Starting phenix.real_space_refine on Tue Mar 3 10:47:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bx7_30235/03_2026/7bx7_30235.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bx7_30235/03_2026/7bx7_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 { model { file = "/net/cci-nas-00/data/ceres_data/7bx7_30235/03_2026/7bx7_30235.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bx7_30235/03_2026/7bx7_30235.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7bx7_30235/03_2026/7bx7_30235.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bx7_30235/03_2026/7bx7_30235.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: B, C, D, E, F Time building chain proxies: 0.21, per 1000 atoms: 0.11 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: 0.08 Conformation dependent library (CDL) restraints added in 49.1 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: 0.04 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: 0.13 Time building geometry restraints manager: 0.10 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' 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: 1.270 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: 0.010 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 2.350 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:4.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.550 ------------------------------------------------------------------------------- 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= 0.454 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 : 15.05 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.009 0.004 ARG C 284 TYR 0.009 0.002 TYR D 260 PHE 0.030 0.005 PHE B 273 Details of bonding type rmsd covalent geometry : bond 0.00937 ( 1950) covalent geometry : angle 0.84056 ( 2592) hydrogen bonds : bond 0.12149 ( 44) hydrogen bonds : angle 7.37013 ( 132) *********************** 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 : 0.039 Fit side-chains REVERT: A 276 MET cc_start: 0.8655 (tpt) cc_final: 0.8296 (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: 0.2292 time to fit residues: 9.9088 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 : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 12 optimal weight: 0.4980 chunk 13 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.4622 r_free = 0.4622 target = 0.190872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.169371 restraints weight = 2364.706| |-----------------------------------------------------------------------------| r_work (start): 0.4401 rms_B_bonded: 2.15 r_work: 0.4323 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.4231 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.4231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2092 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= 0.151 Angle : 0.517 3.977 2592 Z= 0.288 Chirality : 0.037 0.076 174 Planarity : 0.003 0.015 390 Dihedral : 4.066 13.924 294 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.72 % Allowed : 16.67 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.54 (0.19), 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 ARG 0.002 0.001 ARG C 284 TYR 0.009 0.001 TYR F 260 PHE 0.011 0.002 PHE C 281 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 1950) covalent geometry : angle 0.51701 ( 2592) hydrogen bonds : bond 0.01749 ( 44) hydrogen bonds : angle 5.17202 ( 132) *********************** 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 52 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.069 Fit side-chains REVERT: D 289 TYR cc_start: 0.8037 (m-80) cc_final: 0.7817 (m-80) REVERT: D 294 GLN cc_start: 0.7592 (tm-30) cc_final: 0.7368 (tm-30) outliers start: 3 outliers final: 0 residues processed: 49 average time/residue: 0.3125 time to fit residues: 15.8064 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 : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 12 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 11 optimal weight: 0.0030 chunk 3 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 overall best weight: 2.1796 ------------------------------------------------------------------------------- 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 = 0.4490 r_free = 0.4490 target = 0.175911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.152452 restraints weight = 2415.349| |-----------------------------------------------------------------------------| r_work (start): 0.4225 rms_B_bonded: 2.12 r_work: 0.4148 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.4056 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.4056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.051 1950 Z= 0.374 Angle : 0.709 6.369 2592 Z= 0.397 Chirality : 0.039 0.099 174 Planarity : 0.006 0.052 390 Dihedral : 4.573 12.990 294 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.34 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.54 (0.20), residues: 258 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.21 (0.15), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 284 TYR 0.016 0.002 TYR E 260 PHE 0.020 0.004 PHE F 281 Details of bonding type rmsd covalent geometry : bond 0.00812 ( 1950) covalent geometry : angle 0.70908 ( 2592) hydrogen bonds : bond 0.01666 ( 44) hydrogen bonds : angle 4.93896 ( 132) *********************** 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 42 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.070 Fit side-chains REVERT: C 294 GLN cc_start: 0.7891 (tm-30) cc_final: 0.7385 (tm-30) REVERT: D 289 TYR cc_start: 0.8070 (m-80) cc_final: 0.7811 (m-80) REVERT: D 294 GLN cc_start: 0.7540 (tm-30) cc_final: 0.6855 (tm-30) outliers start: 4 outliers final: 1 residues processed: 38 average time/residue: 0.3844 time to fit residues: 15.0006 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 : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 259 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 16 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 3 optimal weight: 0.2980 chunk 12 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 = 0.4615 r_free = 0.4615 target = 0.189949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.167531 restraints weight = 2272.051| |-----------------------------------------------------------------------------| r_work (start): 0.4367 rms_B_bonded: 2.11 r_work: 0.4291 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.4194 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.4194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2735 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= 0.151 Angle : 0.503 3.300 2592 Z= 0.279 Chirality : 0.036 0.074 174 Planarity : 0.003 0.013 390 Dihedral : 4.056 12.990 294 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.001 0.000 ARG F 284 TYR 0.010 0.001 TYR E 266 PHE 0.010 0.002 PHE F 281 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 1950) covalent geometry : angle 0.50275 ( 2592) hydrogen bonds : bond 0.01239 ( 44) hydrogen bonds : angle 4.80544 ( 132) *********************** 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: 4 poor density : 41 time to evaluate : 0.067 Fit side-chains REVERT: B 276 MET cc_start: 0.8901 (OUTLIER) cc_final: 0.8373 (tmm) REVERT: C 294 GLN cc_start: 0.7892 (tm-30) cc_final: 0.7684 (tm-30) REVERT: D 289 TYR cc_start: 0.8082 (m-80) cc_final: 0.7825 (m-80) REVERT: D 294 GLN cc_start: 0.7613 (tm-30) cc_final: 0.7204 (tm-30) outliers start: 4 outliers final: 0 residues processed: 41 average time/residue: 0.2831 time to fit residues: 12.0170 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 : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 276 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 8 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 11 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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 = 0.4523 r_free = 0.4523 target = 0.180204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.156787 restraints weight = 2309.006| |-----------------------------------------------------------------------------| r_work (start): 0.4265 rms_B_bonded: 2.12 r_work: 0.4187 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.4094 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.4094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2664 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= 0.289 Angle : 0.622 5.151 2592 Z= 0.347 Chirality : 0.038 0.088 174 Planarity : 0.004 0.039 390 Dihedral : 4.325 13.652 294 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.002 0.001 ARG B 284 TYR 0.019 0.002 TYR B 266 PHE 0.014 0.003 PHE C 281 Details of bonding type rmsd covalent geometry : bond 0.00624 ( 1950) covalent geometry : angle 0.62184 ( 2592) hydrogen bonds : bond 0.01526 ( 44) hydrogen bonds : angle 4.89170 ( 132) *********************** 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 44 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.085 Fit side-chains REVERT: B 276 MET cc_start: 0.8934 (OUTLIER) cc_final: 0.8551 (tmm) REVERT: D 289 TYR cc_start: 0.8099 (m-80) cc_final: 0.7856 (m-80) REVERT: D 294 GLN cc_start: 0.7635 (tm-30) cc_final: 0.6914 (tm-30) REVERT: F 294 GLN cc_start: 0.7701 (tm-30) cc_final: 0.7191 (tm-30) outliers start: 5 outliers final: 0 residues processed: 39 average time/residue: 0.3797 time to fit residues: 15.2300 Evaluate side-chains 38 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 276 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 15 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 9 optimal weight: 0.4980 chunk 19 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4623 r_free = 0.4623 target = 0.191326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.168780 restraints weight = 2255.376| |-----------------------------------------------------------------------------| r_work (start): 0.4381 rms_B_bonded: 2.11 r_work: 0.4302 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.4208 