Starting phenix.real_space_refine on Tue Mar 3 17:32:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nnt_12483/03_2026/7nnt_12483.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nnt_12483/03_2026/7nnt_12483.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7nnt_12483/03_2026/7nnt_12483.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nnt_12483/03_2026/7nnt_12483.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7nnt_12483/03_2026/7nnt_12483.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nnt_12483/03_2026/7nnt_12483.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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 36 5.16 5 C 4986 2.51 5 N 1263 2.21 5 O 1381 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7666 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2137 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 13, 'TRANS': 265} Chain breaks: 1 Chain: "B" Number of atoms: 2123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2123 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 12, 'TRANS': 259} Chain breaks: 1 Chain: "C" Number of atoms: 1321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1321 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 4, 'TRANS': 164} Chain: "D" Number of atoms: 2085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2085 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 9, 'TRANS': 249} Time building chain proxies: 1.55, per 1000 atoms: 0.20 Number of scatterers: 7666 At special positions: 0 Unit cell: (99.176, 81.972, 111.32, 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 36 16.00 O 1381 8.00 N 1263 7.00 C 4986 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.65 Conformation dependent library (CDL) restraints added in 238.0 milliseconds 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1804 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 0 sheets defined 47.5% 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 'A' and resid 47 through 53 removed outlier: 4.810A pdb=" N LYS A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 82 No H-bonds generated for 'chain 'A' and resid 79 through 82' Processing helix chain 'A' and resid 102 through 105 No H-bonds generated for 'chain 'A' and resid 102 through 105' Processing helix chain 'A' and resid 117 through 130 Processing helix chain 'A' and resid 147 through 158 Processing helix chain 'A' and resid 178 through 193 Processing helix chain 'A' and resid 227 through 230 No H-bonds generated for 'chain 'A' and resid 227 through 230' Processing helix chain 'A' and resid 234 through 240 removed outlier: 3.576A pdb=" N ARG A 239 " --> pdb=" O GLU A 235 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE A 240 " --> pdb=" O MET A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 257 Processing helix chain 'A' and resid 268 through 277 Processing helix chain 'B' and resid 46 through 53 Processing helix chain 'B' and resid 83 through 86 No H-bonds generated for 'chain 'B' and resid 83 through 86' Processing helix chain 'B' and resid 94 through 97 No H-bonds generated for 'chain 'B' and resid 94 through 97' Processing helix chain 'B' and resid 103 through 114 removed outlier: 4.639A pdb=" N GLY B 110 " --> pdb=" O ASP B 106 " (cutoff:3.500A) Proline residue: B 111 - end of helix Processing helix chain 'B' and resid 120 through 132 Processing helix chain 'B' and resid 143 through 145 No H-bonds generated for 'chain 'B' and resid 143 through 145' Processing helix chain 'B' and resid 148 through 158 Processing helix chain 'B' and resid 178 through 192 Processing helix chain 'B' and resid 205 through 211 removed outlier: 3.791A pdb=" N ASP B 210 " --> pdb=" O ASP B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 232 No H-bonds generated for 'chain 'B' and resid 229 through 232' Processing helix chain 'B' and resid 237 through 243 removed outlier: 4.047A pdb=" N HIS B 243 " --> pdb=" O LEU B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 257 Processing helix chain 'B' and resid 270 through 280 Processing helix chain 'C' and resid 13 through 31 Processing helix chain 'C' and resid 44 through 53 Processing helix chain 'C' and resid 57 through 74 Processing helix chain 'C' and resid 83 through 100 Proline residue: C 93 - end of helix Processing helix chain 'C' and resid 107 through 120 Processing helix chain 'C' and