Starting phenix.real_space_refine on Wed Mar 5 14:47:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zf4_60050/03_2025/8zf4_60050.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zf4_60050/03_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_60050/03_2025/8zf4_60050.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zf4_60050/03_2025/8zf4_60050.map" model { file = "/net/cci-nas-00/data/ceres_data/8zf4_60050/03_2025/8zf4_60050.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zf4_60050/03_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-5624/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: 2.31, per 1000 atoms: 1.11 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: 0.56 Conformation dependent library (CDL) restraints added in 281.2 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: 0.20 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: 0.51 Time building geometry restraints manager: 0.67 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: 1.090 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: 0.030 Process input model: 11.300 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.460 ------------------------------------------------------------------------------- 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 2132 Z= 0.390 Angle : 0.945 9.575 2924 Z= 0.507 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 *********************** 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 : 0.212 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 28 average time/residue: 0.2337 time to fit residues: 7.4015 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 : 0.215 ------------------------------------------------------------------------------- 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 = 47)----------------| | 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: 0.3307 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- 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 2132 Z= 0.207 Angle : 0.717 7.382 2924 Z= 0.358 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 *********************** 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 : 0.198 Fit side-chains REVERT: R 112 SER cc_start: 0.8460 (t) cc_final: 0.8248 (p) outliers start: 1 outliers final: 1 residues processed: 35 average time/residue: 0.2713 time to fit residues: 10.4574 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 : 0.233 ------------------------------------------------------------------------------- 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: 0.6980 chunk 5 optimal weight: 0.1980 chunk 23 optimal weight: 0.2980 chunk 16 optimal weight: 0.6980 chunk 8 optimal weight: 0.1980 chunk 7 optimal weight: 0.9980 chunk 11 optimal weight: 0.0040 chunk 0 optimal weight: 1.9990 chunk 17 optimal weight: 0.0970 chunk 1 optimal weight: 0.1980 overall best weight: 0.1390 ------------------------------------------------------------------------------- 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 = 0.3730 r_free = 0.3730 target = 0.129315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.113905 restraints weight = 3125.895| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.70 r_work: 0.3426 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2132 Z= 0.205 Angle : 0.687 8.946 2924 Z= 0.335 Chirality : 0.039 0.126 331 Planarity : 0.007 0.070 374 Dihedral : 4.863 22.315 317 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.45 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 : -3.81 (0.49), residues: 68 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 0.007 0.001 PHE R 107 TYR 0.007 0.001 TYR R 238 ARG 0.006 0.001 ARG R 224 *********************** 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 : 0.222 Fit side-chains REVERT: R 39 LEU cc_start: 0.8534 (tt) cc_final: 0.8330 (tt) REVERT: R 112 SER cc_start: 0.8508 (t) cc_final: 0.8268 (p) outliers start: 3 outliers final: 1 residues processed: 37 average time/residue: 0.2457 time to fit residues: 10.1555 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 : 0.230 ------------------------------------------------------------------------------- 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: 0.2980 chunk 7 optimal weight: 0.2980 chunk 13 optimal weight: 0.4980 chunk 22 optimal weight: 0.3980 chunk 16 optimal weight: 0.3980 chunk 23 optimal weight: 0.2980 chunk 11 optimal weight: 0.3980 chunk 10 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 overall best weight: 0.3380 ------------------------------------------------------------------------------- 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 = 0.3684 r_free = 0.3684 target = 0.125744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.110603 restraints weight = 3065.677| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.64 r_work: 0.3381 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 2132 Z= 0.278 Angle : 0.718 7.392 2924 Z= 0.353 Chirality : 0.041 0.135 331 Planarity : 0.007 0.067 374 Dihedral : 4.986 22.316 317 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 1.63 % Allowed : 11.41 % Favored : 86.96 % 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: 0.50 (0.51), residues: 284 helix: 1.57 (0.37), residues: 216 sheet: None (None), residues: 0 loop : -3.98 (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 0.009 0.001 PHE R 93 TYR 0.010 0.001 TYR R 76 ARG 0.006 0.001 ARG R 224 *********************** 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 : 0.219 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 34 average time/residue: 0.2480 time to fit residues: 9.3923 Evaluate side-chains 35 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.212 ------------------------------------------------------------------------------- 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: 0.5980 chunk 23 optimal weight: 0.1980 chunk 8 optimal weight: 0.1980 chunk 9 optimal weight: 0.1980 chunk 18 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 3 