Starting phenix.real_space_refine on Fri May 9 13:16:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zf4_60050/05_2025/8zf4_60050.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zf4_60050/05_2025/8zf4_60050.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zf4_60050/05_2025/8zf4_60050.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zf4_60050/05_2025/8zf4_60050.map" model { file = "/net/cci-nas-00/data/ceres_data/8zf4_60050/05_2025/8zf4_60050.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zf4_60050/05_2025/8zf4_60050.cif" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 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 13 5.16 5 C 1352 2.51 5 N 356 2.21 5 O 352 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 2073 Number of models: 1 Model: "" Number of chains: 1 Chain: "R" Number of atoms: 2073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2073 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 269} Chain breaks: 1 Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 176 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 9, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 69 Time building chain proxies: 2.09, per 1000 atoms: 1.01 Number of scatterers: 2073 At special positions: 0 Unit cell: (60.45, 66.03, 73.47, 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 13 16.00 O 352 8.00 N 356 7.00 C 1352 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 90 " - pdb=" SG CYS R 168 " distance=2.03 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: 0.52 Conformation dependent library (CDL) restraints added in 272.3 milliseconds 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 528 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 0 sheets defined 77.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'R' and resid 18 through 47 removed outlier: 4.642A pdb=" N LEU R 32 " --> pdb=" O PHE R 28 " (cutoff:3.500A) Proline residue: R 33 - end of helix Processing helix chain 'R' and resid 51 through 79 removed outlier: 4.272A pdb=" N TYR R 55 " --> pdb=" O GLU R 51 " (cutoff:3.500A) Proline residue: R 71 - end of helix Processing helix chain 'R' and resid 86 through 121 removed outlier: 4.094A pdb=" N ARG R 91 " --> pdb=" O PRO R 87 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU R 92 " --> pdb=" O GLY R 88 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TYR R 102 " --> pdb=" O TYR R 98 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA R 105 " --> pdb=" O LEU R 101 " (cutoff:3.500A) Processing helix chain 'R' and resid 129 through 154 removed outlier: 3.770A pdb=" N SER R 133 " --> pdb=" O ARG R 129 " (cutoff:3.500A) Proline residue: R 151 - end of helix Processing helix chain 'R' and resid 177 through 191 Processing helix chain 'R' and resid 193 through 209 removed outlier: 3.602A pdb=" N LEU R 209 " --> pdb=" O LEU R 205 " (cutoff:3.500A) Processing helix chain 'R' and resid 216 through 228 removed outlier: 3.652A pdb=" N ARG R 222 " --> pdb=" O ARG R 218 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL R 223 " --> pdb=" O GLU R 219 " (cutoff:3.500A) Processing helix chain 'R' and resid 229 through 252 Proline residue: R 240 - end of helix Processing helix chain 'R' and resid 264 through 284 removed outlier: 4.428A pdb=" N GLU R 268 " --> pdb=" O GLY R 264 " (cutoff:3.500A) Proline residue: R 273 - end of helix removed outlier: 4.004A pdb=" N ALA R 280 " --> pdb=" O HIS R 276 " (cutoff:3.500A) Processing helix chain 'R' and resid 287 through 294 Processing helix chain 'R' and resid 299 through 303 154 hydrogen bonds defined for protein. 