Starting phenix.real_space_refine on Wed Mar 12 08:30:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nnt_12483/03_2025/7nnt_12483.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nnt_12483/03_2025/7nnt_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7nnt_12483/03_2025/7nnt_12483.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nnt_12483/03_2025/7nnt_12483.map" model { file = "/net/cci-nas-00/data/ceres_data/7nnt_12483/03_2025/7nnt_12483.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nnt_12483/03_2025/7nnt_12483.cif" } resolution = 3.4 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= 0.005 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.26, per 1000 atoms: 0.69 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: 1.82 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.66 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: 1.77 Time building geometry restraints manager: 2.18 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: 1.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 20.920 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.870 ------------------------------------------------------------------------------- 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= 0.304 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 (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: -0.55 (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 TRP 0.038 0.002 TRP D 66 HIS 0.004 0.001 HIS B 41 PHE 0.015 0.002 PHE A 97 TYR 0.012 0.001 TYR D 251 ARG 0.009 0.001 ARG A 113 *********************** 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 : 0.786 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: 0.2295 time to fit residues: 32.5215 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 : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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** A 143 ASN ** B 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.131469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.113639 restraints weight = 10430.867| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.70 r_work: 0.3148 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.0541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7827 Z= 0.277 Angle : 0.545 6.166 10599 Z= 0.278 Chirality : 0.043 0.145 1223 Planarity : 0.005 0.044 1325 Dihedral : 4.395 16.800 1035 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.84 % Allowed : 8.20 % Favored : 90.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.27), residues: 967 helix: 0.63 (0.22), residues: 564 sheet: -1.96 (0.71), residues: 63 loop : -1.28 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 66 HIS 0.004 0.001 HIS B 52 PHE 0.011 0.001 PHE A 13 TYR 0.011 0.001 TYR D 251 ARG 0.006 0.000 ARG B 153 *********************** 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 110 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 103 time to evaluate : 0.895 Fit side-chains REVERT: A 12 THR cc_start: 0.8180 (OUTLIER) cc_final: 0.7962 (m) REVERT: B 41 HIS cc_start: 0.4522 (m-70) cc_final: 0.4230 (m170) REVERT: B 192 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.8512 (tt0) REVERT: C 175 LYS cc_start: 0.8134 (mmmm) cc_final: 0.7650 (mmtt) outliers start: 7 outliers final: 4 residues processed: 106 average time/residue: 0.2074 time to fit residues: 29.7043 Evaluate side-chains 97 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 91 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR 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 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 1 optimal weight: 0.5980 chunk 75 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.132911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.114999 restraints weight = 10542.939| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.72 r_work: 0.3173 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.0778 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= 0.199 Angle : 0.491 5.215 10599 Z= 0.252 Chirality : 0.041 0.137 1223 Planarity : 0.004 0.042 1325 Dihedral : 4.134 14.901 1035 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.33 % Allowed : 10.13 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.27), residues: 967 helix: 0.84 (0.22), residues: 567 sheet: -2.02 (0.70), residues: 63 loop : -1.22 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 66 HIS 0.003 0.001 HIS B 52 PHE 0.010 0.001 PHE A 28 TYR 0.010 0.001 TYR D 251 ARG 0.006 0.000 ARG B 153 *********************** 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 109 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.767 Fit side-chains REVERT: B 41 HIS cc_start: 0.4921 (m90) cc_final: 0.4403 (m170) REVERT: B 192 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.8494 (tt0) REVERT: C 175 LYS cc_start: 0.8178 (mmmm) cc_final: 0.7632 (mmtt) outliers start: 11 outliers final: 9 residues processed: 104 average time/residue: 0.1978 time to fit residues: 27.8718 Evaluate side-chains 99 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR 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 