Starting phenix.real_space_refine on Mon Feb 10 19:49:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bx7_30235/02_2025/7bx7_30235.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bx7_30235/02_2025/7bx7_30235.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7bx7_30235/02_2025/7bx7_30235.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bx7_30235/02_2025/7bx7_30235.map" model { file = "/net/cci-nas-00/data/ceres_data/7bx7_30235/02_2025/7bx7_30235.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bx7_30235/02_2025/7bx7_30235.cif" } resolution = 2.8 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: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 1146 2.51 5 N 348 2.21 5 O 396 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 1896 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 316 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 0.86, per 1000 atoms: 0.45 Number of scatterers: 1896 At special positions: 0 Unit cell: (65.52, 78, 33.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 6 16.00 O 396 8.00 N 348 7.00 C 1146 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: 1.11 Conformation dependent library (CDL) restraints added in 274.0 milliseconds 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 348 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 28.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 253 through 254 Processing sheet with id=AA2, first strand: chain 'A' and resid 260 through 262 Processing sheet with id=AA3, first strand: chain 'A' and resid 265 through 273 Processing sheet with id=AA4, first strand: chain 'A' and resid 279 through 281 removed outlier: 6.666A pdb=" N ASN A 280 " --> pdb=" O PHE B 281 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ASN B 280 " --> pdb=" O PHE C 281 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 253 through 254 Processing sheet with id=AA6, first strand: chain 'D' and resid 260 through 262 Processing sheet with id=AA7, first strand: chain 'D' and resid 265 through 273 Processing sheet with id=AA8, first strand: chain 'D' and resid 279 through 281 removed outlier: 6.618A pdb=" N ASN D 280 " --> pdb=" O PHE E 281 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ASN E 280 " --> pdb=" O PHE F 281 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 44 hydrogen bonds defined for protein. 132 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: 0.46 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 656 1.33 - 1.45: 418 1.45 - 1.56: 864 1.56 - 1.67: 0 1.67 - 1.78: 12 Bond restraints: 1950 Sorted by residual: bond pdb=" CA PHE D 273 " pdb=" CB PHE D 273 " ideal model delta sigma weight residual 1.528 1.502 0.025 1.39e-02 5.18e+03 3.32e+00 bond pdb=" CA PHE E 273 " pdb=" CB PHE E 273 " ideal model delta sigma weight residual 1.528 1.502 0.025 1.39e-02 5.18e+03 3.26e+00 bond pdb=" CA PHE F 273 " pdb=" CB PHE F 273 " ideal model delta sigma weight residual 1.528 1.503 0.025 1.39e-02 5.18e+03 3.20e+00 bond pdb=" CA PHE A 273 " pdb=" CB PHE A 273 " ideal model delta sigma weight residual 1.528 1.503 0.025 1.39e-02 5.18e+03 3.16e+00 bond pdb=" CA PHE B 273 " pdb=" CB PHE B 273 " ideal model delta sigma weight residual 1.528 1.503 0.024 1.39e-02 5.18e+03 3.10e+00 ... (remaining 1945 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 2309 1.20 - 2.40: 217 2.40 - 3.60: 54 3.60 - 4.80: 6 4.80 - 6.00: 6 Bond angle restraints: 2592 Sorted by residual: angle pdb=" CA ARG B 284 " pdb=" CB ARG B 284 " pdb=" CG ARG B 284 " ideal model delta sigma weight residual 114.10 108.10 6.00 2.00e+00 2.50e-01 9.00e+00 angle pdb=" CA ARG C 284 " pdb=" CB ARG C 284 " pdb=" CG ARG C 284 " ideal model delta sigma weight residual 114.10 108.13 5.97 2.00e+00 2.50e-01 8.90e+00 angle pdb=" CA ARG D 284 " pdb=" CB ARG D 284 " pdb=" CG ARG D 284 " ideal model delta sigma weight residual 114.10 108.14 5.96 2.00e+00 2.50e-01 8.88e+00 angle pdb=" CA ARG E 284 " pdb=" CB ARG E 284 " pdb=" CG ARG E 284 " ideal model delta sigma weight residual 114.10 108.16 5.94 2.00e+00 2.50e-01 8.81e+00 angle pdb=" CA ARG F 284 " pdb=" CB ARG F 284 " pdb=" CG ARG F 284 " ideal model delta sigma weight residual 114.10 108.17 5.93 2.00e+00 2.50e-01 8.81e+00 ... (remaining 2587 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.16: 851 11.16 - 22.31: 85 22.31 - 33.47: 54 33.47 - 44.62: 12 44.62 - 55.78: 6 Dihedral angle restraints: 1008 sinusoidal: 372 harmonic: 636 Sorted by residual: dihedral pdb=" CA LYS C 277 " pdb=" CB LYS C 277 " pdb=" CG LYS C 277 " pdb=" CD LYS C 277 " ideal model delta sinusoidal sigma weight residual 180.00 124.22 55.78 3 1.50e+01 4.44e-03 9.37e+00 dihedral pdb=" CA LYS A 277 " pdb=" CB LYS A 277 " pdb=" CG LYS A 277 " pdb=" CD LYS A 277 " ideal model delta sinusoidal sigma weight residual 180.00 124.22 55.78 3 1.50e+01 4.44e-03 9.37e+00 dihedral pdb=" CA LYS D 277 " pdb=" CB LYS D 277 " pdb=" CG LYS D 277 " pdb=" CD LYS D 277 " ideal model delta sinusoidal sigma weight residual 180.00 124.22 55.78 3 