Starting phenix.real_space_refine on Fri Aug 22 12:40:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8feh_29027/08_2025/8feh_29027.cif Found real_map, /net/cci-nas-00/data/ceres_data/8feh_29027/08_2025/8feh_29027.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8feh_29027/08_2025/8feh_29027.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8feh_29027/08_2025/8feh_29027.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8feh_29027/08_2025/8feh_29027.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8feh_29027/08_2025/8feh_29027.map" } resolution = 3.28 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= -0.001 sd= 0.050 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 4 5.16 5 C 1235 2.51 5 N 357 2.21 5 O 397 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 1993 Number of models: 1 Model: "" Number of chains: 1 Chain: "D" Number of atoms: 1993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 1993 Classifications: {'peptide': 268} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 16, 'TRANS': 251} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ASN:plan1': 1, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 17 Time building chain proxies: 0.76, per 1000 atoms: 0.38 Number of scatterers: 1993 At special positions: 0 Unit cell: (66.69, 89.775, 53.01, 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 4 16.00 O 397 8.00 N 357 7.00 C 1235 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: 0.15 Conformation dependent library (CDL) restraints added in 80.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 504 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 4 sheets defined 20.9% alpha, 26.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'D' and resid 101 through 117 removed outlier: 3.540A pdb=" N ARG D 105 " --> pdb=" O THR D 101 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA D 117 " --> pdb=" O ALA D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 126 removed outlier: 3.523A pdb=" N ASP D 126 " --> pdb=" O ILE D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 181 removed outlier: 3.846A pdb=" N GLU D 181 " --> pdb=" O PRO D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 252 removed outlier: 3.518A pdb=" N VAL D 244 " --> pdb=" O GLU D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 262 removed outlier: 3.706A pdb=" N ASP D 259 " --> pdb=" O PRO D 255 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA D 260 " --> pdb=" O LEU D 256 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 6 through 11 removed outlier: 5.920A pdb=" N GLN D 17 " --> pdb=" O ASN D 10 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N SER D 34 " --> pdb=" O ARG D 24 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N VAL D 26 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N VAL D 32 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA D 226 " --> pdb=" O ILE D 204 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 71 through 73 removed outlier: 6.940A pdb=" N THR D 72 " --> pdb=" O THR D 85 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 142 through 147 removed outlier: 5.597A pdb=" N GLN D 153 " --> pdb=" O ASN D 146 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 208 through 209 removed outlier: 3.652A pdb=" N THR D 208 " --> pdb=" O THR D 221 " (cutoff:3.500A) 82 hydrogen bonds defined for protein. 225 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: 0.29 Time building geometry restraints manager: 0.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 654 1.34 - 1.46: 347 1.46 - 1.58: 1016 1.58 - 1.70: 0 1.70 - 1.82: 4 Bond restraints: 2021 Sorted by residual: bond pdb=" N VAL D 202 " pdb=" CA VAL D 202 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.19e-02 7.06e+03 1.07e+01 bond pdb=" N GLN D 223 " pdb=" CA GLN D 223 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.23e-02 6.61e+03 1.01e+01 bond pdb=" N THR D 208 " pdb=" CA THR D 208 " ideal model delta sigma weight residual 1.455 1.495 -0.039 1.25e-02 6.40e+03 9.98e+00 bond pdb=" N ARG D 222 " pdb=" CA ARG D 222 " ideal model delta sigma weight residual 1.457 1.498 -0.040 1.29e-02 6.01e+03 9.78e+00 bond pdb=" N VAL D 220 " pdb=" CA VAL D 220 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.22e-02 6.72e+03 9.76e+00 ... (remaining 2016 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 2530 1.71 - 3.41: 180 3.41 - 5.12: 39 5.12 - 6.82: 5 6.82 - 8.53: 2 Bond angle restraints: 2756 Sorted by residual: angle pdb=" C ALA D 76 " pdb=" N ASN D 77 " pdb=" CA ASN D 77 " ideal model delta sigma weight residual 120.82 129.35 -8.53 1.50e+00 4.44e-01 3.23e+01 angle pdb=" CA ASN D 206 " pdb=" C ASN D 206 " pdb=" N PRO D 207 " ideal model delta sigma weight residual 117.59 121.84 -4.25 1.03e+00 9.43e-01 1.70e+01 angle pdb=" CA GLN D 234 " pdb=" C GLN D 234 " pdb=" O GLN D 234 " ideal model delta sigma weight residual 121.87 117.25 4.62 1.16e+00 7.43e-01 1.59e+01 angle pdb=" C ILE D 204 " pdb=" N GLN D 205 " pdb=" CA GLN D 205 " ideal model delta sigma weight residual 121.02 115.35 5.67 1.48e+00 4.57e-01 1.47e+01 angle pdb=" C GLY D 145 " pdb=" N ASN D 146 " pdb=" CA ASN D 146 " ideal model delta sigma weight residual 121.54 128.84 -7.30 1.91e+00 2.74e-01 1.46e+01 ... (remaining 2751 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 