456 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: 657 1.34 - 1.46: 555 1.46 - 1.59: 904 1.59 - 1.71: 0 1.71 - 1.84: 16 Bond restraints: 2132 Sorted by residual: bond pdb=" CB ASP R 81 " pdb=" CG ASP R 81 " ideal model delta sigma weight residual 1.516 1.432 0.084 2.50e-02 1.60e+03 1.13e+01 bond pdb=" C ARG R 129 " pdb=" N PRO R 130 " ideal model delta sigma weight residual 1.336 1.301 0.035 1.25e-02 6.40e+03 7.67e+00 bond pdb=" C ASP R 81 " pdb=" N VAL R 82 " ideal model delta sigma weight residual 1.331 1.294 0.036 1.40e-02 5.10e+03 6.69e+00 bond pdb=" CA ARG R 129 " pdb=" C ARG R 129 " ideal model delta sigma weight residual 1.524 1.501 0.022 1.26e-02 6.30e+03 3.15e+00 bond pdb=" C ARG R 129 " pdb=" O ARG R 129 " ideal model delta sigma weight residual 1.238 1.217 0.021 1.28e-02 6.10e+03 2.59e+00 ... (remaining 2127 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 2799 1.92 - 3.83: 89 3.83 - 5.75: 27 5.75 - 7.66: 6 7.66 - 9.58: 3 Bond angle restraints: 2924 Sorted by residual: angle pdb=" N PRO R 71 " pdb=" CA PRO R 71 " pdb=" C PRO R 71 " ideal model delta sigma weight residual 110.70 117.07 -6.37 1.22e+00 6.72e-01 2.72e+01 angle pdb=" N ASP R 81 " pdb=" CA ASP R 81 " pdb=" C ASP R 81 " ideal model delta sigma weight residual 111.30 117.61 -6.31 1.36e+00 5.41e-01 2.15e+01 angle pdb=" C ASP R 81 " pdb=" CA ASP R 81 " pdb=" CB ASP R 81 " ideal model delta sigma weight residual 111.95 105.25 6.70 1.50e+00 4.44e-01 2.00e+01 angle pdb=" N GLU R 156 " pdb=" CA GLU R 156 " pdb=" C GLU R 156 " ideal model delta sigma weight residual 110.80 102.42 8.38 2.13e+00 2.20e-01 1.55e+01 angle pdb=" CA PRO R 71 " pdb=" C PRO R 71 " pdb=" N PRO R 72 " ideal model delta sigma weight residual 117.93 122.49 -4.56 1.20e+00 6.94e-01 1.44e+01 ... (remaining 2919 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.52: 1052 12.52 - 25.04: 118 25.04 - 37.56: 44 37.56 - 50.08: 15 50.08 - 62.59: 2 Dihedral angle restraints: 1231 sinusoidal: 401 harmonic: 830 Sorted by residual: dihedral pdb=" CA LEU R 192 " pdb=" C LEU R 192 " pdb=" N LEU R 193 " pdb=" CA LEU R 193 " ideal model delta harmonic sigma weight residual 180.00 157.52 22.48 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA PRO R 71 " pdb=" C PRO R 71 " pdb=" N PRO R 72 " pdb=" CA PRO R 72 " ideal model delta harmonic sigma weight residual 180.00 160.18 19.82 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA PHE R 167 " pdb=" C PHE R 167 " pdb=" N CYS R 168 " pdb=" CA CYS R 168 " ideal model delta harmonic sigma weight residual 180.00 160.67 19.33 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 1228 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 236 0.049 - 0.097: 74 0.097 - 0.145: 20 0.145 - 0.194: 0 0.194 - 0.242: 1 Chirality restraints: 331 Sorted by residual: chirality pdb=" CA PRO R 71 " pdb=" N PRO R 71 " pdb=" C PRO R 71 " pdb=" CB PRO R 71 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA LEU R 19 " pdb=" N LEU R 19 " pdb=" C LEU R 19 " pdb=" CB LEU R 19 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.89e-01 chirality pdb=" CA TYR R 77 " pdb=" N TYR R 77 " pdb=" C TYR R 77 " pdb=" CB TYR R 77 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.54e-01 ... (remaining 328 not shown) Planarity restraints: 374 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO R 20 " -0.056 5.00e-02 4.00e+02 8.39e-02 1.13e+01 pdb=" N PRO R 21 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO R 21 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO R 21 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS R 297 " 0.047 5.00e-02 4.00e+02 7.21e-02 8.33e+00 pdb=" N PRO R 298 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO R 298 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO R 298 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG R 129 " 0.013 2.00e-02 2.50e+03 2.61e-02 6.83e+00 pdb=" C ARG R 129 " -0.045 2.00e-02 2.50e+03 pdb=" O ARG R 129 " 0.017 2.00e-02 2.50e+03 pdb=" N PRO R 130 " 0.015 2.00e-02 2.50e+03 ... (remaining 371 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 571 2.81 - 3.33: 2032 3.33 - 3.86: 3502 3.86 - 4.38: 3706 4.38 - 4.90: 6530 Nonbonded interactions: 16341 Sorted by model distance: nonbonded pdb=" NH2 ARG R 91 " pdb=" O GLY R 155 " model vdw 2.290 3.120 nonbonded pdb=" O LEU R 209 " pdb=" NH1 ARG R 220 " model vdw 2.337 3.120 nonbonded pdb=" CE2 TYR R 77 " pdb=" ND1 HIS R 276 " model vdw 2.342 3.420 nonbonded pdb=" O GLY R 31 " pdb=" N ASN R 35 " model vdw 2.368 3.120 nonbonded pdb=" O ASP R 16 " pdb=" O TYR R 77 " model vdw 2.429 3.040 ... (remaining 16336 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: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 10.210 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 