHE 0.008 0.001 PHE A 273 TYR 0.031 0.002 TYR A 299 ARG 0.001 0.000 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.352 Fit side-chains REVERT: A 35 TYR cc_start: 0.6949 (m-10) cc_final: 0.6683 (m-10) REVERT: A 169 MET cc_start: 0.8543 (tpp) cc_final: 0.7931 (ttm) REVERT: A 202 MET cc_start: 0.8204 (mmm) cc_final: 0.7625 (mmm) REVERT: A 215 TYR cc_start: 0.8074 (t80) cc_final: 0.7769 (t80) REVERT: A 362 MET cc_start: 0.7390 (ttm) cc_final: 0.6970 (ttm) outliers start: 4 outliers final: 2 residues processed: 62 average time/residue: 0.1466 time to fit residues: 11.4657 Evaluate side-chains 54 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 167 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 10 optimal weight: 0.0970 chunk 2 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 5 optimal weight: 0.4980 chunk 28 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.127852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.102214 restraints weight = 4209.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.104416 restraints weight = 2962.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.106046 restraints weight = 2354.219| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3196 Z= 0.212 Angle : 0.616 8.146 4349 Z= 0.315 Chirality : 0.039 0.139 540 Planarity : 0.005 0.074 533 Dihedral : 8.243 79.802 481 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.46 % Allowed : 17.23 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.42), residues: 415 helix: 1.21 (0.28), residues: 352 sheet: None (None), residues: 0 loop : -3.21 (0.65), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 32 PHE 0.008 0.001 PHE A 273 TYR 0.039 0.002 TYR A 299 ARG 0.001 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.308 Fit side-chains REVERT: A 169 MET cc_start: 0.8517 (tpp) cc_final: 0.7872 (ttm) REVERT: A 276 ARG cc_start: 0.8464 (mtm-85) cc_final: 0.8045 (mtm-85) REVERT: A 298 ILE cc_start: 0.8529 (OUTLIER) cc_final: 0.8279 (tt) REVERT: A 362 MET cc_start: 0.7490 (ttm) cc_final: 0.6989 (ttm) outliers start: 8 outliers final: 4 residues processed: 63 average time/residue: 0.1448 time to fit residues: 11.4037 Evaluate side-chains 56 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 167 TYR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 298 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 19 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 24 optimal weight: 0.0870 chunk 5 optimal weight: 0.3980 chunk 16 optimal weight: 0.3980 chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.129002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.103256 restraints weight = 4151.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.105367 restraints weight = 2897.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.106873 restraints weight = 2289.462| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3196 Z= 0.207 Angle : 0.607 6.972 4349 Z= 0.313 Chirality : 0.039 0.136 540 Planarity : 0.005 0.077 533 Dihedral : 7.629 75.399 481 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.77 % Allowed : 18.77 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.43), residues: 415 helix: 1.47 (0.28), residues: 352 sheet: None (None), residues: 0 loop : -3.08 (0.68), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 114 PHE 0.008 0.001 PHE A 273 TYR 0.036 0.002 TYR A 299 ARG 0.001 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.305 Fit side-chains REVERT: A 169 MET cc_start: 0.8523 (tpp) cc_final: 0.7880 (ttm) REVERT: A 276 ARG cc_start: 0.8450 (mtm-85) cc_final: 0.8013 (mtm-85) REVERT: A 298 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8184 (tt) REVERT: A 362 MET cc_start: 0.7527 (ttm) cc_final: 0.6939 (ttm) outliers start: 9 outliers final: 3 residues processed: 63 average time/residue: 0.1443 time to fit residues: 11.3184 Evaluate side-chains 55 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 298 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 1 optimal weight: 0.0570 chunk 24 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.126048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.100364 restraints weight = 4325.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.102437 restraints weight = 3037.