15.84: 1120 15.84 - 31.68: 100 31.68 - 47.51: 25 47.51 - 63.35: 3 63.35 - 79.18: 5 Dihedral angle restraints: 1253 sinusoidal: 475 harmonic: 778 Sorted by residual: dihedral pdb=" CA LYS D 182 " pdb=" C LYS D 182 " pdb=" N ARG D 183 " pdb=" CA ARG D 183 " ideal model delta harmonic sigma weight residual -180.00 -163.44 -16.56 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA ILE D 122 " pdb=" C ILE D 122 " pdb=" N ASP D 123 " pdb=" CA ASP D 123 " ideal model delta harmonic sigma weight residual 180.00 164.04 15.96 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" CG ARG D 222 " pdb=" CD ARG D 222 " pdb=" NE ARG D 222 " pdb=" CZ ARG D 222 " ideal model delta sinusoidal sigma weight residual -180.00 -137.90 -42.10 2 1.50e+01 4.44e-03 9.59e+00 ... (remaining 1250 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 261 0.075 - 0.151: 62 0.151 - 0.226: 8 0.226 - 0.301: 2 0.301 - 0.376: 1 Chirality restraints: 334 Sorted by residual: chirality pdb=" CA ILE D 204 " pdb=" N ILE D 204 " pdb=" C ILE D 204 " pdb=" CB ILE D 204 " both_signs ideal model delta sigma weight residual False 2.43 2.81 -0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" CA VAL D 228 " pdb=" N VAL D 228 " pdb=" C VAL D 228 " pdb=" CB VAL D 228 " both_signs ideal model delta sigma weight residual False 2.44 2.71 -0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CB ILE D 68 " pdb=" CA ILE D 68 " pdb=" CG1 ILE D 68 " pdb=" CG2 ILE D 68 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 331 not shown) Planarity restraints: 366 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS D 203 " 0.012 2.00e-02 2.50e+03 2.52e-02 6.35e+00 pdb=" C LYS D 203 " -0.044 2.00e-02 2.50e+03 pdb=" O LYS D 203 " 0.017 2.00e-02 2.50e+03 pdb=" N ILE D 204 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 9 " 0.009 2.00e-02 2.50e+03 1.87e-02 3.50e+00 pdb=" C GLY D 9 " -0.032 2.00e-02 2.50e+03 pdb=" O GLY D 9 " 0.012 2.00e-02 2.50e+03 pdb=" N ASN D 10 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL D 41 " -0.026 5.00e-02 4.00e+02 3.88e-02 2.41e+00 pdb=" N PRO D 42 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO D 42 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 42 " -0.022 5.00e-02 4.00e+02 ... (remaining 363 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 644 2.83 - 3.35: 1828 3.35 - 3.87: 3322 3.87 - 4.38: 3580 4.38 - 4.90: 6222 Nonbonded interactions: 15596 Sorted by model distance: nonbonded pdb=" O THR D 97 " pdb=" OG SER D 100 " model vdw 2.317 3.040 nonbonded pdb=" OG1 THR D 101 " pdb=" OE1 GLU D 104 " model vdw 2.320 3.040 nonbonded pdb=" CG1 VAL D 220 " pdb=" OE1 GLN D 223 " model vdw 2.369 3.460 nonbonded pdb=" O ARG D 57 " pdb=" NZ LYS D 60 " model vdw 2.398 3.120 nonbonded pdb=" O SER D 236 " pdb=" NH1 ARG D 241 " model vdw 2.398 3.120 ... (remaining 15591 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 8.430 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 4.270 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.040 2021 Z= 0.462 Angle : 1.022 8.528 2756 Z= 0.650 Chirality : 0.067 0.376 334 Planarity : 0.006 0.039 366 Dihedral : 14.169 79.183 749 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 1.83 % Allowed : 10.55 % Favored : 87.61 % 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 aren not related in a simple way. whole: -3.45 (0.43), residues: 266 helix: -3.25 (0.50), residues: 41 sheet: -1.30 (0.51), residues: 97 loop : -2.73 (0.42), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 245 TYR 0.010 0.002 TYR D 198 PHE 0.009 0.002 PHE D 230 Details of bonding type rmsd covalent geometry : bond 0.00790 ( 2021) covalent geometry : angle 1.02199 ( 2756) hydrogen bonds : bond 0.25938 ( 82) hydrogen bonds : angle 9.52295 ( 225) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.086 Fit side-chains REVERT: D 91 ASP cc_start: 0.6774 (t70) cc_final: 0.6401 (t0) outliers start: 4 outliers final: 0 residues processed: 33 average time/residue: 0.0735 time to fit residues: 2.8156 Evaluate side-chains 13 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 12 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 17 GLN ** D 173 GLN ** 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 = 0.3319 r_free = 0.3319 target = 0.043491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.035530 restraints weight = 12908.536| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 5.00 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.4670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2021 Z= 0.211 Angle : 0.710 6.371 2756 Z= 0.378 Chirality : 0.048 0.144 334 Planarity : 0.005 0.050 366 Dihedral : 4.544 22.329 289 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.75 % Allowed : 16.06 % Favored : 81.19 % 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 aren not related in a simple way. whole: -2.89 (0.44), residues: 266 helix: -1.66 (0.64), residues: 52 sheet: -1.34 (0.49), residues: 99 loop : -2.47 (0.43), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 193 TYR 0.010 0.002 TYR D 89 PHE 0.009 0.002 PHE D 94 Details of bonding type rmsd covalent geometry : bond 0.00436 ( 2021) covalent geometry : angle 0.70970 ( 2756) hydrogen bonds : bond 0.03659 ( 82) hydrogen bonds : angle 5.86983 ( 225) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 11 time to evaluate : 0.082 Fit side-chains REVERT: D 87 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.8148 (mm-40) outliers start: 6 outliers final: 1 residues processed: 16 average time/residue: 0.0639 time to fit residues: 1.2911 Evaluate side-chains 10 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 8 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 87 GLN Chi-restraints excluded: chain D residue 115 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 4 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 chunk 11 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 30.0000 chunk 18 optimal weight: 9.9990 chunk 12 optimal weight: 0.9980 chunk 14 optimal weight: 0.3980 chunk 2 optimal weight: 9.9990 overall best weight: 4.