resid 128 through 134 Processing helix chain 'C' and resid 138 through 145 Processing helix chain 'C' and resid 148 through 161 Proline residue: C 153 - end of helix Processing helix chain 'C' and resid 164 through 167 No H-bonds generated for 'chain 'C' and resid 164 through 167' Processing helix chain 'D' and resid 23 through 36 Processing helix chain 'D' and resid 41 through 58 Processing helix chain 'D' and resid 62 through 69 Processing helix chain 'D' and resid 73 through 84 Processing helix chain 'D' and resid 103 through 117 Processing helix chain 'D' and resid 132 through 144 Processing helix chain 'D' and resid 153 through 182 Proline residue: D 168 - end of helix Processing helix chain 'D' and resid 195 through 198 No H-bonds generated for 'chain 'D' and resid 195 through 198' Processing helix chain 'D' and resid 201 through 225 Proline residue: D 206 - end of helix Processing helix chain 'D' and resid 243 through 250 removed outlier: 4.882A pdb=" N ILE D 247 " --> pdb=" O LYS D 243 " (cutoff:3.500A) Proline residue: D 248 - end of helix No H-bonds generated for 'chain 'D' and resid 243 through 250' Processing helix chain 'D' and resid 256 through 262 269 hydrogen bonds defined for protein. 807 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: 0.87 Time building geometry restraints manager: 0.85 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: 2409 1.34 - 1.46: 1151 1.46 - 1.57: 4199 1.57 - 1.69: 0 1.69 - 1.81: 68 Bond restraints: 7827 Sorted by residual: bond pdb=" C ILE A 244 " pdb=" N PRO A 245 " ideal model delta sigma weight residual 1.331 1.347 -0.016 1.21e-02 6.83e+03 1.72e+00 bond pdb=" SD MET C 157 " pdb=" CE MET C 157 " ideal model delta sigma weight residual 1.791 1.760 0.031 2.50e-02 1.60e+03 1.57e+00 bond pdb=" CB TRP C 108 " pdb=" CG TRP C 108 " ideal model delta sigma weight residual 1.498 1.465 0.033 3.10e-02 1.04e+03 1.15e+00 bond pdb=" CB VAL B 8 " pdb=" CG1 VAL B 8 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.04e+00 bond pdb=" CG LEU D 164 " pdb=" CD1 LEU D 164 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 1.00e+00 ... (remaining 7822 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 10307 1.61 - 3.22: 224 3.22 - 4.84: 49 4.84 - 6.45: 17 6.45 - 8.06: 2 Bond angle restraints: 10599 Sorted by residual: angle pdb=" N GLY B 62 " pdb=" CA GLY B 62 " pdb=" C GLY B 62 " ideal model delta sigma weight residual 110.56 114.74 -4.18 1.36e+00 5.41e-01 9.44e+00 angle pdb=" C ASP A 217 " pdb=" N ASP A 218 " pdb=" CA ASP A 218 " ideal model delta sigma weight residual 121.54 127.05 -5.51 1.91e+00 2.74e-01 8.31e+00 angle pdb=" N ILE C 151 " pdb=" CA ILE C 151 " pdb=" C ILE C 151 " ideal model delta sigma weight residual 113.42 110.06 3.36 1.17e+00 7.31e-01 8.23e+00 angle pdb=" CB MET C 21 " pdb=" CG MET C 21 " pdb=" SD MET C 21 " ideal model delta sigma weight residual 112.70 120.76 -8.06 3.00e+00 1.11e-01 7.22e+00 angle pdb=" C PHE D 149 " pdb=" N LYS D 150 " pdb=" CA LYS D 150 " ideal model delta sigma weight residual 122.08 125.97 -3.89 1.47e+00 4.63e-01 7.01e+00 ... (remaining 10594 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.07: 4004 14.07 - 28.15: 471 28.15 - 42.22: 144 42.22 - 56.29: 26 56.29 - 70.37: 10 Dihedral angle restraints: 4655 sinusoidal: 1855 harmonic: 2800 Sorted by residual: dihedral pdb=" CA ASP A 25 " pdb=" CB ASP A 25 " pdb=" CG ASP A 25 " pdb=" OD1 ASP A 25 " ideal model delta sinusoidal sigma weight residual -30.00 -88.58 58.58 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CA LEU A 216 " pdb=" C LEU A 216 " pdb=" N ASP A 217 " pdb=" CA ASP A 217 " ideal model delta harmonic sigma weight residual 180.00 163.68 16.32 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CA ASN B 113 " pdb=" C ASN B 113 " pdb=" N PHE B 114 " pdb=" CA PHE B 114 " ideal model delta harmonic sigma weight residual 180.00 163.79 16.21 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 4652 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 1114 0.079 - 0.157: 107 0.157 - 0.236: 1 0.236 - 0.315: 0 0.315 - 0.394: 1 Chirality restraints: 1223 Sorted by residual: chirality pdb=" CB ILE A 5 " pdb=" CA ILE A 5 " pdb=" CG1 ILE A 5 " pdb=" CG2 ILE A 5 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.87e+00 chirality pdb=" CB ILE C 105 " pdb=" CA ILE C 105 " pdb=" CG1 ILE C 105 " pdb=" CG2 ILE C 105 