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.103956 restraints weight = 2412.518| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3196 Z= 0.230 Angle : 0.631 8.416 4349 Z= 0.323 Chirality : 0.040 0.154 540 Planarity : 0.005 0.081 533 Dihedral : 7.546 76.228 481 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.15 % Allowed : 20.62 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.43), residues: 415 helix: 1.59 (0.28), residues: 351 sheet: None (None), residues: 0 loop : -2.89 (0.70), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 40 PHE 0.009 0.001 PHE A 273 TYR 0.034 0.002 TYR A 299 ARG 0.001 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.350 Fit side-chains REVERT: A 169 MET cc_start: 0.8541 (tpp) cc_final: 0.7892 (ttm) REVERT: A 298 ILE cc_start: 0.8512 (OUTLIER) cc_final: 0.8240 (tt) REVERT: A 362 MET cc_start: 0.7557 (ttm) cc_final: 0.6975 (ttm) outliers start: 7 outliers final: 3 residues processed: 59 average time/residue: 0.1474 time to fit residues: 10.8489 Evaluate side-chains 53 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 298 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 35 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.140280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.114620 restraints weight = 4239.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.117357 restraints weight = 2731.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.119235 restraints weight = 2063.612| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3196 Z= 0.255 Angle : 0.642 7.716 4349 Z= 0.331 Chirality : 0.040 0.150 540 Planarity : 0.005 0.082 533 Dihedral : 7.618 76.794 481 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.38 % Allowed : 20.62 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.39 (0.42), residues: 415 helix: 1.55 (0.28), residues: 352 sheet: None (None), residues: 0 loop : -2.71 (0.72), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 40 PHE 0.010 0.001 PHE A 273 TYR 0.032 0.002 TYR A 299 ARG 0.001 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.338 Fit side-chains REVERT: A 169 MET cc_start: 0.8565 (tpp) cc_final: 0.7921 (ttm) REVERT: A 276 ARG cc_start: 0.8363 (mtm-85) cc_final: 0.7929 (mtm-85) REVERT: A 298 ILE cc_start: 0.8467 (OUTLIER) cc_final: 0.8192 (tt) REVERT: A 323 PHE cc_start: 0.8083 (OUTLIER) cc_final: 0.7478 (t80) REVERT: A 362 MET cc_start: 0.7553 (ttm) cc_final: 0.6986 (ttm) outliers start: 11 outliers final: 5 residues processed: 62 average time/residue: 0.1468 time to fit residues: 11.4383 Evaluate side-chains 57 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 392 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 38 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 8 optimal weight: 0.3980 chunk 37 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 29 optimal weight: 0.4980 chunk 32 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.125335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.100050 restraints weight = 4209.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.102035 restraints weight = 3002.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.103484 restraints weight = 2410.118| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3196 Z= 0.232 Angle : 0.633 7.438 4349 Z= 0.326 Chirality : 0.039 0.156 540 Planarity : 0.005 0.082 533 Dihedral : 7.465 73.646 481 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.77 % Allowed : 20.92 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.43), residues: 415 helix: 1.70 (0.28), residues: 352 sheet: None (None), residues: 0 loop : -2.70 (0.71), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 40 PHE 0.009 0.001 PHE A 273 TYR 0.032 0.002 TYR A 299 ARG 0.001 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.328 Fit side-chains REVERT: A 169 MET cc_start: 0.8537 (tpp) cc_final: 0.7915 (ttm) REVERT: A 276 ARG cc_start: 0.8375 (mtm-85) cc_final: 0.7947 (mtm-85) REVERT: A 298 ILE cc_start: 0.8501 (OUTLIER) cc_final: 0.8240 (tt) REVERT: A 323 PHE cc_start: 0.8093 (OUTLIER) cc_final: 0.7500 (t80) REVERT: A 362 MET cc_start: 0.7563 (ttm) cc_final: 0.6973 (ttm) outliers start: 9 outliers final: 5 residues processed: 61 average time/residue: 0.1354 time to fit residues: 10.2798 Evaluate side-chains 57 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 392 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 5 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 32 optimal weight: 0.1980 chunk 36 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.135871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.108974 restraints weight = 4291.