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 205 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.040783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.032993 restraints weight = 13310.559| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 4.88 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.7604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 2021 Z= 0.252 Angle : 0.675 6.182 2756 Z= 0.363 Chirality : 0.046 0.132 334 Planarity : 0.005 0.052 366 Dihedral : 4.462 21.070 289 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.83 % Allowed : 18.81 % Favored : 79.36 % 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 aren not related in a simple way. whole: -2.40 (0.48), residues: 266 helix: -0.89 (0.68), residues: 52 sheet: -1.09 (0.51), residues: 101 loop : -2.33 (0.50), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 109 TYR 0.007 0.002 TYR D 99 PHE 0.006 0.001 PHE D 96 Details of bonding type rmsd covalent geometry : bond 0.00542 ( 2021) covalent geometry : angle 0.67499 ( 2756) hydrogen bonds : bond 0.04188 ( 82) hydrogen bonds : angle 5.72398 ( 225) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 9 time to evaluate : 0.089 Fit side-chains REVERT: D 87 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7972 (mm110) outliers start: 4 outliers final: 3 residues processed: 13 average time/residue: 0.0309 time to fit residues: 0.6401 Evaluate side-chains 8 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 4 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 87 GLN Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 229 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 11 optimal weight: 8.9990 chunk 15 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 7 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 = 0.3218 r_free = 0.3218 target = 0.040583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.033070 restraints weight = 13201.112| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 4.81 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.8052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2021 Z= 0.168 Angle : 0.575 5.965 2756 Z= 0.309 Chirality : 0.045 0.163 334 Planarity : 0.003 0.016 366 Dihedral : 3.956 19.222 289 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.83 % Allowed : 22.02 % Favored : 76.15 % 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 aren not related in a simple way. whole: -2.12 (0.49), residues: 266 helix: -0.37 (0.72), residues: 52 sheet: -1.01 (0.52), residues: 100 loop : -2.20 (0.50), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 245 TYR 0.004 0.001 TYR D 99 PHE 0.009 0.001 PHE D 94 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 2021) covalent geometry : angle 0.57547 ( 2756) hydrogen bonds : bond 0.03345 ( 82) hydrogen bonds : angle 5.23465 ( 225) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 8 time to evaluate : 0.089 Fit side-chains REVERT: D 247 GLU cc_start: 0.9545 (pt0) cc_final: 0.9246 (pt0) outliers start: 4 outliers final: 2 residues processed: 12 average time/residue: 0.0332 time to fit residues: 0.6287 Evaluate side-chains 7 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 5 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 168 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 23 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 21 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 13 optimal weight: 0.0870 overall best weight: 1.7564 ------------------------------------------------------------------------------- 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 = 0.3255 r_free = 0.3255 target = 0.041198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.033754 restraints weight = 12733.774| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 4.86 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.8299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2021 Z= 0.134 Angle : 0.547 5.636 2756 Z= 0.296 Chirality : 0.044 0.151 334 Planarity : 0.003 0.014 366 Dihedral : 3.810 18.734 289 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.92 % Allowed : 24.77 % Favored : 74.31 % 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 aren not related in a simple way. whole: -1.91 (0.49), residues: 266 helix: -0.05 (0.73), residues: 51 sheet: -0.83 (0.53), residues: 99 loop : -2.20 (0.50), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 245 TYR 0.011 0.001 TYR D 89 PHE 0.008 0.001 PHE D 94 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 