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.4208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 1950 Z= 0.154 Angle : 0.496 2.934 2592 Z= 0.275 Chirality : 0.036 0.085 174 Planarity : 0.002 0.014 390 Dihedral : 4.032 13.716 294 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 1.15 % Allowed : 19.54 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.39 (0.21), residues: 258 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.10 (0.16), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 284 TYR 0.014 0.001 TYR B 266 PHE 0.012 0.002 PHE C 273 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 1950) covalent geometry : angle 0.49610 ( 2592) hydrogen bonds : bond 0.01281 ( 44) hydrogen bonds : angle 4.91928 ( 132) *********************** 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 42 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.068 Fit side-chains REVERT: B 276 MET cc_start: 0.8955 (OUTLIER) cc_final: 0.8576 (tmm) REVERT: D 289 TYR cc_start: 0.8082 (m-80) cc_final: 0.7837 (m-80) REVERT: D 294 GLN cc_start: 0.7634 (tm-30) cc_final: 0.6983 (tm-30) REVERT: F 294 GLN cc_start: 0.7708 (tm-30) cc_final: 0.7207 (tm-30) outliers start: 2 outliers final: 0 residues processed: 40 average time/residue: 0.3082 time to fit residues: 12.7403 Evaluate side-chains 36 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 35 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 276 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 22 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.4604 r_free = 0.4604 target = 0.189288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.166344 restraints weight = 2261.313| |-----------------------------------------------------------------------------| r_work (start): 0.4358 rms_B_bonded: 2.13 r_work: 0.4278 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.4186 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.4186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2931 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= 0.183 Angle : 0.519 3.547 2592 Z= 0.288 Chirality : 0.036 0.085 174 Planarity : 0.003 0.016 390 Dihedral : 3.979 13.153 294 Min Nonbonded Distance : 2.486 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.35 (0.21), residues: 258 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.07 (0.16), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 284 TYR 0.021 0.002 TYR E 266 PHE 0.011 0.002 PHE C 281 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 1950) covalent geometry : angle 0.51919 ( 2592) hydrogen bonds : bond 0.01257 ( 44) hydrogen bonds : angle 4.87735 ( 132) *********************** 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 42 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.069 Fit side-chains REVERT: B 276 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.8552 (tmm) REVERT: D 294 GLN cc_start: 0.7658 (tm-30) cc_final: 0.6978 (tm-30) REVERT: F 294 GLN cc_start: 0.7704 (tm-30) cc_final: 0.7125 (tm-30) outliers start: 3 outliers final: 0 residues processed: 40 average time/residue: 0.3235 time to fit residues: 13.3440 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 : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 276 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 13 optimal weight: 3.9990 chunk 2 optimal weight: 0.1980 chunk 18 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.189397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.166087 restraints weight = 2248.523| |-----------------------------------------------------------------------------| r_work (start): 0.4358 rms_B_bonded: 2.14 r_work: 0.4274 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.4182 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.4182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 1950 Z= 0.202 Angle : 0.543 3.688 2592 Z= 0.302 Chirality : 0.037 0.093 174 Planarity : 0.003 0.020 390 Dihedral : 4.036 14.021 294 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.34 (0.22), residues: 258 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.06 (0.17), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 284 TYR 0.025 0.002 TYR B 266 PHE 0.011 0.002 PHE C 281 Details of bonding type rmsd covalent geometry : bond 0.00431 ( 1950) covalent geometry : angle 0.54264 ( 2592) hydrogen bonds : bond 0.01406 ( 44) hydrogen bonds : angle 5.03307 ( 132) *********************** 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 45 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 43 time to evaluate : 0.067 Fit side-chains REVERT: B 276 MET cc_start: 0.8954 (OUTLIER) cc_final: 0.8563 (tmm) REVERT: F 294 GLN cc_start: 0.7729 (tm-30) cc_final: 0.7148 (tm-30) outliers start: 2 outliers final: 0 residues processed: 43 average time/residue: 0.2809 time to fit residues: 12.4916 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 : 0.064 ------------------------------------------------------------------------------- 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 5 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 