1.50e+01 4.44e-03 9.37e+00 ... (remaining 1005 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.019: 70 0.019 - 0.038: 40 0.038 - 0.056: 40 0.056 - 0.074: 12 0.074 - 0.093: 12 Chirality restraints: 174 Sorted by residual: chirality pdb=" CA PHE B 273 " pdb=" N PHE B 273 " pdb=" C PHE B 273 " pdb=" CB PHE B 273 " both_signs ideal model delta sigma weight residual False 2.51 2.60 -0.09 2.00e-01 2.50e+01 2.16e-01 chirality pdb=" CA PHE A 273 " pdb=" N PHE A 273 " pdb=" C PHE A 273 " pdb=" CB PHE A 273 " both_signs ideal model delta sigma weight residual False 2.51 2.60 -0.09 2.00e-01 2.50e+01 2.08e-01 chirality pdb=" CA PHE F 273 " pdb=" N PHE F 273 " pdb=" C PHE F 273 " pdb=" CB PHE F 273 " both_signs ideal model delta sigma weight residual False 2.51 2.60 -0.09 2.00e-01 2.50e+01 2.02e-01 ... (remaining 171 not shown) Planarity restraints: 390 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 273 " -0.008 2.00e-02 2.50e+03 1.41e-02 3.48e+00 pdb=" CG PHE B 273 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE B 273 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE B 273 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE B 273 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE B 273 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE B 273 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 273 " -0.008 2.00e-02 2.50e+03 1.40e-02 3.42e+00 pdb=" CG PHE D 273 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE D 273 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE D 273 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE D 273 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE D 273 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE D 273 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 273 " -0.008 2.00e-02 2.50e+03 1.39e-02 3.40e+00 pdb=" CG PHE A 273 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE A 273 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 273 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE A 273 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 273 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 273 " 0.000 2.00e-02 2.50e+03 ... (remaining 387 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 492 2.76 - 3.30: 1669 3.30 - 3.83: 3459 3.83 - 4.37: 4027 4.37 - 4.90: 7450 Nonbonded interactions: 17097 Sorted by model distance: nonbonded pdb=" NH1 ARG D 284 " pdb=" OD2 ASP E 262 " model vdw 2.228 3.120 nonbonded pdb=" NH1 ARG B 284 " pdb=" OD2 ASP C 262 " model vdw 2.288 3.120 nonbonded pdb=" NH1 ARG A 284 " pdb=" OD2 ASP B 262 " model vdw 2.305 3.120 nonbonded pdb=" O SER B 285 " pdb=" OG SER B 285 " model vdw 2.318 3.040 nonbonded pdb=" O SER A 285 " pdb=" OG SER A 285 " model vdw 2.319 3.040 ... (remaining 17092 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.300 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 9.920 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 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 : 0.009 0.040 1950 Z= 0.603 Angle : 0.841 6.000 2592 Z= 0.485 Chirality : 0.039 0.093 174 Planarity : 0.004 0.016 390 Dihedral : 12.960 55.780 660 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Rotamer: Outliers : 0.00 % Allowed : 13.79 % Favored : 86.21 % 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: -5.83 (0.18), residues: 258 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.44 (0.13), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.030 0.005 PHE B 273 TYR 0.009 0.002 TYR D 260 ARG 0.009 0.004 ARG C 284 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.188 Fit side-chains REVERT: A 276 MET cc_start: 0.8655 (tpt) cc_final: 0.8297 (tmm) REVERT: C 294 GLN cc_start: 0.7650 (tm-30) cc_final: 0.7326 (tm-30) REVERT: D 289 TYR cc_start: 0.7782 (m-80) cc_final: 0.7494 (m-80) REVERT: D 294 GLN cc_start: 0.7753 (tm-30) cc_final: 0.7535 (tm-30) REVERT: E 276 MET cc_start: 0.8825 (tpt) cc_final: 0.8319 (tpt) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.8299 time to fit residues: 35.9195 Evaluate side-chains 34 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN A 269 GLN B 265 ASN B 269 GLN C 265 ASN C 269 GLN D 265 ASN D 269 GLN E 265 ASN E 269 GLN F 269 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.186953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.165260 restraints weight = 2353.333| |-----------------------------------------------------------------------------| r_work (start): 0.4363 rms_B_bonded: 2.13 r_work: 0.4287 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.4197 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.4197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 1950 Z= 0.237 Angle : 0.548 4.029 2592 Z= 0.306 Chirality : 0.037 0.076 174 Planarity : 0.003 0.015 390 Dihedral : 4.162 14.054 294 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.30 % Allowed : 16.09 % Favored : 81.61 % 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: -5.56 (0.19), residues: 258 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.23 (0.15), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.002 PHE C 281 TYR 0.009 0.001 TYR F 260 ARG 0.002 0.001 ARG C 284 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.192 Fit side-chains REVERT: D 289 TYR cc_start: 0.8054 (m-80) cc_final: 0.7808 (m-80) REVERT: D 294 GLN cc_start: 0.7592 (tm-30) cc_final: 0.7369 (tm-30) outliers start: 4 outliers final: 0 residues processed: 49 average time/residue: 0.6337 time to fit residues: 32.1038 Evaluate side-chains 39 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 10 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 3 optimal weight: 0.0070 chunk 15 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.7804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 265 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.178401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.155134 restraints weight = 2343.628| |-----------------------------------------------------------------------------| r_work (start): 0.4260 rms_B_bonded: 2.09 r_work: 0.4186 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.4095 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.4095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 1950 Z= 0.439 Angle : 0.665 5.919 2592 Z= 0.372 Chirality : 0.038 0.090 174 Planarity : 0.005 0.041 390 Dihedral : 4.404 13.232 294 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 2.30 % Allowed : 19.54 % Favored : 78.16 % 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: -5.54 (0.20), residues: 258 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.22 (0.15), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.018 0.003 PHE F 281 TYR 0.016 0.002 TYR E 260 ARG 0.002 0.001 ARG C 284 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.204 Fit side-chains REVERT: C 294 GLN cc_start: 0.7896 (tm-30) cc_final: 0.7380 (tm-30) REVERT: D 289 TYR cc_start: 0.8041 (m-80) cc_final: 0.7775 (m-80) REVERT: D 294 GLN cc_start: 0.7585 (tm-30) cc_final: 0.6882 (tm-30) outliers start: 4 outliers final: 0 residues processed: 42 average time/residue: 0.7239 time to fit residues: 31.3246 Evaluate side-chains 38 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 4 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 = 0.4592 r_free = 0.4592 target = 0.188197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.165330 restraints weight = 2256.158| |-----------------------------------------------------------------------------| r_work (start): 0.4343 rms_B_bonded: 2.13 r_work: 0.4264 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.4171 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.4171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 1950 Z= 0.260 Angle : 0.536 3.780 2592 Z= 0.298 Chirality : 0.036 0.076 174 Planarity : 0.003 0.015 390 Dihedral : 4.143 13.288 294 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 2.30 % Allowed : 18.39 % Favored : 79.31 % 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: -5.49 (0.20), residues: 258 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.18 (0.15), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.002 PHE F 281 TYR 0.012 0.001 TYR E 260 ARG 0.001 0.000 ARG F 284 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.208 Fit side-chains REVERT: B 276 MET cc_start: 0.8892 (tmm) cc_final: 0.8568 (tmm) REVERT: D 289 TYR cc_start: 0.8124 (m-80) cc_final: 0.7881 (m-80) REVERT: D 294 GLN cc_start: 0.7576 (tm-30) cc_final: 0.7178 (tm-30) REVERT: F 294 GLN cc_start: 0.7645 (tm-30) cc_final: 0.7253 (tm-30) outliers start: 4 outliers final: 1 residues processed: 42 average time/residue: 0.7067 time to fit residues: 30.6816 Evaluate side-chains 40 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 259 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 280 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.184748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.161503 restraints weight = 2280.916| |-----------------------------------------------------------------------------| r_work (start): 0.4310 rms_B_bonded: 2.12 r_work: 0.4228 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.4133 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.4133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 1950 Z= 0.334 Angle : 0.575 4.315 2592 Z= 0.321 Chirality : 0.037 0.081 174 Planarity : 0.004 0.026 390 Dihedral : 4.215 12.400 294 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 3.45 % Allowed : 16.09 % Favored : 80.46 % 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: -5.45 (0.21), residues: 258 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.15 (0.16), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.003 PHE C 281 TYR 0.015 0.002 TYR E 266 ARG 0.002 0.000 ARG F 284 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.207 Fit side-chains REVERT: B 276 MET cc_start: 0.8905 (OUTLIER) cc_final: 0.8294 (tmm) REVERT: D 289 TYR cc_start: 0.8090 (m-80) cc_final: 0.7829 (m-80) REVERT: D 294 GLN cc_start: 0.7579 (tm-30) cc_final: 