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 18 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3502 r_free = 0.3502 target = 0.133059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.115135 restraints weight = 10455.185| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.71 r_work: 0.3169 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.0881 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= 0.206 Angle : 0.486 5.108 10599 Z= 0.249 Chirality : 0.041 0.133 1223 Planarity : 0.004 0.041 1325 Dihedral : 4.036 14.329 1035 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.33 % Allowed : 11.94 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.27), residues: 967 helix: 1.00 (0.22), residues: 567 sheet: -1.93 (0.77), residues: 53 loop : -1.23 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 128 HIS 0.003 0.001 HIS B 52 PHE 0.009 0.001 PHE A 28 TYR 0.010 0.001 TYR D 251 ARG 0.008 0.000 ARG B 153 *********************** 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 : 0.865 Fit side-chains REVERT: A 140 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8457 (mp0) REVERT: A 183 LEU cc_start: 0.8598 (mt) cc_final: 0.8306 (mt) REVERT: B 41 HIS cc_start: 0.4839 (m90) cc_final: 0.4481 (m170) REVERT: B 192 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.8467 (tt0) REVERT: C 175 LYS cc_start: 0.8243 (mmmm) cc_final: 0.7708 (mmtt) outliers start: 11 outliers final: 8 residues processed: 99 average time/residue: 0.2121 time to fit residues: 28.3797 Evaluate side-chains 101 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 16 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 chunk 67 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 25 optimal weight: 0.4980 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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** C 31 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.130050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.111955 restraints weight = 10606.349| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.73 r_work: 0.3150 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.0952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7827 Z= 0.261 Angle : 0.508 5.688 10599 Z= 0.260 Chirality : 0.042 0.129 1223 Planarity : 0.004 0.042 1325 Dihedral : 4.075 14.449 1035 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.93 % Allowed : 13.27 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.28), residues: 967 helix: 0.99 (0.22), residues: 567 sheet: -2.00 (0.77), residues: 53 loop : -1.21 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 128 HIS 0.003 0.001 HIS B 52 PHE 0.011 0.001 PHE A 28 TYR 0.011 0.001 TYR D 251 ARG 0.008 0.000 ARG B 153 *********************** 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 111 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.809 Fit side-chains REVERT: A 140 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8478 (mp0) REVERT: A 183 LEU cc_start: 0.8618 (mt) cc_final: 0.8325 (mt) REVERT: B 192 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.8483 (tt0) REVERT: C 31 GLN cc_start: 0.8552 (mm-40) cc_final: 0.8245 (mm-40) REVERT: C 87 LEU cc_start: 0.8565 (tp) cc_final: 0.8241 (tp) REVERT: C 175 LYS cc_start: 0.8268 (mmmm) cc_final: 0.7702 (mmtt) outliers start: 16 outliers final: 11 residues processed: 103 average time/residue: 0.1969 time to fit residues: 27.7864 Evaluate side-chains 104 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR 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 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 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 1 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 = 0.130950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.112926 restraints weight = 10559.042| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.72 r_work: 0.3125 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 7827 Z= 0.356 Angle : 0.564 6.881 10599 Z= 0.289 Chirality : 0.044 0.134 1223 Planarity : 0.005 0.042 1325 Dihedral : 4.285 15.804 1035 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.29 % Allowed : 14.48 % 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 (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: -0.10 (0.28), residues: 967 helix: 0.87 (0.22), residues: 565 sheet: -2.28 (0.68), residues: 63 loop : -1.12 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 94 HIS 0.004 0.001 HIS B 52 PHE 0.014 0.002 PHE A 28 TYR 0.013 0.001 TYR D 251 ARG 0.008 0.000 ARG B 153 *********************** 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 112 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 1.253 Fit side-chains REVERT: A 13 PHE cc_start: 0.8321 (OUTLIER) cc_final: 0.7462 (m-10) REVERT: A 183 LEU cc_start: 0.8731 (mt) cc_final: 0.8426 (mt) REVERT: B 192 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8532 (tt0) REVERT: C 31 GLN cc_start: 0.8622 (mm-40) cc_final: 0.8403 (mm-40) REVERT: C 175 LYS cc_start: 0.8298 (mmmm) cc_final: 0.7702 (mmtt) outliers start: 19 outliers final: 14 residues processed: 102 average time/residue: 0.2471 time to fit residues: 34.5864 Evaluate side-chains 