Starting phenix.real_space_refine on Wed Mar 5 14:39:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bx7_30235/03_2025/7bx7_30235.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bx7_30235/03_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_30235/03_2025/7bx7_30235.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bx7_30235/03_2025/7bx7_30235.map" model { file = "/net/cci-nas-00/data/ceres_data/7bx7_30235/03_2025/7bx7_30235.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bx7_30235/03_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-5624/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: 0.87, per 1000 atoms: 0.46 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: 0.95 Conformation dependent library (CDL) restraints added in 225.6 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: 0.26 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: 0.43 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: 1.22 - 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: 1.170 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 9.740 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: 0.000 Load rotamer database and sin/cos tables:13.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.820 ------------------------------------------------------------------------------- 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 : 0.349 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: 0.8246 time to fit residues: 35.6906 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 : 0.238 ------------------------------------------------------------------------------- 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: 0.4286 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.4196 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.4196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 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 : 0.179 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: 0.7587 (tm-30) cc_final: 0.7366 (tm-30) outliers start: 4 outliers final: 0 residues processed: 49 average time/residue: 0.6724 time to fit residues: 34.0156 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 : 0.219 ------------------------------------------------------------------------------- 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: 0.6980 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: 1.7404 ------------------------------------------------------------------------------- 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 = 0.4508 r_free = 0.4508 target = 0.178394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.155249 restraints weight = 2347.298| |-----------------------------------------------------------------------------| r_work (start): 0.4261 rms_B_bonded: 2.09 r_work: 0.4187 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.4098 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.4098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2163 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= 0.430 Angle : 0.662 5.903 2592 Z= 0.370 Chirality : 0.038 0.090 174 Planarity : 0.005 0.040 390 Dihedral : 4.389 13.271 294 Min Nonbonded Distance : 2.424 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 F 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 : 0.206 Fit side-chains REVERT: C 294 GLN cc_start: 0.7899 (tm-30) cc_final: 0.7382 (tm-30) REVERT: D 289 TYR cc_start: 0.8034 (m-80) cc_final: 0.7766 (m-80) REVERT: D 294 GLN cc_start: 0.7579 (tm-30) cc_final: 0.6875 (tm-30) outliers start: 4 outliers final: 0 residues processed: 42 average time/residue: 0.6831 time to fit residues: 29.6235 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 : 0.194 ------------------------------------------------------------------------------- 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: 2.9990 chunk 6 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 22 optimal weight: 0.3980 chunk 18 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.4602 r_free = 0.4602 target = 0.188726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.166063 restraints weight = 2261.303| |-----------------------------------------------------------------------------| r_work (start): 0.4357 rms_B_bonded: 2.13 r_work: 0.4276 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.4182 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.4182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 1950 Z= 0.234 Angle : 0.519 3.463 2592 Z= 0.288 Chirality : 0.036 0.076 174 Planarity : 0.003 0.013 390 Dihedral : 4.089 13.260 294 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 1.72 % Allowed : 18.97 % 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: -5.48 (0.20), residues: 258 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.17 (0.15), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.002 PHE F 281 TYR 0.011 0.001 TYR E 260 ARG 0.001 0.001 ARG C 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 45 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.201 Fit side-chains REVERT: B 276 MET cc_start: 0.8884 (tmm) cc_final: 0.8573 (tmm) REVERT: D 289 TYR cc_start: 0.8114 (m-80) cc_final: 0.7854 (m-80) REVERT: D 294 GLN cc_start: 0.7546 (tm-30) cc_final: 0.7148 (tm-30) REVERT: F 294 GLN cc_start: 0.7670 (tm-30) cc_final: 0.7265 (tm-30) outliers start: 3 outliers final: 0 residues processed: 42 average time/residue: 