optimal weight: 0.0020 chunk 26 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 overall best weight: 0.2388 ------------------------------------------------------------------------------- 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 = 0.3700 r_free = 0.3700 target = 0.126865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.111761 restraints weight = 3099.958| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.64 r_work: 0.3397 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 2132 Z= 0.235 Angle : 0.676 6.447 2924 Z= 0.336 Chirality : 0.040 0.132 331 Planarity : 0.007 0.066 374 Dihedral : 4.855 22.068 317 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % 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: 0.74 (0.51), residues: 284 helix: 1.80 (0.37), residues: 212 sheet: None (None), residues: 0 loop : -3.79 (0.46), residues: 72 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 107 TYR 0.010 0.001 TYR R 76 ARG 0.006 0.001 ARG R 225 *********************** 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 36 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.199 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 34 average time/residue: 0.2432 time to fit residues: 9.1630 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 : 0.198 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 2 optimal weight: 0.0270 chunk 22 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 23 optimal weight: 0.1980 chunk 10 optimal weight: 0.6980 chunk 6 optimal weight: 0.0980 chunk 3 optimal weight: 0.4980 chunk 4 optimal weight: 0.0980 chunk 15 optimal weight: 1.9990 overall best weight: 0.1838 ------------------------------------------------------------------------------- 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 = 0.3716 r_free = 0.3716 target = 0.127911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.112535 restraints weight = 3089.220| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.72 r_work: 0.3406 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2132 Z= 0.212 Angle : 0.663 7.010 2924 Z= 0.332 Chirality : 0.040 0.130 331 Planarity : 0.007 0.065 374 Dihedral : 4.752 22.326 317 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 2.72 % Allowed : 11.96 % 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: 1.04 (0.52), residues: 284 helix: 1.94 (0.37), residues: 217 sheet: None (None), residues: 0 loop : -3.82 (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 107 TYR 0.009 0.001 TYR R 76 ARG 0.006 0.001 ARG R 225 *********************** 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: 5 poor density : 33 time to evaluate : 0.202 Fit side-chains REVERT: R 51 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6776 (pp20) outliers start: 5 outliers final: 2 residues processed: 36 average time/residue: 0.2530 time to fit residues: 10.1315 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 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 51 GLU Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 236 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 18 optimal weight: 0.0670 chunk 13 optimal weight: 0.7980 chunk 27 optimal weight: 0.4980 chunk 5 optimal weight: 0.5980 chunk 14 optimal weight: 0.4980 chunk 15 optimal weight: 0.6980 chunk 20 optimal weight: 0.3980 chunk 23 optimal weight: 0.0980 chunk 12 optimal weight: 0.8980 chunk 10 optimal weight: 0.1980 chunk 8 optimal weight: 0.2980 overall best weight: 0.2118 ------------------------------------------------------------------------------- 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 = 0.3716 r_free = 0.3716 target = 0.127910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.112719 restraints weight = 3119.605| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.68 r_work: 0.3410 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 2132 Z= 0.234 Angle : 0.669 6.624 2924 Z= 0.333 Chirality : 0.040 0.130 331 Planarity : 0.007 0.064 374 Dihedral : 4.724 22.401 317 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 2.72 % Allowed : 13.04 % 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: 1.04 (0.52), residues: 284 helix: 1.95 (0.37), residues: 217 sheet: None (None), residues: 0 loop : -3.84 (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 0.011 0.001 TYR R 76 ARG 0.007 0.001 ARG R 224 *********************** 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 39 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.234 Fit side-chains REVERT: R 51 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6763 (pp20) outliers start: 5 outliers final: 4 residues processed: 36 average time/residue: 0.2740 time to fit residues: 11.0085 Evaluate side-chains 37 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.337 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain R residue 236 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 27 optimal weight: 0.1980 chunk 22 optimal weight: 0.0970 chunk 12 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 25 optimal weight: 0.4980 chunk 24 optimal weight: 0.9980 chunk 18 optimal weight: 0.3980 chunk 13 optimal weight: 0.5980 chunk 23 optimal weight: 0.2980 chunk 11 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 overall best weight: 0.2978 ------------------------------------------------------------------------------- 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 = 0.3699 r_free = 0.3699 target = 0.126628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.111186 restraints weight = 3164.100| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.73 r_work: 0.3386 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 2132 Z= 0.271 Angle : 0.692 7.445 2924 Z= 0.347 Chirality : 0.041 0.146 331 Planarity : 0.007 0.063 374 Dihedral : 4.824 22.342 317 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 2.72 % Allowed : 13.04 % 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: 0.76 (0.51), residues: 284 helix: 1.71 (0.36), residues: 219 sheet: None (None), residues: 