Starting phenix.real_space_refine on Wed Jun 4 10:18:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8feh_29027/06_2025/8feh_29027.cif Found real_map, /net/cci-nas-00/data/ceres_data/8feh_29027/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8feh_29027/06_2025/8feh_29027.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8feh_29027/06_2025/8feh_29027.map" model { file = "/net/cci-nas-00/data/ceres_data/8feh_29027/06_2025/8feh_29027.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8feh_29027/06_2025/8feh_29027.cif" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'TYR:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 17 Time building chain proxies: 3.17, per 1000 atoms: 1.59 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: 0.53 Conformation dependent library (CDL) restraints added in 271.4 milliseconds 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: 0.28 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: 0.49 Time building geometry restraints manager: 0.62 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: 5.370 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: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 11.950 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.090 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.45 (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 PHE 0.009 0.002 PHE D 230 TYR 0.010 0.002 TYR D 198 ARG 0.003 0.000 ARG D 245 Details of bonding type rmsd hydrogen bonds : bond 0.25938 ( 82) hydrogen bonds : angle 9.52295 ( 225) covalent geometry : bond 0.00790 ( 2021) covalent geometry : angle 1.02199 ( 2756) *********************** 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 : 0.245 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: 0.1591 time to fit residues: 6.1852 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 : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 21 optimal weight: 5.9990 chunk 19 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 7 optimal weight: 0.0000 chunk 12 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 overall best weight: 3.3992 ------------------------------------------------------------------------------- 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 = 0.3305 r_free = 0.3305 target = 0.043278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.035324 restraints weight = 12580.776| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 4.91 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.5413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 2021 Z= 0.231 Angle : 0.746 6.159 2756 Z= 0.398 Chirality : 0.048 0.146 334 Planarity : 0.005 0.042 366 Dihedral : 4.677 21.506 289 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.21 % Allowed : 16.06 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.43), residues: 266 helix: -1.72 (0.62), residues: 52 sheet: -1.41 (0.48), residues: 102 loop : -2.62 (0.43), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.002 PHE D 94 TYR 0.011 0.002 TYR D 89 ARG 0.007 0.001 ARG D 193 Details of bonding type rmsd hydrogen bonds : bond 0.04124 ( 82) hydrogen bonds : angle 5.98831 ( 225) covalent geometry : bond 0.00496 ( 2021) covalent geometry : angle 0.74573 ( 2756) *********************** 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 18 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 11 time to evaluate : 0.229 Fit side-chains REVERT: D 87 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.8260 (mm110) outliers start: 7 outliers final: 2 residues processed: 17 average time/residue: 0.1283 time to fit residues: 2.8112 Evaluate side-chains 9 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 6 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 87 GLN Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 168 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 15 optimal weight: 9.9990 chunk 24 optimal weight: 0.9990 chunk 22 optimal weight: 8.9990 chunk 23 optimal weight: 0.0470 chunk 1 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 87 GLN D 173 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.041952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.034450 restraints weight = 13096.491| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 4.90 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.6257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2021 Z= 0.139 Angle : 0.565 5.603 2756 Z= 0.307 Chirality : 0.044 0.133 334 Planarity : 0.003 0.019 366 Dihedral : 3.921 19.324 289 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.46 % Allowed : 16.51 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.47), residues: 266 helix: -0.88 (0.69), residues: 52 sheet: -1.03 (0.52), residues: 100 loop : -2.32 (0.46), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.001 PHE D 94 TYR 0.003 0.001 TYR D 268 ARG 0.002 0.000 ARG D 241 Details of bonding type rmsd hydrogen bonds : bond 0.03576 ( 82) hydrogen bonds : angle 5.38429 ( 225) covalent geometry : bond 0.00299 ( 2021) covalent geometry : angle 0.56470 ( 2756) *********************** 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 11 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 10 time to evaluate : 0.251 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 11 average time/residue: 0.0894 time to fit residues: 1.5466 Evaluate side-chains 6 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 5 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 24 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 3 optimal weight: 10.