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.30e-01 chirality pdb=" CA ASP A 218 " pdb=" N ASP A 218 " pdb=" C ASP A 218 " pdb=" CB ASP A 218 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.80e-01 ... (remaining 1220 not shown) Planarity restraints: 1325 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 66 " 0.020 2.00e-02 2.50e+03 1.45e-02 5.25e+00 pdb=" CG TRP D 66 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP D 66 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP D 66 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 66 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP D 66 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 66 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 66 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 66 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP D 66 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY C 92 " 0.032 5.00e-02 4.00e+02 4.83e-02 3.74e+00 pdb=" N PRO C 93 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO C 93 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 93 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 266 " 0.032 5.00e-02 4.00e+02 4.81e-02 3.70e+00 pdb=" N PRO B 267 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 267 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 267 " 0.027 5.00e-02 4.00e+02 ... (remaining 1322 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1164 2.75 - 3.29: 7630 3.29 - 3.83: 12777 3.83 - 4.36: 15345 4.36 - 4.90: 26126 Nonbonded interactions: 63042 Sorted by model distance: nonbonded pdb=" OD2 ASP A 104 " pdb=" NH1 ARG D 237 " model vdw 2.218 3.120 nonbonded pdb=" OH TYR D 30 " pdb=" OG1 THR D 256 " model vdw 2.228 3.040 nonbonded pdb=" O MET C 133 " pdb=" NH1 ARG D 115 " model vdw 2.344 3.120 nonbonded pdb=" OG1 THR A 12 " pdb=" OD2 ASP A 60 " model vdw 2.346 3.040 nonbonded pdb=" O PRO B 164 " pdb=" OH TYR B 191 " model vdw 2.357 3.040 ... (remaining 63037 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 1.300 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: 0.020 Set scattering table: 0.010 Process input model: 7.110 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 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 : 0.005 0.036 7827 Z= 0.197 Angle : 0.656 8.061 10599 Z= 0.358 Chirality : 0.046 0.394 1223 Planarity : 0.005 0.048 1325 Dihedral : 13.716 70.367 2851 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.27), residues: 967 helix: 0.46 (0.22), residues: 564 sheet: -1.90 (0.71), residues: 63 loop : -1.34 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 113 TYR 0.012 0.001 TYR D 251 PHE 0.015 0.002 PHE A 97 TRP 0.038 0.002 TRP D 66 HIS 0.004 0.001 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00474 ( 7827) covalent geometry : angle 0.65629 (10599) hydrogen bonds : bond 0.04241 ( 269) hydrogen bonds : angle 4.14056 ( 807) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.358 Fit side-chains REVERT: B 41 HIS cc_start: 0.3493 (m-70) cc_final: 0.3240 (m-70) REVERT: C 175 LYS cc_start: 0.8033 (mmmm) cc_final: 0.7676 (mmtt) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.0933 time to fit residues: 13.2269 Evaluate side-chains 92 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.1980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 ASN B 41 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.126388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.106249 restraints weight = 10517.499| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.05 r_work: 0.3044 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.0660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7827 Z= 0.108 Angle : 0.489 5.376 10599 Z= 0.250 Chirality : 0.041 0.142 1223 Planarity : 0.004 0.042 1325 Dihedral : 4.174 15.424 1035 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.72 % Allowed : 7.00 % Favored : 92.