0 loop : -3.99 (0.47), 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 0.008 0.001 PHE R 97 TYR 0.013 0.001 TYR R 76 ARG 0.007 0.001 ARG R 225 *********************** 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: 5 poor density : 35 time to evaluate : 0.220 Fit side-chains REVERT: R 51 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.6757 (pp20) REVERT: R 169 TYR cc_start: 0.8021 (OUTLIER) cc_final: 0.6712 (m-80) outliers start: 5 outliers final: 2 residues processed: 37 average time/residue: 0.2496 time to fit residues: 10.2853 Evaluate side-chains 39 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.228 ------------------------------------------------------------------------------- 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 236 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 0.3980 chunk 9 optimal weight: 0.2980 chunk 7 optimal weight: 0.0050 chunk 27 optimal weight: 0.0270 chunk 8 optimal weight: 0.1980 chunk 14 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 3 optimal weight: 0.0170 chunk 21 optimal weight: 0.1980 chunk 6 optimal weight: 0.2980 chunk 0 optimal weight: 0.9990 overall best weight: 0.0890 ------------------------------------------------------------------------------- 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 = 0.3752 r_free = 0.3752 target = 0.130885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.115646 restraints weight = 3150.452| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.78 r_work: 0.3447 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2132 Z= 0.189 Angle : 0.656 6.876 2924 Z= 0.329 Chirality : 0.039 0.131 331 Planarity : 0.007 0.063 374 Dihedral : 4.586 22.300 317 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 3.26 % Allowed : 14.13 % 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: 1.18 (0.52), residues: 284 helix: 2.04 (0.37), residues: 217 sheet: None (None), residues: 0 loop : -3.78 (0.48), 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 0.008 0.001 PHE R 167 TYR 0.008 0.001 TYR R 76 ARG 0.005 0.001 ARG R 225 *********************** 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 42 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.202 Fit side-chains REVERT: R 51 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6832 (pp20) REVERT: R 159 HIS cc_start: 0.7054 (m90) cc_final: 0.6487 (m90) outliers start: 6 outliers final: 3 residues processed: 39 average time/residue: 0.2275 time to fit residues: 9.9090 Evaluate side-chains 37 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.229 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 25 optimal weight: 0.2980 chunk 9 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 5 optimal weight: 0.0870 chunk 23 optimal weight: 0.0870 chunk 8 optimal weight: 0.0980 chunk 14 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 11 optimal weight: 0.0070 chunk 6 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 overall best weight: 0.1154 ------------------------------------------------------------------------------- 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 = 0.3754 r_free = 0.3754 target = 0.131100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.115754 restraints weight = 3140.180| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.78 r_work: 0.3445 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2132 Z= 0.198 Angle : 0.676 7.316 2924 Z= 0.337 Chirality : 0.039 0.161 331 Planarity : 0.007 0.062 374 Dihedral : 4.556 22.726 317 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 1.63 % Allowed : 16.30 % Favored : 82.07 % 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: 1.22 (0.52), residues: 284 helix: 2.08 (0.37), residues: 217 sheet: None (None), residues: 0 loop : -3.79 (0.48), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 195 HIS 0.007 0.001 HIS R 276 PHE 0.011 0.002 PHE R 125 TYR 0.011 0.001 TYR R 77 ARG 0.007 0.001 ARG R 224 ********************** 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 39 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.216 Fit side-chains REVERT: R 91 ARG cc_start: 0.7237 (ttp-170) cc_final: 0.6767 (ttm-80) REVERT: R 159 HIS cc_start: 0.7023 (m90) cc_final: 0.6430 (m90) REVERT: R 169 TYR cc_start: 0.7966 (OUTLIER) cc_final: 0.6781 (m-80) outliers start: 3 outliers final: 2 residues processed: 37 average time/residue: 0.2466 time to fit residues: 10.1580 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 : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 GLN Chi-restraints excluded: chain R residue 169 TYR Chi-restraints excluded: chain R residue 181 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 19 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 2 optimal weight: 0.0470 chunk 16 optimal weight: 0.0770 chunk 13 optimal weight: 0.2980 chunk 27 optimal weight: 0.3980 chunk 14 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 21 optimal weight: 0.3980 chunk 25 optimal weight: 0.9980 chunk 23 optimal weight: 0.1980 overall best weight: 0.2036 ------------------------------------------------------------------------------- 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 = 0.129358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.113861 restraints weight = 3121.929| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.77 r_work: 0.3420 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 2132 Z= 0.227 Angle : 0.690 7.225 2924 Z= 0.344 Chirality : 0.040 0.149 331 Planarity : 0.007 0.062 374 Dihedral : 4.662 22.209 317 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 1.63 % Allowed : 16.30 % Favored : 82.07 % 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: 1.98 (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 0.006 0.001 TRP R 195 HIS 0.010 0.002 HIS R 276 PHE 0.010 0.002 PHE R 125 TYR 0.014 0.001 TYR R 275 ARG 0.007 0.001 ARG R 224 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1822.26 seconds wall clock time: 31 minutes 59.06 seconds (1919.06 seconds total)