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 173 GLN D 205 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.041100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.033587 restraints weight = 12618.597| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 4.77 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.7859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 2021 Z= 0.177 Angle : 0.595 6.090 2756 Z= 0.320 Chirality : 0.046 0.141 334 Planarity : 0.003 0.019 366 Dihedral : 3.914 20.539 289 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.92 % Allowed : 18.81 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.49), residues: 266 helix: -0.38 (0.72), residues: 52 sheet: -1.03 (0.51), residues: 103 loop : -2.24 (0.50), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.002 PHE D 94 TYR 0.008 0.001 TYR D 89 ARG 0.001 0.000 ARG D 222 Details of bonding type rmsd hydrogen bonds : bond 0.03246 ( 82) hydrogen bonds : angle 5.30015 ( 225) covalent geometry : bond 0.00382 ( 2021) covalent geometry : angle 0.59522 ( 2756) *********************** 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 8 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 6 time to evaluate : 0.254 Fit side-chains REVERT: D 225 TYR cc_start: 0.8448 (m-10) cc_final: 0.8226 (m-10) outliers start: 2 outliers final: 1 residues processed: 8 average time/residue: 0.0760 time to fit residues: 1.1381 Evaluate side-chains 6 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 5 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 11 optimal weight: 10.0000 chunk 16 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 18 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 2 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 = 0.3274 r_free = 0.3274 target = 0.041668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.034105 restraints weight = 12919.097| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 4.87 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.8068 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= 0.125 Angle : 0.520 5.696 2756 Z= 0.279 Chirality : 0.044 0.129 334 Planarity : 0.003 0.015 366 Dihedral : 3.645 18.080 289 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.92 % Allowed : 20.18 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.49), residues: 266 helix: -0.10 (0.72), residues: 52 sheet: -0.70 (0.55), residues: 97 loop : -2.18 (0.49), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE D 94 TYR 0.008 0.001 TYR D 89 ARG 0.001 0.000 ARG D 241 Details of bonding type rmsd hydrogen bonds : bond 0.03016 ( 82) hydrogen bonds : angle 5.09330 ( 225) covalent geometry : bond 0.00271 ( 2021) covalent geometry : angle 0.52044 ( 2756) *********************** 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 : 0.233 Fit side-chains REVERT: D 225 TYR cc_start: 0.8431 (m-10) cc_final: 0.8201 (m-10) outliers start: 2 outliers final: 1 residues processed: 9 average time/residue: 0.0687 time to fit residues: 1.1164 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 : 0.248 ------------------------------------------------------------------------------- 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 8 optimal weight: 10.0000 chunk 11 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 9 optimal weight: 8.9990 chunk 14 optimal weight: 0.0010 chunk 22 optimal weight: 3.9990 overall best weight: 1.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 173 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.041531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.034168 restraints weight = 12865.487| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 4.83 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.8277 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= 0.121 Angle : 0.529 5.684 2756 Z= 0.284 Chirality : 0.044 0.132 334 Planarity : 0.003 0.016 366 Dihedral : 3.576 18.081 289 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.38 % Allowed : 19.72 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.50), residues: 266 helix: 0.11 (0.74), residues: 51 sheet: -0.64 (0.56), residues: 97 loop : -2.19 (0.48), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE D 94 TYR 0.007 0.001 TYR D 89 ARG 0.002 0.000 ARG D 245 Details of bonding type rmsd hydrogen bonds : bond 0.03071 ( 82) hydrogen bonds : angle 5.15316 ( 225) covalent geometry : bond 0.00263 ( 2021) covalent geometry : angle 0.52890 ( 2756) *********************** 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 8 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 5 time to evaluate : 0.250 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 8 average time/residue: 0.1430 time to fit residues: 1.6945 Evaluate side-chains 6 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 5 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 14 optimal weight: 0.0020 chunk 15 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 7 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 3 optimal weight: 9.9990 chunk 6 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 overall best weight: 1.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 173 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.041658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.034246 restraints weight = 12718.798| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 4.90 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.8427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2021 Z= 0.117 Angle : 0.525 5.619 2756 Z= 0.286 Chirality : 0.044 0.135 334 Planarity : 0.003 0.027 366 Dihedral : 3.621 17.991 289 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.38 % Allowed : 19.72 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.50), residues: 266 helix: 0.24 (0.74), residues: 51 sheet: -0.61 (0.55), residues: 97 loop : -2.13 (0.49), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.001 PHE D 94 TYR 0.003 0.001 TYR D 198 ARG 0.002 0.000 ARG D 245 Details of bonding type rmsd hydrogen bonds : bond 0.02890 ( 82) hydrogen bonds : angle 4.99980 ( 225) covalent geometry : bond 0.00251 ( 2021) covalent geometry : angle 0.52505 ( 2756) *********************** 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 : 0.246 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 8 average time/residue: 0.0736 time to fit residues: 1.0954 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 : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 53 SER 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 17 optimal weight: 8.9990 chunk 7 optimal weight: 0.0050 chunk 6 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 