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.27), residues: 967 helix: 0.82 (0.22), residues: 567 sheet: -1.87 (0.71), residues: 63 loop : -1.26 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 153 TYR 0.009 0.001 TYR D 251 PHE 0.010 0.001 PHE C 61 TRP 0.020 0.001 TRP D 66 HIS 0.003 0.001 HIS B 52 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 7827) covalent geometry : angle 0.48923 (10599) hydrogen bonds : bond 0.03467 ( 269) hydrogen bonds : angle 3.81248 ( 807) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 103 time to evaluate : 0.255 Fit side-chains REVERT: A 140 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8354 (mp0) REVERT: B 41 HIS cc_start: 0.4661 (m90) cc_final: 0.4026 (m170) REVERT: B 192 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.8285 (tt0) REVERT: C 87 LEU cc_start: 0.8428 (tp) cc_final: 0.8138 (tp) REVERT: C 175 LYS cc_start: 0.8066 (mmmm) cc_final: 0.7489 (mmtt) outliers start: 6 outliers final: 3 residues processed: 107 average time/residue: 0.0855 time to fit residues: 12.5142 Evaluate side-chains 93 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 88 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain B residue 192 GLN Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 190 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 94 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.130867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.112966 restraints weight = 10519.666| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.71 r_work: 0.3148 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.0750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 7827 Z= 0.201 Angle : 0.561 6.828 10599 Z= 0.286 Chirality : 0.044 0.139 1223 Planarity : 0.005 0.044 1325 Dihedral : 4.272 16.003 1035 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.57 % Allowed : 10.01 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.27), residues: 967 helix: 0.79 (0.22), residues: 565 sheet: -2.02 (0.71), residues: 63 loop : -1.16 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 153 TYR 0.012 0.001 TYR D 251 PHE 0.013 0.001 PHE A 28 TRP 0.014 0.002 TRP D 66 HIS 0.004 0.001 HIS B 52 Details of bonding type rmsd covalent geometry : bond 0.00504 ( 7827) covalent geometry : angle 0.56097 (10599) hydrogen bonds : bond 0.04063 ( 269) hydrogen bonds : angle 3.93560 ( 807) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.288 Fit side-chains REVERT: B 192 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.8540 (tt0) REVERT: C 175 LYS cc_start: 0.8209 (mmmm) cc_final: 0.7672 (mmtt) outliers start: 13 outliers final: 11 residues processed: 99 average time/residue: 0.0941 time to fit residues: 12.6719 Evaluate side-chains 99 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 192 GLN Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain C residue 108 TRP Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 190 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 71 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 69 optimal weight: 0.0980 chunk 28 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.131218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.113203 restraints weight = 10691.327| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.73 r_work: 0.3151 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.0878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7827 Z= 0.174 Angle : 0.528 6.251 10599 Z= 0.270 Chirality : 0.043 0.135 1223 Planarity : 0.004 0.042 1325 Dihedral : 4.213 15.088 1035 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.33 % Allowed : 12.06 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.27), residues: 967 helix: 0.83 (0.22), residues: 565 sheet: -2.16 (0.69), residues: 63 loop : -1.14 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 153 TYR 0.012 0.001 TYR D 251 PHE 0.012 0.001 PHE A 28 TRP 0.013 0.001 TRP D 66 HIS 0.003 0.001 HIS B 52 Details of bonding type rmsd covalent geometry : bond 0.00432 ( 7827) covalent geometry : angle 0.52765 (10599) hydrogen bonds : bond 0.03889 ( 269) hydrogen bonds : angle 3.91944 ( 807) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.271 Fit side-chains REVERT: B 192 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.8505 (tt0) REVERT: C 175 LYS cc_start: 0.8212 (mmmm) cc_final: 0.7664 (mmtt) outliers start: 11 outliers final: 8 residues processed: 99 average time/residue: 0.0942 time to fit residues: 12.4020 Evaluate side-chains 97 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain B residue 192 GLN Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain C residue 108 TRP Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 190 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 40 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 26 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 94 