0.6919 time to fit residues: 30.0245 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 : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4609 r_free = 0.4609 target = 0.189918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.166753 restraints weight = 2263.547| |-----------------------------------------------------------------------------| r_work (start): 0.4360 rms_B_bonded: 2.13 r_work: 0.4275 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.4180 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.4180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 1950 Z= 0.238 Angle : 0.508 3.350 2592 Z= 0.283 Chirality : 0.036 0.081 174 Planarity : 0.003 0.013 390 Dihedral : 3.992 12.496 294 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 1.72 % Allowed : 17.82 % 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: -5.40 (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 0.011 0.002 PHE C 281 TYR 0.014 0.001 TYR B 266 ARG 0.001 0.001 ARG C 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 41 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.199 Fit side-chains REVERT: B 276 MET cc_start: 0.8883 (OUTLIER) cc_final: 0.8283 (tmm) REVERT: D 294 GLN cc_start: 0.7541 (tm-30) cc_final: 0.6956 (tm-30) REVERT: F 294 GLN cc_start: 0.7651 (tm-30) cc_final: 0.7142 (tm-30) outliers start: 3 outliers final: 1 residues processed: 38 average time/residue: 0.7078 time to fit residues: 27.7597 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 : 0.161 ------------------------------------------------------------------------------- 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: 5.9990 chunk 19 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 = 0.4547 r_free = 0.4547 target = 0.183987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.160511 restraints weight = 2289.042| |-----------------------------------------------------------------------------| r_work (start): 0.4301 rms_B_bonded: 2.15 r_work: 0.4218 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.4124 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.4124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 1950 Z= 0.377 Angle : 0.597 4.623 2592 Z= 0.333 Chirality : 0.038 0.094 174 Planarity : 0.004 0.033 390 Dihedral : 4.274 13.975 294 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 2.87 % Allowed : 17.24 % 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: -5.41 (0.21), residues: 258 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.12 (0.16), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.003 PHE C 281 TYR 0.022 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 46 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.239 Fit side-chains REVERT: B 276 MET cc_start: 0.8932 (OUTLIER) cc_final: 0.8617 (tmm) REVERT: D 294 GLN cc_start: 0.7605 (tm-30) cc_final: 0.6954 (tm-30) REVERT: F 294 GLN cc_start: 0.7708 (tm-30) cc_final: 0.7198 (tm-30) outliers start: 5 outliers final: 1 residues processed: 42 average time/residue: 0.6949 time to fit residues: 30.2346 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 : 0.205 ------------------------------------------------------------------------------- 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: 4.9990 chunk 7 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.4596 r_free = 0.4596 target = 0.189314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.166259 restraints weight = 2234.246| |-----------------------------------------------------------------------------| r_work (start): 0.4357 rms_B_bonded: 2.11 r_work: 0.4272 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.4179 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.4179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 1950 Z= 0.275 Angle : 0.534 3.632 2592 Z= 0.297 Chirality : 0.036 0.091 174 Planarity : 0.003 0.018 390 Dihedral : 4.127 14.592 294 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.30 % Allowed : 18.97 % 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: -5.31 (0.22), residues: 258 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.04 (0.16), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.002 PHE C 281 TYR 0.020 0.002 TYR B 266 ARG 0.002 0.000 ARG C 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 44 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.184 Fit side-chains REVERT: B 276 MET cc_start: 0.8966 (OUTLIER) cc_final: 0.8306 (tmm) REVERT: D 294 GLN cc_start: 0.7570 (tm-30) cc_final: 0.6928 (tm-30) REVERT: F 294 GLN cc_start: 0.7681 (tm-30) cc_final: 0.7107 (tm-30) outliers start: 4 outliers final: 1 residues processed: 41 average time/residue: 0.6662 time to fit residues: 28.2271 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 : 0.196 ------------------------------------------------------------------------------- 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: 4.9990 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 14 optimal weight: 0.0980 chunk 7 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 ASN ** D 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.188227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.164677 restraints weight = 2283.274| |-----------------------------------------------------------------------------| r_work (start): 0.4349 rms_B_bonded: 2.20 r_work: 0.4265 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.4171 