105 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.842 ------------------------------------------------------------------------------- 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 12 THR Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain A residue 140 GLU 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 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 26 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 94 optimal weight: 0.0770 chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 overall best weight: 1.1344 ------------------------------------------------------------------------------- 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 = 0.3478 r_free = 0.3478 target = 0.131144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.113270 restraints weight = 10555.110| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.71 r_work: 0.3182 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7827 Z= 0.217 Angle : 0.502 8.362 10599 Z= 0.255 Chirality : 0.041 0.128 1223 Planarity : 0.004 0.041 1325 Dihedral : 4.080 14.640 1035 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.81 % Allowed : 15.08 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.28), residues: 967 helix: 1.05 (0.22), residues: 567 sheet: -2.13 (0.76), residues: 53 loop : -1.16 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 128 HIS 0.003 0.001 HIS B 52 PHE 0.010 0.001 PHE A 28 TYR 0.012 0.001 TYR D 251 ARG 0.010 0.000 ARG B 153 *********************** 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 112 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.911 Fit side-chains REVERT: A 140 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8490 (mp0) REVERT: A 183 LEU cc_start: 0.8607 (mt) cc_final: 0.8293 (mt) REVERT: B 192 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8486 (tt0) REVERT: C 31 GLN cc_start: 0.8565 (mm-40) cc_final: 0.8353 (mm-40) REVERT: C 175 LYS cc_start: 0.8322 (mmmm) cc_final: 0.7735 (mmtt) outliers start: 15 outliers final: 10 residues processed: 105 average time/residue: 0.1910 time to fit residues: 27.8484 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 : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 140 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 6 optimal weight: 0.7980 chunk 40 optimal weight: 0.1980 chunk 36 optimal weight: 0.6980 chunk 48 optimal weight: 0.4980 chunk 63 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 chunk 65 optimal weight: 0.0050 chunk 7 optimal weight: 0.0970 chunk 33 optimal weight: 0.8980 chunk 13 optimal weight: 0.0870 overall best weight: 0.1770 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 HIS A 143 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.136309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.118443 restraints weight = 10549.261| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.73 r_work: 0.3220 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7827 Z= 0.124 Angle : 0.464 8.618 10599 Z= 0.238 Chirality : 0.039 0.124 1223 Planarity : 0.004 0.040 1325 Dihedral : 3.744 17.068 1035 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.57 % Allowed : 16.28 % 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 (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: 0.45 (0.28), residues: 967 helix: 1.34 (0.23), residues: 567 sheet: -2.02 (0.77), residues: 53 loop : -1.03 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 161 HIS 0.002 0.000 HIS D 265 PHE 0.007 0.001 PHE C 61 TYR 0.011 0.001 TYR B 12 ARG 0.006 0.000 ARG B 153 *********************** 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 116 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.765 Fit side-chains REVERT: A 13 PHE cc_start: 0.8359 (OUTLIER) cc_final: 0.7330 (m-10) REVERT: A 140 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8400 (mp0) REVERT: A 188 LYS cc_start: 0.8028 (ttpp) cc_final: 0.7792 (ttpp) REVERT: A 236 MET cc_start: 0.8869 (tmm) cc_final: 0.8337 (tmm) REVERT: A 263 ASP cc_start: 0.7103 (m-30) cc_final: 0.6622 (t0) REVERT: B 192 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.8319 (tt0) REVERT: C 87 LEU cc_start: 0.8447 (tp) cc_final: 0.8105 (tp) REVERT: C 175 LYS cc_start: 0.8248 (mmmm) cc_final: 0.7667 (mmtt) REVERT: D 75 MET cc_start: 0.6702 (tmm) cc_final: 0.6500 (tmm) outliers start: 13 outliers final: 8 residues processed: 107 average time/residue: 0.1869 time to fit residues: 27.7529 Evaluate side-chains 106 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain A residue 140 GLU 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 0.1980 chunk 81 optimal weight: 0.0870 chunk 51 optimal weight: 0.9990 chunk 26 optimal weight: 0.3980 chunk 24 optimal weight: 0.1980 chunk 25 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 overall best weight: 0.3158 ------------------------------------------------------------------------------- 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 = 0.3533 r_free = 0.3533 target = 0.135704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.117791 restraints weight = 10581.242| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.73 