optimal weight: 0.0770 chunk 10 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 overall best weight: 0.6940 ------------------------------------------------------------------------------- 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 = 0.3512 r_free = 0.3512 target = 0.133857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.115959 restraints weight = 10467.696| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.71 r_work: 0.3182 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7827 Z= 0.103 Angle : 0.464 5.044 10599 Z= 0.239 Chirality : 0.040 0.127 1223 Planarity : 0.004 0.040 1325 Dihedral : 3.929 14.001 1035 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.69 % Allowed : 13.27 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.28), residues: 967 helix: 1.12 (0.22), residues: 566 sheet: -2.00 (0.77), residues: 53 loop : -1.09 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 153 TYR 0.010 0.001 TYR B 12 PHE 0.008 0.001 PHE C 61 TRP 0.012 0.001 TRP B 128 HIS 0.002 0.001 HIS B 52 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 7827) covalent geometry : angle 0.46425 (10599) hydrogen bonds : bond 0.03378 ( 269) hydrogen bonds : angle 3.72031 ( 807) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.254 Fit side-chains REVERT: A 140 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8438 (mp0) REVERT: B 192 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.8406 (tt0) REVERT: C 87 LEU cc_start: 0.8522 (tp) cc_final: 0.8219 (tp) REVERT: C 175 LYS cc_start: 0.8239 (mmmm) cc_final: 0.7687 (mmtt) outliers start: 14 outliers final: 7 residues processed: 105 average time/residue: 0.0782 time to fit residues: 11.5170 Evaluate side-chains 97 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain B residue 192 GLN Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain C residue 108 TRP Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 190 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 22 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN A 143 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.128625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.110632 restraints weight = 10690.509| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.72 r_work: 0.3117 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 7827 Z= 0.235 Angle : 0.586 7.288 10599 Z= 0.299 Chirality : 0.045 0.140 1223 Planarity : 0.005 0.041 1325 Dihedral : 4.300 15.486 1035 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.29 % Allowed : 14.11 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.28), residues: 967 helix: 0.89 (0.22), residues: 564 sheet: -2.31 (0.67), residues: 63 loop : -1.07 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 153 TYR 0.013 0.001 TYR D 251 PHE 0.014 0.002 PHE A 28 TRP 0.013 0.002 TRP D 94 HIS 0.004 0.001 HIS D 95 Details of bonding type rmsd covalent geometry : bond 0.00589 ( 7827) covalent geometry : angle 0.58598 (10599) hydrogen bonds : bond 0.04328 ( 269) hydrogen bonds : angle 3.97293 ( 807) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.305 Fit side-chains REVERT: A 13 PHE cc_start: 0.8471 (OUTLIER) cc_final: 0.7628 (m-10) REVERT: B 192 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.8534 (tt0) REVERT: C 175 LYS cc_start: 0.8368 (mmmm) cc_final: 0.7803 (mmtt) outliers start: 19 outliers final: 13 residues processed: 103 average time/residue: 0.0919 time to fit residues: 12.7509 Evaluate side-chains 104 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 192 GLN Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 108 TRP Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 144 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 9 optimal weight: 0.9980 chunk 88 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 13 optimal weight: 0.3980 chunk 54 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.132410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.114575 restraints weight = 10489.387| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.71 r_work: 0.3181 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7827 Z= 0.110 Angle : 0.485 6.178 10599 Z= 0.247 Chirality : 0.041 0.125 1223 Planarity : 0.004 0.041 1325 Dihedral : 3.996 14.711 1035 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.57 % Allowed : 15.20 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.28), residues: 