overall best weight: 2.8002 ------------------------------------------------------------------------------- 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 = 0.3202 r_free = 0.3202 target = 0.040140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.032578 restraints weight = 13319.401| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 4.88 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.8703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2021 Z= 0.173 Angle : 0.557 6.192 2756 Z= 0.299 Chirality : 0.044 0.139 334 Planarity : 0.003 0.022 366 Dihedral : 3.777 17.036 289 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.83 % Allowed : 20.18 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.50), residues: 266 helix: 0.26 (0.73), residues: 51 sheet: -0.57 (0.54), residues: 99 loop : -2.13 (0.50), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE D 94 TYR 0.005 0.001 TYR D 198 ARG 0.004 0.000 ARG D 245 Details of bonding type rmsd hydrogen bonds : bond 0.03096 ( 82) hydrogen bonds : angle 5.16972 ( 225) covalent geometry : bond 0.00377 ( 2021) covalent geometry : angle 0.55662 ( 2756) *********************** 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: 4 poor density : 4 time to evaluate : 0.247 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 8 average time/residue: 0.0660 time to fit residues: 1.0374 Evaluate side-chains 5 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 3 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 68 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 15 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 8.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 173 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.040867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.033352 restraints weight = 13259.592| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 4.91 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.8818 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= 0.121 Angle : 0.524 6.177 2756 Z= 0.283 Chirality : 0.044 0.146 334 Planarity : 0.003 0.017 366 Dihedral : 3.599 17.306 289 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.92 % Allowed : 21.10 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.50), residues: 266 helix: 0.37 (0.74), residues: 51 sheet: -0.51 (0.55), residues: 97 loop : -2.13 (0.49), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE D 94 TYR 0.011 0.001 TYR D 89 ARG 0.002 0.000 ARG D 245 Details of bonding type rmsd hydrogen bonds : bond 0.02893 ( 82) hydrogen bonds : angle 4.98241 ( 225) covalent geometry : bond 0.00261 ( 2021) covalent geometry : angle 0.52400 ( 2756) *********************** 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 8 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 6 time to evaluate : 0.254 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 8 average time/residue: 0.1431 time to fit residues: 1.6749 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 : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 68 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 9 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 13 optimal weight: 0.0040 chunk 11 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 10 optimal weight: 0.0670 chunk 1 optimal weight: 9.9990 overall best weight: 1.3734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 173 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.040520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.032880 restraints weight = 13170.425| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 4.76 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.8883 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= 0.119 Angle : 0.539 6.063 2756 Z= 0.293 Chirality : 0.044 0.141 334 Planarity : 0.003 0.016 366 Dihedral : 3.572 17.153 289 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.38 % Allowed : 21.10 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.50), residues: 266 helix: 0.35 (0.73), residues: 51 sheet: -0.42 (0.55), residues: 97 loop : -2.12 (0.49), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.001 PHE D 94 TYR 0.003 0.001 TYR D 225 ARG 0.002 0.000 ARG D 245 Details of bonding type rmsd hydrogen bonds : bond 0.02950 ( 82) hydrogen bonds : angle 5.11251 ( 225) covalent geometry : bond 0.00259 ( 2021) covalent geometry : angle 0.53856 ( 2756) ********************** 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 8 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 5 time to evaluate : 0.228 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 8 average time/residue: 0.1319 time to fit residues: 1.5439 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 : 0.229 ------------------------------------------------------------------------------- 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 19 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 0.3980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 173 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.040305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.032710 restraints weight = 13340.392| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 4.75 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.9021 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= 0.132 Angle : 0.541 6.092 2756 Z= 0.294 Chirality : 0.044 0.142 334 Planarity : 0.003 0.016 366 Dihedral : 3.606 17.001 289 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.38 % Allowed : 21.10 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.50), residues: 266 helix: 0.34 (0.73), residues: 51 sheet: -0.43 (0.55), residues: 99 loop : -2.02 (0.50), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.001 PHE D 94 TYR 0.011 0.001 TYR D 89 ARG 0.002 0.000 ARG D 245 Details of bonding type rmsd hydrogen bonds : bond 0.02901 ( 82) hydrogen bonds : angle 5.14569 ( 225) covalent geometry : bond 0.00289 ( 2021) covalent geometry : angle 0.54133 ( 2756) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1433.21 seconds wall clock time: 25 minutes 38.12 seconds (1538.12 seconds total)