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 : 0.006 0.084 2133 Z= 0.272 Angle : 0.948 9.575 2926 Z= 0.508 Chirality : 0.049 0.242 331 Planarity : 0.009 0.084 374 Dihedral : 13.233 62.594 700 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 0.54 % Allowed : 0.00 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.59 (0.49), residues: 284 helix: 0.65 (0.37), residues: 210 sheet: None (None), residues: 0 loop : -3.50 (0.52), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP R 195 HIS 0.006 0.001 HIS R 276 PHE 0.013 0.002 PHE R 93 TYR 0.014 0.002 TYR R 76 ARG 0.007 0.001 ARG R 160 Details of bonding type rmsd hydrogen bonds : bond 0.11775 ( 154) hydrogen bonds : angle 5.48062 ( 456) SS BOND : bond 0.00078 ( 1) SS BOND : angle 3.14123 ( 2) covalent geometry : bond 0.00618 ( 2132) covalent geometry : angle 0.94493 ( 2924) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 27 time to evaluate : 0.211 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 28 average time/residue: 0.2251 time to fit residues: 7.1188 Evaluate side-chains 25 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 23 optimal weight: 0.2980 chunk 21 optimal weight: 0.2980 chunk 11 optimal weight: 0.0050 chunk 7 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 8 optimal weight: 0.1980 chunk 13 optimal weight: 0.0970 chunk 16 optimal weight: 0.4980 chunk 25 optimal weight: 0.8980 chunk 17 optimal weight: 0.1980 chunk 27 optimal weight: 0.0570 overall best weight: 0.1110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 45 GLN R 149 ASN R 159 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.129478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.113752 restraints weight = 3139.933| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.73 r_work: 0.3422 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2133 Z= 0.140 Angle : 0.719 7.382 2926 Z= 0.359 Chirality : 0.040 0.128 331 Planarity : 0.008 0.074 374 Dihedral : 5.217 23.155 317 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 0.54 % Allowed : 7.07 % Favored : 92.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.14 (0.50), residues: 284 helix: 1.36 (0.37), residues: 209 sheet: None (None), residues: 0 loop : -3.77 (0.47), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 195 HIS 0.005 0.001 HIS R 276 PHE 0.006 0.001 PHE R 107 TYR 0.007 0.001 TYR R 76 ARG 0.006 0.001 ARG R 224 Details of bonding type rmsd hydrogen bonds : bond 0.03745 ( 154) hydrogen bonds : angle 4.53459 ( 456) SS BOND : bond 0.00182 ( 1) SS BOND : angle 2.29819 ( 2) covalent geometry : bond 0.00319 ( 2132) covalent geometry : angle 0.71652 ( 2924) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 35 time to evaluate : 0.216 Fit side-chains REVERT: R 112 SER cc_start: 0.8460 (t) cc_final: 0.8249 (p) outliers start: 1 outliers final: 1 residues processed: 35 average time/residue: 0.2535 time to fit residues: 9.8643 Evaluate side-chains 34 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 236 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 26 optimal weight: 0.4980 chunk 3 optimal weight: 0.8980 chunk 5 optimal weight: 0.0870 chunk 23 optimal weight: 0.3980 chunk 16 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 11 optimal weight: 0.0170 chunk 0 optimal weight: 1.9990 chunk 17 optimal weight: 0.0980 chunk 1 optimal weight: 0.0980 overall best weight: 0.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 149 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.129333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.113914 restraints weight = 3124.908| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 1.69 r_work: 0.3426 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2133 Z= 0.137 Angle : 0.687 8.848 2926 Z= 0.336 Chirality : 0.039 0.127 331 Planarity : 0.007 0.070 374 Dihedral : 4.858 22.282 317 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 1.63 % Allowed : 9.24 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.74 (0.51), residues: 284 helix: 1.72 (0.37), residues: 216 sheet: None (None), residues: 0 loop : -3.80 (0.49), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 195 HIS 0.003 0.001 HIS R 276 PHE 0.007 