967 helix: 1.16 (0.23), residues: 566 sheet: -2.07 (0.77), residues: 53 loop : -1.04 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 153 TYR 0.012 0.001 TYR B 12 PHE 0.009 0.001 PHE A 28 TRP 0.013 0.001 TRP B 128 HIS 0.002 0.000 HIS B 52 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 7827) covalent geometry : angle 0.48512 (10599) hydrogen bonds : bond 0.03487 ( 269) hydrogen bonds : angle 3.73573 ( 807) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.281 Fit side-chains REVERT: A 13 PHE cc_start: 0.8479 (OUTLIER) cc_final: 0.7591 (m-10) REVERT: A 140 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8488 (mp0) REVERT: A 188 LYS cc_start: 0.8059 (ttpp) cc_final: 0.7827 (ttpp) REVERT: B 192 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.8436 (tt0) REVERT: C 94 MET cc_start: 0.8735 (ttm) cc_final: 0.8531 (ttm) REVERT: C 175 LYS cc_start: 0.8305 (mmmm) cc_final: 0.7724 (mmtt) outliers start: 13 outliers final: 8 residues processed: 102 average time/residue: 0.0826 time to fit residues: 11.7213 Evaluate side-chains 101 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain B residue 192 GLN Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 108 TRP Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 144 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 60 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 82 optimal weight: 0.5980 chunk 66 optimal weight: 5.9990 chunk 12 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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 = 0.3482 r_free = 0.3482 target = 0.131422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.113481 restraints weight = 10687.046| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.72 r_work: 0.3142 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7827 Z= 0.178 Angle : 0.537 6.623 10599 Z= 0.274 Chirality : 0.043 0.129 1223 Planarity : 0.004 0.041 1325 Dihedral : 4.096 14.234 1035 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.69 % Allowed : 16.04 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.28), residues: 967 helix: 1.08 (0.22), residues: 564 sheet: -2.10 (0.77), residues: 53 loop : -1.04 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 153 TYR 0.012 0.001 TYR D 251 PHE 0.012 0.001 PHE A 28 TRP 0.012 0.001 TRP B 128 HIS 0.003 0.001 HIS B 52 Details of bonding type rmsd covalent geometry : bond 0.00445 ( 7827) covalent geometry : angle 0.53746 (10599) hydrogen bonds : bond 0.03911 ( 269) hydrogen bonds : angle 3.83334 ( 807) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.306 Fit side-chains REVERT: A 13 PHE cc_start: 0.8526 (OUTLIER) cc_final: 0.7630 (m-10) REVERT: A 188 LYS cc_start: 0.8079 (ttpp) cc_final: 0.7843 (ttpp) REVERT: A 195 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8566 (pp) REVERT: B 192 GLN cc_start: 0.8763 (OUTLIER) cc_final: 0.8500 (tt0) REVERT: C 87 LEU cc_start: 0.8580 (tp) cc_final: 0.8293 (tp) REVERT: C 175 LYS cc_start: 0.8326 (mmmm) cc_final: 0.7747 (mmtt) outliers start: 14 outliers final: 9 residues processed: 98 average time/residue: 0.0898 time to fit residues: 12.0596 Evaluate side-chains 103 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain B residue 192 GLN Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 108 TRP Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 144 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 39 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 4 optimal weight: 0.4980 chunk 34 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 89 optimal weight: 0.0060 chunk 78 optimal weight: 7.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- 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 = 0.3521 r_free = 0.3521 target = 0.134470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.116583 restraints weight = 10520.096| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.71 r_work: 0.3199 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7827 Z= 0.103 Angle : 0.477 5.724 10599 Z= 0.244 Chirality : 0.040 0.128 1223 Planarity : 0.004 0.041 1325 Dihedral : 3.869 14.806 1035 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.69 % Allowed : 15.92 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.28), residues: 967 helix: 1.29 (0.23), residues: 566 sheet: -2.01 (0.77), residues: 53 loop : -1.02 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 