2021) covalent geometry : angle 0.54675 ( 2756) hydrogen bonds : bond 0.03250 ( 82) hydrogen bonds : angle 5.05572 ( 225) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 9 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 7 time to evaluate : 0.082 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 9 average time/residue: 0.0287 time to fit residues: 0.4563 Evaluate side-chains 5 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 4 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 5 optimal weight: 0.6980 chunk 23 optimal weight: 7.9990 chunk 14 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 4 optimal weight: 0.0470 chunk 7 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 overall best weight: 1.5484 ------------------------------------------------------------------------------- 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 = 0.3248 r_free = 0.3248 target = 0.041114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.033643 restraints weight = 12810.871| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 4.86 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.8442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2021 Z= 0.126 Angle : 0.545 5.718 2756 Z= 0.295 Chirality : 0.044 0.146 334 Planarity : 0.003 0.015 366 Dihedral : 3.700 18.850 289 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.92 % Allowed : 24.77 % Favored : 74.31 % 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 aren not related in a simple way. whole: -1.79 (0.50), residues: 266 helix: 0.05 (0.73), residues: 51 sheet: -0.73 (0.54), residues: 99 loop : -2.13 (0.50), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 245 TYR 0.003 0.001 TYR D 99 PHE 0.008 0.001 PHE D 94 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 2021) covalent geometry : angle 0.54501 ( 2756) hydrogen bonds : bond 0.03127 ( 82) hydrogen bonds : angle 5.07373 ( 225) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 7 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 5 time to evaluate : 0.081 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 7 average time/residue: 0.0304 time to fit residues: 0.4128 Evaluate side-chains 6 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 4 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 168 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 23 optimal weight: 7.9990 chunk 18 optimal weight: 9.9990 chunk 5 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 11 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 13 optimal weight: 8.9990 chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 17 optimal weight: 0.4980 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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 = 0.3254 r_free = 0.3254 target = 0.041245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.033849 restraints weight = 12756.457| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 4.87 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.8633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2021 Z= 0.116 Angle : 0.524 5.513 2756 Z= 0.284 Chirality : 0.044 0.138 334 Planarity : 0.003 0.016 366 Dihedral : 3.559 18.345 289 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.38 % Allowed : 24.31 % Favored : 74.31 % 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 aren not related in a simple way. whole: -1.63 (0.50), residues: 266 helix: 0.22 (0.74), residues: 51 sheet: -0.64 (0.55), residues: 98 loop : -2.04 (0.50), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 245 TYR 0.012 0.001 TYR D 89 PHE 0.009 0.001 PHE D 94 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 2021) covalent geometry : angle 0.52447 ( 2756) hydrogen bonds : bond 0.02950 ( 82) hydrogen bonds : angle 4.90613 ( 225) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 8 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 5 time to evaluate : 0.083 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 8 average time/residue: 0.0288 time to fit residues: 0.4226 Evaluate side-chains 5 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 4 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 3 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 21 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 14 optimal weight: 10.0000 chunk 4 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 = 0.3241 r_free = 0.3241 target = 0.040940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.033437 restraints weight = 13045.621| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 4.93 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.8706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2021 Z= 0.118 Angle : 0.535 5.576 2756 Z= 0.293 Chirality : 0.044 0.149 334 Planarity : 0.003 0.024 366 Dihedral : 3.639 18.436 289 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.92 % Allowed : 23.85 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.52 (0.50), residues: 266 helix: 0.29 (0.74), residues: 51 sheet: -0.56 (0.55), residues: 98 loop : -1.98 (0.50), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 245 TYR 0.003 0.001 TYR D 225 PHE 0.008 0.001 PHE D 94 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 2021) covalent geometry : angle 0.53476 ( 2756) hydrogen bonds : bond 0.02905 ( 82) hydrogen bonds : angle 4.87587 ( 225) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 8 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 6 time to evaluate : 0.086 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 8 average time/residue: 0.0633 time to fit residues: 0.7026 Evaluate side-chains 8 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 6 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 85 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 17 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 3 optimal weight: 8.9990 chunk 13 optimal weight: 0.0970 chunk 21 optimal weight: 0.0040 chunk 2 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 overall best weight: 1.2194 ------------------------------------------------------------------------------- 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 = 0.3239 r_free = 0.3239 target = 0.040986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.033581 restraints weight = 12770.478| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 4.81 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.8830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 2021 Z= 0.114 Angle : 0.523 5.559 2756 Z= 0.285 Chirality : 0.044 0.137 334 Planarity : 0.003 0.020 366 Dihedral : 3.610 18.307 289 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.92 % Allowed : 24.77 % Favored : 74.31 % 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 aren not related in a simple way. whole: -1.40 (0.50), residues: 266 helix: 0.41 (0.74), residues: 51 sheet: -0.41 (0.55), residues: 98 loop : -1.98 (0.50), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 245 TYR 0.012 0.001 TYR D 89 PHE 0.009 0.001 PHE D 94 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 2021) covalent geometry : angle 0.52283 ( 2756) hydrogen bonds : bond 0.02817 ( 82) hydrogen bonds : angle 4.68404 ( 225) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 9 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 7 time to evaluate : 0.048 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 9 average time/residue: 0.0484 time to fit residues: 0.6203 Evaluate side-chains 9 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 7 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 85 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 8 optimal weight: 0.8980 chunk 16 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 20 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 22 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 = 0.3222 r_free = 0.3222 target = 0.040643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.033034 restraints weight = 13368.580| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 4.99 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.8935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2021 Z= 0.129 Angle : 0.529 5.584 2756 Z= 0.288 Chirality : 0.044 0.137 334 Planarity : 0.003 0.017 366 Dihedral : 3.662 18.032 289 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.38 % Allowed : 24.31 % Favored : 74.31 % 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 aren not related in a simple way. whole: -1.33 (0.50), residues: 266 helix: 0.44 (0.74), residues: 51 sheet: -0.33 (0.56), residues: 98 loop : -1.96 (0.50), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 245 TYR 0.004 0.001 TYR D 198 PHE 0.008 0.001 PHE D 94 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 2021) covalent geometry : angle 0.52941 ( 2756) hydrogen bonds : bond 0.02918 ( 82) hydrogen bonds : angle 4.79967 ( 225) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 7 time to evaluate : 0.048 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 10 average time/residue: 0.0459 time to fit residues: 0.6002 Evaluate side-chains 10 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 7 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 85 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 17 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 21 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- 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 = 0.3205 r_free = 0.3205 target = 0.040137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.032682 restraints weight = 13489.508| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 4.91 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.9108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 2021 Z= 0.219 Angle : 0.596 6.003 2756 Z= 0.321 Chirality : 0.045 0.149 334 Planarity : 0.003 0.019 366 Dihedral : 4.012 18.091 289 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.38 % Allowed : 24.31 % Favored : 74.31 % 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 aren not related in a simple way. whole: -1.45 (0.51), residues: 266 helix: 0.12 (0.73), residues: 52 sheet: -0.41 (0.55), residues: 100 loop : -1.95 (0.52), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 245 TYR 0.015 0.001 TYR D 89 PHE 0.006 0.001 PHE D 94 Details of bonding type rmsd covalent geometry : bond 0.00480 ( 2021) covalent geometry : angle 0.59559 ( 2756) hydrogen bonds : bond 0.03216 ( 82) hydrogen bonds : angle 5.12262 ( 225) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 759.06 seconds wall clock time: 13 minutes 41.57 seconds (821.57 seconds total)