0.001 PHE R 107 TYR 0.007 0.001 TYR R 238 ARG 0.007 0.001 ARG R 224 Details of bonding type rmsd hydrogen bonds : bond 0.03515 ( 154) hydrogen bonds : angle 4.37324 ( 456) SS BOND : bond 0.00232 ( 1) SS BOND : angle 2.00209 ( 2) covalent geometry : bond 0.00315 ( 2132) covalent geometry : angle 0.68571 ( 2924) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.215 Fit side-chains REVERT: R 39 LEU cc_start: 0.8542 (tt) cc_final: 0.8340 (tt) REVERT: R 112 SER cc_start: 0.8510 (t) cc_final: 0.8270 (p) outliers start: 3 outliers final: 1 residues processed: 37 average time/residue: 0.2251 time to fit residues: 9.3318 Evaluate side-chains 34 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 181 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 12 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 7 optimal weight: 0.1980 chunk 13 optimal weight: 0.8980 chunk 22 optimal weight: 0.4980 chunk 16 optimal weight: 0.1980 chunk 23 optimal weight: 0.5980 chunk 11 optimal weight: 0.3980 chunk 10 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 overall best weight: 0.3780 ------------------------------------------------------------------------------- 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 = 0.3679 r_free = 0.3679 target = 0.125288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.110181 restraints weight = 3063.584| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.63 r_work: 0.3374 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 2133 Z= 0.191 Angle : 0.732 7.422 2926 Z= 0.360 Chirality : 0.042 0.132 331 Planarity : 0.007 0.068 374 Dihedral : 5.035 22.475 317 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 1.63 % Allowed : 11.96 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.42 (0.51), residues: 284 helix: 1.51 (0.37), residues: 216 sheet: None (None), residues: 0 loop : -4.00 (0.47), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 195 HIS 0.002 0.001 HIS R 276 PHE 0.010 0.001 PHE R 93 TYR 0.011 0.001 TYR R 76 ARG 0.006 0.001 ARG R 224 Details of bonding type rmsd hydrogen bonds : bond 0.04089 ( 154) hydrogen bonds : angle 4.54898 ( 456) SS BOND : bond 0.00126 ( 1) SS BOND : angle 1.99014 ( 2) covalent geometry : bond 0.00460 ( 2132) covalent geometry : angle 0.73078 ( 2924) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.222 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 34 average time/residue: 0.2479 time to fit residues: 9.3858 Evaluate side-chains 33 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 30 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 169 TYR Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 236 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 5 optimal weight: 0.6980 chunk 23 optimal weight: 0.1980 chunk 8 optimal weight: 0.2980 chunk 9 optimal weight: 0.1980 chunk 18 optimal weight: 0.2980 chunk 24 optimal weight: 0.4980 chunk 19 optimal weight: 0.5980 chunk 3 optimal weight: 0.0370 chunk 26 optimal weight: 0.4980 chunk 15 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 overall best weight: 0.2058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 149 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.127401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.112197 restraints weight = 3099.900| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.66 r_work: 0.3403 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2133 Z= 0.147 Angle : 0.668 6.370 2926 Z= 0.332 Chirality : 0.040 0.130 331 Planarity : 0.007 0.066 374 Dihedral : 4.826 22.209 317 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 1.63 % Allowed : 13.59 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.64 (0.52), residues: 284 helix: 1.73 (0.37), residues: 215 sheet: None (None), residues: 0 loop : -4.07 (0.46), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 195 HIS 0.002 0.000 HIS R 276 PHE 0.008 0.001 PHE R 107 TYR 0.010 0.001 TYR R 76 ARG 0.005 0.001 ARG R 225 Details of bonding type rmsd hydrogen bonds : bond 0.03599 ( 154) hydrogen bonds : angle 4.42699 ( 456) SS BOND : bond 0.00183 ( 1) SS BOND : angle 1.76122 ( 2) covalent geometry : bond 0.00344 ( 2132) covalent geometry : angle 0.66638 ( 