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.4171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 1950 Z= 0.298 Angle : 0.552 3.710 2592 Z= 0.308 Chirality : 0.036 0.090 174 Planarity : 0.003 0.022 390 Dihedral : 4.159 14.260 294 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 1.72 % Allowed : 19.54 % 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: -5.31 (0.22), residues: 258 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.04 (0.17), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.002 PHE E 281 TYR 0.024 0.002 TYR B 266 ARG 0.001 0.000 ARG F 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 41 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.163 Fit side-chains REVERT: B 276 MET cc_start: 0.8951 (OUTLIER) cc_final: 0.8288 (tmm) REVERT: D 294 GLN cc_start: 0.7553 (tm-30) cc_final: 0.6899 (tm-30) REVERT: F 294 GLN cc_start: 0.7702 (tm-30) cc_final: 0.7126 (tm-30) outliers start: 3 outliers final: 2 residues processed: 39 average time/residue: 0.6922 time to fit residues: 27.8936 Evaluate side-chains 41 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain E 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: 1.9990 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN ** D 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.181179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.157033 restraints weight = 2386.090| |-----------------------------------------------------------------------------| r_work (start): 0.4277 rms_B_bonded: 2.19 r_work: 0.4196 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.4106 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.4106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.047 1950 Z= 0.490 Angle : 0.670 5.344 2592 Z= 0.375 Chirality : 0.038 0.098 174 Planarity : 0.005 0.050 390 Dihedral : 4.459 14.850 294 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 2.30 % Allowed : 18.97 % 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: -5.36 (0.22), residues: 258 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.08 (0.17), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.014 0.003 PHE C 281 TYR 0.034 0.003 TYR E 266 ARG 0.003 0.001 ARG D 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 41 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.212 Fit side-chains REVERT: B 276 MET cc_start: 0.8940 (OUTLIER) cc_final: 0.8274 (tmm) REVERT: D 294 GLN cc_start: 0.7665 (tm-30) cc_final: 0.6884 (tm-30) REVERT: F 294 GLN cc_start: 0.7772 (tm-30) cc_final: 0.7188 (tm-30) outliers start: 4 outliers final: 2 residues processed: 39 average time/residue: 0.6713 time to fit residues: 27.0742 Evaluate side-chains 38 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain E 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: 0.5980 chunk 0 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 261 ASN D 267 ASN ** D 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.191732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.168488 restraints weight = 2285.141| |-----------------------------------------------------------------------------| r_work (start): 0.4380 rms_B_bonded: 2.20 r_work: 0.4299 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.4201 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.4201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 1950 Z= 0.238 Angle : 0.535 5.233 2592 Z= 0.297 Chirality : 0.037 0.083 174 Planarity : 0.003 0.013 390 Dihedral : 4.070 14.002 294 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 1.72 % Allowed : 20.11 % 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: -5.32 (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 0.010 0.002 PHE E 281 TYR 0.027 0.002 TYR E 266 ARG 0.001 0.000 ARG C 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 44 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.198 Fit side-chains REVERT: B 276 MET cc_start: 0.8966 (OUTLIER) cc_final: 0.8587 (tmm) REVERT: D 294 GLN cc_start: 0.7556 (tm-30) cc_final: 0.6772 (tm-30) REVERT: F 294 GLN cc_start: 0.7749 (tm-30) cc_final: 0.7178 (tm-30) outliers start: 3 outliers final: 1 residues processed: 41 average time/residue: 0.6306 time to fit residues: 26.7701 Evaluate side-chains 42 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain C residue 259 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 10 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 4 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.183446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.159172 restraints weight = 2259.232| |-----------------------------------------------------------------------------| r_work (start): 0.4293 rms_B_bonded: 2.19 r_work: 0.4211 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.4115 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 1950 Z= 0.417 Angle : 0.634 4.982 2592 Z= 0.355 Chirality : 0.038 0.094 174 Planarity : 0.005 0.043 390 Dihedral : 4.356 14.681 294 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % 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: -5.36 (0.22), residues: 258 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.08 (0.17), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.014 0.003 PHE C 281 TYR 0.040 0.003 TYR E 266 ARG 0.002 0.001 ARG D 284 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1868.95 seconds wall clock time: 32 minutes 52.83 seconds (1972.83 seconds total)