153 TYR 0.011 0.001 TYR B 12 PHE 0.008 0.001 PHE C 61 TRP 0.012 0.001 TRP B 128 HIS 0.002 0.000 HIS B 226 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 7827) covalent geometry : angle 0.47734 (10599) hydrogen bonds : bond 0.03397 ( 269) hydrogen bonds : angle 3.70125 ( 807) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.251 Fit side-chains REVERT: A 13 PHE cc_start: 0.8548 (OUTLIER) cc_final: 0.7558 (m-10) REVERT: A 188 LYS cc_start: 0.8035 (ttpp) cc_final: 0.7802 (ttpp) REVERT: A 195 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8586 (pp) REVERT: B 192 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.8391 (tt0) REVERT: C 175 LYS cc_start: 0.8283 (mmmm) cc_final: 0.7697 (mmtt) outliers start: 14 outliers final: 9 residues processed: 96 average time/residue: 0.0850 time to fit residues: 11.3258 Evaluate side-chains 100 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain B residue 192 GLN Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain C residue 108 TRP Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 190 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 22 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 83 optimal weight: 0.6980 overall best weight: 0.8786 ------------------------------------------------------------------------------- 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 = 0.3516 r_free = 0.3516 target = 0.134006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.116098 restraints weight = 10526.182| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.71 r_work: 0.3189 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7827 Z= 0.119 Angle : 0.487 6.097 10599 Z= 0.247 Chirality : 0.041 0.127 1223 Planarity : 0.004 0.040 1325 Dihedral : 3.836 14.584 1035 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.69 % Allowed : 15.92 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.28), residues: 967 helix: 1.33 (0.22), residues: 567 sheet: -1.93 (0.78), residues: 53 loop : -1.01 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 153 TYR 0.013 0.001 TYR B 12 PHE 0.010 0.001 PHE C 61 TRP 0.011 0.001 TRP B 128 HIS 0.002 0.000 HIS B 52 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 7827) covalent geometry : angle 0.48733 (10599) hydrogen bonds : bond 0.03468 ( 269) hydrogen bonds : angle 3.68646 ( 807) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.267 Fit side-chains REVERT: A 13 PHE cc_start: 0.8608 (OUTLIER) cc_final: 0.7618 (m-10) REVERT: A 188 LYS cc_start: 0.8045 (ttpp) cc_final: 0.7803 (ttpp) REVERT: A 195 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8578 (pp) REVERT: B 192 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.8407 (tt0) REVERT: C 87 LEU cc_start: 0.8506 (tp) cc_final: 0.8187 (tp) REVERT: C 175 LYS cc_start: 0.8279 (mmmm) cc_final: 0.7718 (mmtt) outliers start: 14 outliers final: 9 residues processed: 100 average time/residue: 0.0880 time to fit residues: 12.1477 Evaluate side-chains 103 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain B residue 192 GLN Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 108 TRP Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 144 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 63 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3500 r_free = 0.3500 target = 0.132627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.114754 restraints weight = 10559.398| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.69 r_work: 0.3173 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7827 Z= 0.153 Angle : 0.515 6.154 10599 Z= 0.262 Chirality : 0.042 0.128 1223 Planarity : 0.004 0.045 1325 Dihedral : 3.925 14.482 1035 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.93 % Allowed : 15.92 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.28), residues: 967 helix: 1.30 (0.22), residues: 564 sheet: -1.95 (0.77), residues: 53 loop : -0.96 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 153 TYR 0.012 0.001 TYR B 12 PHE 0.011 0.001 PHE C 61 TRP 0.012 0.001 TRP B 128 HIS 0.003 0.001 HIS B 52 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 7827) covalent geometry : angle 0.51458 (10599) hydrogen bonds : bond 0.03724 ( 269) hydrogen bonds : angle 3.76068 ( 807) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1713.02 seconds wall clock time: 30 minutes 0.29 seconds (1800.29 seconds total)