2924) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.209 Fit side-chains REVERT: R 112 SER cc_start: 0.8540 (t) cc_final: 0.8289 (p) outliers start: 3 outliers final: 2 residues processed: 35 average time/residue: 0.2313 time to fit residues: 9.0529 Evaluate side-chains 36 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 169 TYR Chi-restraints excluded: chain R residue 181 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 2 optimal weight: 0.0970 chunk 22 optimal weight: 0.0770 chunk 0 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 23 optimal weight: 0.0970 chunk 10 optimal weight: 0.5980 chunk 6 optimal weight: 0.2980 chunk 3 optimal weight: 0.3980 chunk 4 optimal weight: 0.1980 chunk 15 optimal weight: 1.9990 overall best weight: 0.1534 ------------------------------------------------------------------------------- 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 = 0.3723 r_free = 0.3723 target = 0.128576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.113143 restraints weight = 3103.319| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 1.74 r_work: 0.3416 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2133 Z= 0.134 Angle : 0.657 6.944 2926 Z= 0.328 Chirality : 0.039 0.132 331 Planarity : 0.007 0.066 374 Dihedral : 4.714 22.694 317 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 2.17 % Allowed : 12.50 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.06 (0.52), residues: 284 helix: 1.99 (0.37), residues: 216 sheet: None (None), residues: 0 loop : -3.85 (0.48), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 195 HIS 0.002 0.001 HIS R 276 PHE 0.007 0.001 PHE R 107 TYR 0.009 0.001 TYR R 76 ARG 0.006 0.001 ARG R 225 Details of bonding type rmsd hydrogen bonds : bond 0.03367 ( 154) hydrogen bonds : angle 4.31959 ( 456) SS BOND : bond 0.00208 ( 1) SS BOND : angle 1.62212 ( 2) covalent geometry : bond 0.00315 ( 2132) covalent geometry : angle 0.65629 ( 2924) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.220 Fit side-chains REVERT: R 51 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6791 (pp20) REVERT: R 112 SER cc_start: 0.8559 (t) cc_final: 0.8314 (p) outliers start: 4 outliers final: 1 residues processed: 37 average time/residue: 0.2373 time to fit residues: 9.8596 Evaluate side-chains 33 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 51 GLU Chi-restraints excluded: chain R residue 181 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 18 optimal weight: 0.0970 chunk 13 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 5 optimal weight: 0.0870 chunk 14 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 23 optimal weight: 0.1980 chunk 12 optimal weight: 0.2980 chunk 10 optimal weight: 0.3980 chunk 8 optimal weight: 0.3980 overall best weight: 0.2156 ------------------------------------------------------------------------------- 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 = 0.3720 r_free = 0.3720 target = 0.128244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.112784 restraints weight = 3104.905| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.73 r_work: 0.3405 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 2133 Z= 0.150 Angle : 0.669 7.098 2926 Z= 0.334 Chirality : 0.040 0.134 331 Planarity : 0.007 0.064 374 Dihedral : 4.713 22.312 317 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 2.17 % Allowed : 13.04 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.06 (0.52), residues: 284 helix: 1.96 (0.37), residues: 217 sheet: None (None), residues: 0 loop : -3.83 (0.47), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 195 HIS 0.002 0.001 HIS R 276 PHE 0.008 0.001 PHE R 97 TYR 0.012 0.001 TYR R 76 ARG 0.007 0.001 ARG R 224 Details of bonding type rmsd hydrogen bonds : bond 0.03544 ( 154) hydrogen bonds : angle 4.35635 ( 456) SS BOND : bond 0.00178 ( 1) SS BOND : angle 1.67059 ( 2) covalent geometry : bond 0.00370 ( 2132) covalent geometry : angle 0.66810 ( 2924) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.209 Fit side-chains REVERT: R 51 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.6781 (pp20) REVERT: R 112 SER cc_start: 0.8512 (t) cc_final: 0.8303 (p) outliers