0.6862 (tm-30) REVERT: F 294 GLN cc_start: 0.7729 (tm-30) cc_final: 0.7224 (tm-30) outliers start: 6 outliers final: 1 residues processed: 39 average time/residue: 0.7240 time to fit residues: 29.1586 Evaluate side-chains 40 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 38 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain C residue 259 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 8 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 overall best weight: 1.3182 ------------------------------------------------------------------------------- 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 = 0.4556 r_free = 0.4556 target = 0.184719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.161366 restraints weight = 2280.803| |-----------------------------------------------------------------------------| r_work (start): 0.4305 rms_B_bonded: 2.14 r_work: 0.4226 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.4132 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.4132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 1950 Z= 0.348 Angle : 0.585 4.357 2592 Z= 0.326 Chirality : 0.037 0.099 174 Planarity : 0.004 0.030 390 Dihedral : 4.303 14.028 294 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 2.30 % Allowed : 17.82 % Favored : 79.89 % 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: -5.40 (0.21), residues: 258 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.11 (0.16), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.003 PHE F 281 TYR 0.019 0.002 TYR B 266 ARG 0.002 0.001 ARG F 284 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.208 Fit side-chains REVERT: B 276 MET cc_start: 0.8959 (OUTLIER) cc_final: 0.8522 (tmm) REVERT: D 289 TYR cc_start: 0.8104 (m-80) cc_final: 0.7875 (m-80) REVERT: D 294 GLN cc_start: 0.7597 (tm-30) cc_final: 0.6893 (tm-30) REVERT: E 280 ASN cc_start: 0.8846 (t0) cc_final: 0.8269 (t0) REVERT: F 294 GLN cc_start: 0.7714 (tm-30) cc_final: 0.7207 (tm-30) outliers start: 4 outliers final: 1 residues processed: 41 average time/residue: 0.6729 time to fit residues: 28.5262 Evaluate side-chains 38 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 36 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain C residue 259 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 18 optimal weight: 0.1980 chunk 7 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4650 r_free = 0.4650 target = 0.194489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.172095 restraints weight = 2219.216| |-----------------------------------------------------------------------------| r_work (start): 0.4413 rms_B_bonded: 2.10 r_work: 0.4334 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.4241 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.4241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 1950 Z= 0.187 Angle : 0.481 2.661 2592 Z= 0.266 Chirality : 0.036 0.083 174 Planarity : 0.002 0.012 390 Dihedral : 3.973 13.929 294 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.87 % Allowed : 18.39 % Favored : 78.74 % 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: -5.30 (0.22), residues: 258 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.03 (0.17), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.002 PHE C 273 TYR 0.015 0.001 TYR E 266 ARG 0.001 0.000 ARG B 284 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.211 Fit side-chains REVERT: B 276 MET cc_start: 0.8975 (OUTLIER) cc_final: 0.8605 (tmm) REVERT: F 294 GLN cc_start: 0.7682 (tm-30) cc_final: 0.7107 (tm-30) outliers start: 5 outliers final: 1 residues processed: 37 average time/residue: 0.6307 time to fit residues: 24.1975 Evaluate side-chains 37 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain C residue 259 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 4 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 3 optimal weight: 0.2980 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 261 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.183423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.159738 restraints weight = 2304.861| |-----------------------------------------------------------------------------| r_work (start): 0.4300 rms_B_bonded: 2.14 r_work: 0.4214 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.4122 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.4122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 1950 Z= 0.397 Angle : 0.613 4.704 2592 Z= 0.343 Chirality : 0.038 0.097 174 Planarity : 0.004 0.039 390 Dihedral : 4.310 14.623 294 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 1.15 % Allowed : 20.11 % Favored : 78.74 % 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: -5.32 (0.22), residues: 258 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.05 (0.17), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.003 PHE C 281 TYR 0.029 0.002 TYR E 266 ARG 0.002 0.001 ARG D 284 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 37 time to evaluate : 0.206 Fit side-chains REVERT: B 276 MET cc_start: 0.8933 (OUTLIER) cc_final: 0.8570 (tmm) REVERT: D 294 GLN cc_start: 0.7622 (tm-30) cc_final: 0.6859 (tm-30) REVERT: F 294 GLN cc_start: 0.7733 (tm-30) cc_final: 0.7154 (tm-30) outliers start: 2 outliers final: 0 residues processed: 37 average time/residue: 0.7911 time to fit residues: 30.1757 Evaluate side-chains 37 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 36 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 276 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 23 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.4595 r_free = 0.4595 target = 0.188914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.165456 restraints weight = 2330.673| |-----------------------------------------------------------------------------| r_work (start): 0.4351 rms_B_bonded: 2.18 r_work: 0.4270 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.4173 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.4173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 1950 Z= 0.285 Angle : 0.546 3.625 2592 Z= 0.304 Chirality : 0.037 0.085 174 Planarity : 0.003 0.022 390 Dihedral : 4.144 14.102 294 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 1.15 % Allowed : 20.69 % Favored : 78.16 % 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: -5.33 (0.22), residues: 258 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.05 (0.17), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.002 PHE C 281 TYR 0.027 0.002 TYR E 266 ARG 0.001 0.000 ARG F 284 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 41 time to evaluate : 0.210 Fit side-chains REVERT: B 276 MET cc_start: 0.8973 (OUTLIER) cc_final: 0.8584 (tmm) REVERT: D 294 GLN cc_start: 0.7566 (tm-30) cc_final: 0.6793 (tm-30) REVERT: F 294 GLN cc_start: 0.7718 (tm-30) cc_final: 0.7147 (tm-30) outliers start: 2 outliers final: 0 residues processed: 41 average time/residue: 0.7196 time to fit residues: 30.4814 Evaluate side-chains 39 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 276 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 17 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 14 optimal weight: 0.0970 chunk 18 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 261 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.190265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.166738 restraints weight = 2269.010| |-----------------------------------------------------------------------------| r_work (start): 0.4361 rms_B_bonded: 2.17 r_work: 0.4282 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.4185 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.4185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 1950 Z= 0.263 Angle : 0.540 4.229 2592 Z= 0.301 Chirality : 0.037 0.084 174 Planarity : 0.003 0.019 390 Dihedral : 4.067 14.163 294 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 1.15 % Allowed : 21.26 % Favored : 77.59 % 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: -5.30 (0.22), residues: 258 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.03 (0.17), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.002 PHE C 281 TYR 0.031 0.002 TYR E 266 ARG 0.001 0.000 ARG D 284 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 39 time to evaluate : 0.192 Fit side-chains REVERT: B 276 MET cc_start: 0.8969 (OUTLIER) cc_final: 0.8581 (tmm) REVERT: F 294 GLN cc_start: 0.7740 (tm-30) cc_final: 0.7168 (tm-30) outliers start: 2 outliers final: 0 residues processed: 40 average time/residue: 0.6530 time to fit residues: 27.0255 Evaluate side-chains 39 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 276 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 10 optimal weight: 0.0980 chunk 3 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 2 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 16 optimal weight: 0.0030 chunk 6 optimal weight: 0.9980 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 267 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.197843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.175257 restraints weight = 2204.991| |-----------------------------------------------------------------------------| r_work (start): 0.4453 rms_B_bonded: 2.17 r_work: 0.4366 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.4270 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.4270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1950 Z= 0.162 Angle : 0.477 4.061 2592 Z= 0.266 Chirality : 0.036 0.077 174 Planarity : 0.002 0.013 390 Dihedral : 3.825 14.354 294 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.57 % Allowed : 21.84 % Favored : 77.59 % 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: -5.24 (0.23), residues: 258 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.99 (0.17), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.002 PHE A 263 TYR 0.025 0.002 TYR E 266 ARG 0.001 0.000 ARG E 284 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1839.05 seconds wall clock time: 33 minutes 41.09 seconds (2021.09 seconds total)