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.111843 restraints weight = 2697.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.113883 restraints weight = 2015.677| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3196 Z= 0.234 Angle : 0.661 9.580 4349 Z= 0.333 Chirality : 0.040 0.168 540 Planarity : 0.005 0.084 533 Dihedral : 7.405 71.853 481 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.77 % Allowed : 21.85 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.43), residues: 415 helix: 1.72 (0.28), residues: 352 sheet: None (None), residues: 0 loop : -2.67 (0.71), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 40 PHE 0.010 0.001 PHE A 273 TYR 0.032 0.002 TYR A 299 ARG 0.001 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.351 Fit side-chains REVERT: A 169 MET cc_start: 0.8543 (tpp) cc_final: 0.7935 (ttm) REVERT: A 276 ARG cc_start: 0.8340 (mtm-85) cc_final: 0.7893 (mtm-85) REVERT: A 298 ILE cc_start: 0.8460 (OUTLIER) cc_final: 0.8199 (tt) REVERT: A 323 PHE cc_start: 0.8099 (OUTLIER) cc_final: 0.7504 (t80) REVERT: A 362 MET cc_start: 0.7575 (ttm) cc_final: 0.6966 (ttm) outliers start: 9 outliers final: 6 residues processed: 60 average time/residue: 0.1437 time to fit residues: 10.7281 Evaluate side-chains 60 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 392 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 12 optimal weight: 0.0370 chunk 25 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.130151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.103238 restraints weight = 4317.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.105770 restraints weight = 2925.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.107299 restraints weight = 2292.651| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3196 Z= 0.243 Angle : 0.662 9.008 4349 Z= 0.336 Chirality : 0.040 0.179 540 Planarity : 0.005 0.083 533 Dihedral : 7.364 69.656 481 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.46 % Allowed : 22.77 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.43), residues: 415 helix: 1.69 (0.28), residues: 352 sheet: None (None), residues: 0 loop : -2.63 (0.72), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS A 40 PHE 0.010 0.001 PHE A 273 TYR 0.031 0.002 TYR A 299 ARG 0.001 0.000 ARG A 177 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.335 Fit side-chains REVERT: A 169 MET cc_start: 0.8549 (tpp) cc_final: 0.7955 (ttm) REVERT: A 276 ARG cc_start: 0.8288 (mtm-85) cc_final: 0.7849 (mtm-85) REVERT: A 298 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8178 (tt) REVERT: A 323 PHE cc_start: 0.8117 (OUTLIER) cc_final: 0.7491 (t80) REVERT: A 362 MET cc_start: 0.7573 (ttm) cc_final: 0.6963 (ttm) outliers start: 8 outliers final: 5 residues processed: 58 average time/residue: 0.1627 time to fit residues: 11.8142 Evaluate side-chains 57 residues out of total 325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 392 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 17 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 15 optimal weight: 0.0470 chunk 29 optimal weight: 0.6980 chunk 35 optimal weight: 0.0980 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.128408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.102681 restraints weight = 4171.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.104891 restraints weight = 2884.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.106460 restraints weight = 2262.273| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3196 Z= 0.209 Angle : 0.646 9.472 4349 Z= 0.326 Chirality : 0.039 0.173 540 Planarity : 0.005 0.079 533 Dihedral : 7.165 64.975 481 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.46 % Allowed : 22.46 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.43), residues: 415 helix: 1.81 (0.28), residues: 352 sheet: None (None), residues: 0 loop : -2.53 (0.73), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 40 PHE 0.009 0.001 PHE A 273 TYR 0.032 0.002 TYR A 299 ARG 0.001 0.000 ARG A 177 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1350.02 seconds wall clock time: 24 minutes 23.30 seconds (1463.30 seconds total)