start: 4 outliers final: 3 residues processed: 36 average time/residue: 0.2600 time to fit residues: 10.3450 Evaluate side-chains 38 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 GLN Chi-restraints excluded: chain R residue 51 GLU Chi-restraints excluded: chain R residue 169 TYR Chi-restraints excluded: chain R residue 181 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 27 optimal weight: 0.0970 chunk 22 optimal weight: 0.4980 chunk 12 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 18 optimal weight: 0.2980 chunk 13 optimal weight: 0.7980 chunk 23 optimal weight: 0.2980 chunk 11 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.3578 ------------------------------------------------------------------------------- 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 = 0.3686 r_free = 0.3686 target = 0.125578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.110318 restraints weight = 3183.708| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.68 r_work: 0.3374 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 2133 Z= 0.188 Angle : 0.702 6.929 2926 Z= 0.351 Chirality : 0.042 0.136 331 Planarity : 0.007 0.063 374 Dihedral : 4.918 23.158 317 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 3.26 % Allowed : 12.50 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.66 (0.51), residues: 284 helix: 1.66 (0.36), residues: 219 sheet: None (None), residues: 0 loop : -4.10 (0.46), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 195 HIS 0.002 0.001 HIS R 276 PHE 0.009 0.001 PHE R 97 TYR 0.014 0.001 TYR R 76 ARG 0.007 0.001 ARG R 224 Details of bonding type rmsd hydrogen bonds : bond 0.03915 ( 154) hydrogen bonds : angle 4.50446 ( 456) SS BOND : bond 0.00127 ( 1) SS BOND : angle 1.90330 ( 2) covalent geometry : bond 0.00463 ( 2132) covalent geometry : angle 0.70011 ( 2924) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.201 Fit side-chains REVERT: R 51 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6727 (pp20) REVERT: R 57 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7463 (tp) REVERT: R 169 TYR cc_start: 0.7986 (OUTLIER) cc_final: 0.6685 (m-80) outliers start: 6 outliers final: 2 residues processed: 37 average time/residue: 0.2131 time to fit residues: 8.8644 Evaluate side-chains 38 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 GLN Chi-restraints excluded: chain R residue 51 GLU Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 169 TYR Chi-restraints excluded: chain R residue 236 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 0.2980 chunk 9 optimal weight: 0.0980 chunk 7 optimal weight: 0.6980 chunk 27 optimal weight: 0.0270 chunk 8 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 13 optimal weight: 0.3980 chunk 3 optimal weight: 0.0050 chunk 21 optimal weight: 0.2980 chunk 6 optimal weight: 0.0980 chunk 0 optimal weight: 1.9990 overall best weight: 0.1052 ------------------------------------------------------------------------------- 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 = 0.3741 r_free = 0.3741 target = 0.130095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.114959 restraints weight = 3169.964| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.70 r_work: 0.3439 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2133 Z= 0.131 Angle : 0.655 6.648 2926 Z= 0.328 Chirality : 0.039 0.125 331 Planarity : 0.007 0.063 374 Dihedral : 4.607 22.371 317 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 2.17 % Allowed : 14.67 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.11 (0.52), residues: 284 helix: 2.01 (0.37), residues: 217 sheet: None (None), residues: 0 loop : -3.86 (0.46), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 142 HIS 0.002 0.000 HIS R 276 PHE 0.009 0.001 PHE R 167 TYR 0.008 0.001 TYR R 76 ARG 0.007 0.001 ARG R 225 Details of bonding type rmsd hydrogen bonds : bond 0.03219 ( 154) hydrogen bonds : angle 4.27937 ( 456) SS BOND : bond 0.00212 ( 1) SS BOND : angle 1.50481 ( 2) covalent geometry : bond 0.00304 ( 2132) covalent geometry : angle 0.65381 ( 2924) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.200 Fit side-chains REVERT: R 51 GLU cc_start: 0.7263 (OUTLIER) cc_final: 0.6845 (pp20) REVERT: R 159 HIS cc_start: 0.7040 (m90) cc_final: 0.6450 (m90) outliers start: 4 outliers final: 2 residues processed: 39 average time/residue: 0.2272 time to fit residues: 9.8564 Evaluate side-chains 37 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 GLN Chi-restraints excluded: chain R residue 51 GLU Chi-restraints excluded: chain R residue 236 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 25 optimal weight: 0.0030 chunk 9 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 23 optimal weight: 0.0970 chunk 8 optimal weight: 0.0980 chunk 14 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 11 optimal weight: 0.0870 chunk 6 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 overall best weight: 0.1766 ------------------------------------------------------------------------------- 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 = 0.3734 r_free = 0.3734 target = 0.129453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.113993 restraints weight = 3134.034| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.76 r_work: 0.3421 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2133 Z= 0.144 Angle : 0.688 7.456 2926 Z= 0.344 Chirality : 0.040 0.164 331 Planarity : 0.007 0.063 374 Dihedral : 4.631 22.457 317 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 1.63 % Allowed : 15.76 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.07 (0.52), residues: 284 helix: 1.99 (0.37), residues: 217 sheet: None (None), residues: 0 loop : -3.88 (0.46), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 195 HIS 0.009 0.002 HIS R 276 PHE 0.014 0.002 PHE R 125 TYR 0.011 0.001 TYR R 77 ARG 0.008 0.001 ARG R 224 Details of bonding type rmsd hydrogen bonds : bond 0.03376 ( 154) hydrogen bonds : angle 4.31393 ( 456) SS BOND : bond 0.00172 ( 1) SS BOND : angle 1.56566 ( 2) covalent geometry : bond 0.00348 ( 2132) covalent geometry : angle 0.68734 ( 2924) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.244 Fit side-chains REVERT: R 51 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6841 (pp20) REVERT: R 159 HIS cc_start: 0.7066 (m90) cc_final: 0.6443 (m90) outliers start: 3 outliers final: 2 residues processed: 37 average time/residue: 0.2712 time to fit residues: 11.2294 Evaluate side-chains 38 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 GLN Chi-restraints excluded: chain R residue 51 GLU Chi-restraints excluded: chain R residue 236 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 19 optimal weight: 0.0970 chunk 15 optimal weight: 1.9990 chunk 2 optimal weight: 0.0870 chunk 16 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 27 optimal weight: 0.3980 chunk 14 optimal weight: 1.9990 chunk 24 optimal weight: 0.3980 chunk 21 optimal weight: 0.1980 chunk 25 optimal weight: 0.7980 chunk 23 optimal weight: 0.1980 overall best weight: 0.1956 ------------------------------------------------------------------------------- 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 = 0.3730 r_free = 0.3730 target = 0.129259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.113668 restraints weight = 3118.959| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.76 r_work: 0.3419 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 2133 Z= 0.147 Angle : 0.688 7.261 2926 Z= 0.344 Chirality : 0.040 0.150 331 Planarity : 0.007 0.063 374 Dihedral : 4.696 22.318 317 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 1.63 % Allowed : 15.76 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.02 (0.52), residues: 284 helix: 1.95 (0.37), residues: 217 sheet: None (None), residues: 0 loop : -3.92 (0.45), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 195 HIS 0.011 0.002 HIS R 276 PHE 0.014 0.002 PHE R 125 TYR 0.015 0.001 TYR R 275 ARG 0.007 0.001 ARG R 224 Details of bonding type rmsd hydrogen bonds : bond 0.03416 ( 154) hydrogen bonds : angle 4.32939 ( 456) SS BOND : bond 0.00161 ( 1) SS BOND : angle 1.57690 ( 2) covalent geometry : bond 0.00356 ( 2132) covalent geometry : angle 0.68686 ( 2924) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1779.51 seconds wall clock time: 31 minutes 22.83 seconds (1882.83 seconds total)