r_work: 0.3226 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7827 Z= 0.135 Angle : 0.471 8.566 10599 Z= 0.237 Chirality : 0.040 0.124 1223 Planarity : 0.004 0.039 1325 Dihedral : 3.634 17.263 1035 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.21 % Allowed : 16.89 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.28), residues: 967 helix: 1.54 (0.23), residues: 561 sheet: -1.90 (0.77), residues: 53 loop : -0.82 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 108 HIS 0.001 0.000 HIS B 226 PHE 0.010 0.001 PHE C 61 TYR 0.010 0.001 TYR B 12 ARG 0.008 0.000 ARG B 153 *********************** 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 108 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.867 Fit side-chains REVERT: A 13 PHE cc_start: 0.8355 (OUTLIER) cc_final: 0.7342 (m-10) REVERT: A 140 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8413 (mp0) REVERT: A 188 LYS cc_start: 0.7988 (ttpp) cc_final: 0.7743 (ttpp) REVERT: A 236 MET cc_start: 0.8859 (tmm) cc_final: 0.8322 (tmm) REVERT: A 263 ASP cc_start: 0.7032 (m-30) cc_final: 0.6669 (t0) REVERT: B 192 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.8330 (tt0) REVERT: C 87 LEU cc_start: 0.8440 (tp) cc_final: 0.8079 (tp) REVERT: C 175 LYS cc_start: 0.8216 (mmmm) cc_final: 0.7671 (mmtt) outliers start: 10 outliers final: 6 residues processed: 101 average time/residue: 0.1944 time to fit residues: 27.2526 Evaluate side-chains 104 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain B residue 192 GLN Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain D residue 14 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 74 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 93 optimal weight: 0.3980 chunk 71 optimal weight: 0.8980 chunk 65 optimal weight: 0.1980 chunk 54 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3542 r_free = 0.3542 target = 0.136284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.118334 restraints weight = 10502.412| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.71 r_work: 0.3221 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7827 Z= 0.164 Angle : 0.492 8.369 10599 Z= 0.247 Chirality : 0.040 0.127 1223 Planarity : 0.004 0.038 1325 Dihedral : 3.616 18.326 1035 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.33 % Allowed : 17.13 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.28), residues: 967 helix: 1.51 (0.23), residues: 567 sheet: -1.79 (0.78), residues: 53 loop : -0.81 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 128 HIS 0.002 0.001 HIS B 242 PHE 0.010 0.001 PHE C 61 TYR 0.013 0.001 TYR D 30 ARG 0.008 0.000 ARG B 153 ********************** 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 106 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.790 Fit side-chains REVERT: A 13 PHE cc_start: 0.8357 (OUTLIER) cc_final: 0.7413 (m-10) REVERT: A 140 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8413 (mp0) REVERT: A 188 LYS cc_start: 0.7991 (ttpp) cc_final: 0.7745 (ttpp) REVERT: A 236 MET cc_start: 0.8865 (tmm) cc_final: 0.8319 (tmm) REVERT: A 263 ASP cc_start: 0.7077 (m-30) cc_final: 0.6613 (t0) REVERT: B 192 GLN cc_start: 0.8612 (OUTLIER) cc_final: 0.8367 (tt0) REVERT: C 87 LEU cc_start: 0.8494 (tp) cc_final: 0.8123 (tp) REVERT: C 175 LYS cc_start: 0.8238 (mmmm) cc_final: 0.7713 (mmtt) outliers start: 11 outliers final: 8 residues processed: 100 average time/residue: 0.1895 time to fit residues: 26.2132 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 : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain A residue 140 GLU 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 D residue 14 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 3 optimal weight: 1.9990 chunk 86 optimal weight: 0.2980 chunk 53 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 chunk 90 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 55 optimal weight: 0.0980 chunk 18 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 65 optimal weight: 0.0970 overall best weight: 0.3778 ------------------------------------------------------------------------------- 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 = 0.3556 r_free = 0.3556 target = 0.137510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.119558 restraints weight = 10486.311| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.71 r_work: 0.3241 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1688 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= 0.142 Angle : 0.484 8.394 10599 Z= 0.242 Chirality : 0.040 0.129 1223 Planarity : 0.004 0.039 1325 Dihedral : 3.547 19.540 1035 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.57 % Allowed : 17.01 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.88 (0.28), residues: 967 helix: 1.60 (0.23), residues: 560 sheet: -1.68 (0.79), residues: 53 loop : -0.66 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 128 HIS 0.003 0.000 HIS B 242 PHE 0.010 0.001 PHE C 61 TYR 0.018 0.001 TYR D 30 ARG 0.008 0.000 ARG B 153 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3619.32 seconds wall clock time: 62 minutes 50.99 seconds (3770.99 seconds total)