23 optimal weight: 0.1980 chunk 10 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4636 r_free = 0.4636 target = 0.192819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.169464 restraints weight = 2249.660| |-----------------------------------------------------------------------------| r_work (start): 0.4389 rms_B_bonded: 2.17 r_work: 0.4304 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.4207 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.4207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.3149 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= 0.167 Angle : 0.510 3.093 2592 Z= 0.284 Chirality : 0.036 0.087 174 Planarity : 0.003 0.014 390 Dihedral : 3.900 13.628 294 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.001 0.000 ARG F 284 TYR 0.025 0.002 TYR B 266 PHE 0.010 0.002 PHE C 281 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 1950) covalent geometry : angle 0.51017 ( 2592) hydrogen bonds : bond 0.01379 ( 44) hydrogen bonds : angle 5.02909 ( 132) *********************** 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 39 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 37 time to evaluate : 0.070 Fit side-chains REVERT: B 276 MET cc_start: 0.8964 (OUTLIER) cc_final: 0.8359 (tmm) REVERT: F 294 GLN cc_start: 0.7713 (tm-30) cc_final: 0.7133 (tm-30) outliers start: 2 outliers final: 0 residues processed: 38 average time/residue: 0.2764 time to fit residues: 10.8715 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 : 0.072 ------------------------------------------------------------------------------- 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: 2.9990 chunk 23 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 22 optimal weight: 0.0470 overall best weight: 0.9484 ------------------------------------------------------------------------------- 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 = 0.4624 r_free = 0.4624 target = 0.191536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.167902 restraints weight = 2267.171| |-----------------------------------------------------------------------------| r_work (start): 0.4376 rms_B_bonded: 2.18 r_work: 0.4292 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.4196 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.4196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 1950 Z= 0.192 Angle : 0.542 3.532 2592 Z= 0.302 Chirality : 0.037 0.089 174 Planarity : 0.003 0.018 390 Dihedral : 3.954 13.437 294 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.05 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.30 (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 ARG 0.001 0.000 ARG F 284 TYR 0.033 0.002 TYR E 266 PHE 0.010 0.002 PHE C 281 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 1950) covalent geometry : angle 0.54162 ( 2592) hydrogen bonds : bond 0.01480 ( 44) hydrogen bonds : angle 5.07756 ( 132) ********************** 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 : 0.047 Fit side-chains REVERT: B 276 MET cc_start: 0.8943 (OUTLIER) cc_final: 0.8591 (tmm) REVERT: F 294 GLN cc_start: 0.7723 (tm-30) cc_final: 0.7140 (tm-30) outliers start: 2 outliers final: 0 residues processed: 39 average time/residue: 0.2836 time to fit residues: 11.4365 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 : 0.062 ------------------------------------------------------------------------------- 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: 1.9990 chunk 2 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 12 optimal weight: 0.0040 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 overall best weight: 0.7192 ------------------------------------------------------------------------------- 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 = 0.4653 r_free = 0.4653 target = 0.195395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.172070 restraints weight = 2279.018| |-----------------------------------------------------------------------------| r_work (start): 0.4411 rms_B_bonded: 2.20 r_work: 0.4327 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.4234 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.4234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 1950 Z= 0.157 Angle : 0.513 4.148 2592 Z= 0.285 Chirality : 0.037 0.084 174 Planarity : 0.003 0.014 390 Dihedral : 3.821 12.979 294 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.57 % Allowed : 21.26 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.27 (0.23), residues: 258 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.01 (0.17), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 284 TYR 0.032 0.002 TYR E 266 PHE 0.009 0.002 PHE C 281 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 1950) covalent geometry : angle 0.51297 ( 2592) hydrogen bonds : bond 0.01496 ( 44) hydrogen bonds : angle 5.05958 ( 132) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 910.92 seconds wall clock time: 16 minutes 57.46 seconds (1017.46 seconds total)