Starting phenix.real_space_refine on Wed Feb 12 08:27:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nnt_12483/02_2025/7nnt_12483.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nnt_12483/02_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_12483/02_2025/7nnt_12483.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nnt_12483/02_2025/7nnt_12483.map" model { file = "/net/cci-nas-00/data/ceres_data/7nnt_12483/02_2025/7nnt_12483.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nnt_12483/02_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-5592/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: 4.90, per 1000 atoms: 0.64 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: 1.74 Conformation dependent library (CDL) restraints added in 1.0 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: 1.72 Time building geometry restraints manager: 2.05 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: 0.940 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 19.510 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.570 ------------------------------------------------------------------------------- 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 : 0.892 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: 0.2371 time to fit residues: 33.2254 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 : 0.835 ------------------------------------------------------------------------------- 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 = 0.131468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.113614 restraints weight = 10430.941| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.71 r_work: 0.3157 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 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 6.165 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 : 0.966 Fit side-chains REVERT: A 12 THR cc_start: 0.8181 (OUTLIER) cc_final: 0.7960 (m) REVERT: B 41 HIS cc_start: 0.4546 (m-70) cc_final: 0.4242 (m170) REVERT: B 192 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.8535 (tt0) REVERT: C 175 LYS cc_start: 0.8153 (mmmm) cc_final: 0.7685 (mmtt) outliers start: 7 outliers final: 4 residues processed: 106 average time/residue: 0.2174 time to fit residues: 31.0072 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 : 0.910 ------------------------------------------------------------------------------- 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: 0.9990 chunk 75 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 47 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- 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 = 0.3502 r_free = 0.3502 target = 0.133059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.115226 restraints weight = 10537.437| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.71 r_work: 0.3170 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.0773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7827 Z= 0.189 Angle : 0.488 5.246 10599 Z= 0.250 Chirality : 0.041 0.137 1223 Planarity : 0.004 0.042 1325 Dihedral : 4.130 14.907 1035 Min Nonbonded Distance : 2.558 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: -0.12 (0.27), residues: 967 helix: 0.85 (0.22), residues: 567 sheet: -2.02 (0.70), residues: 63 loop : -1.21 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 66 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 0.005 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 : 0.898 Fit side-chains REVERT: A 140 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8453 (mp0) REVERT: B 41 HIS cc_start: 0.4860 (m90) cc_final: 0.4329 (m170) REVERT: B 192 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.8476 (tt0) REVERT: C 175 LYS cc_start: 0.8226 (mmmm) cc_final: 0.7690 (mmtt) outliers start: 11 outliers final: 7 residues processed: 104 average time/residue: 0.2183 time to fit residues: 30.8615 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 : 0.902 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 10 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3510 r_free = 0.3510 target = 0.133794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.115876 restraints weight = 10432.480| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.71 r_work: 0.3181 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.0925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7827 Z= 0.181 Angle : 0.473 5.087 10599 Z= 0.243 Chirality : 0.041 0.132 1223 Planarity : 0.004 0.041 1325 Dihedral : 3.960 14.191 1035 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.33 % Allowed : 11.58 % Favored : 87.09 % 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: 0.12 (0.28), residues: 967 helix: 1.07 (0.22), residues: 567 sheet: -1.93 (0.77), residues: 53 loop : -1.20 (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 0.007 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 107 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.869 Fit side-chains REVERT: A 140 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8402 (mp0) REVERT: B 41 HIS cc_start: 0.4666 (m90) cc_final: 0.4354 (m170) REVERT: B 192 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.8416 (tt0) REVERT: C 175 LYS cc_start: 0.8223 (mmmm) cc_final: 0.7691 (mmtt) REVERT: D 116 PHE cc_start: 0.8909 (m-80) cc_final: 0.8590 (m-10) outliers start: 11 outliers final: 8 residues processed: 101 average time/residue: 0.2080 time to fit residues: 28.6717 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 : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 16 optimal weight: 0.0980 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: 0.9990 chunk 39 optimal weight: 0.0370 chunk 68 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 overall best weight: 0.8262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.133378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.115322 restraints weight = 10506.766| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.72 r_work: 0.3196 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7827 Z= 0.174 Angle : 0.466 5.694 10599 Z= 0.238 Chirality : 0.041 0.129 1223 Planarity : 0.004 0.040 1325 Dihedral : 3.849 13.794 1035 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.57 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 (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: 0.31 (0.28), residues: 967 helix: 1.23 (0.22), residues: 567 sheet: -1.88 (0.78), residues: 53 loop : -1.13 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 128 HIS 0.003 0.001 HIS B 52 PHE 0.009 0.001 PHE A 28 TYR 0.009 0.001 TYR D 251 ARG 0.005 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 108 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.820 Fit side-chains REVERT: A 140 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8435 (mp0) REVERT: B 41 HIS cc_start: 0.5070 (m90) cc_final: 0.4847 (m170) REVERT: B 192 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.8435 (tt0) REVERT: C 87 LEU cc_start: 0.8499 (tp) cc_final: 0.8140 (tp) REVERT: C 175 LYS cc_start: 0.8225 (mmmm) cc_final: 0.7706 (mmtt) REVERT: D 116 PHE cc_start: 0.8934 (m-80) cc_final: 0.8595 (m-10) outliers start: 14 outliers final: 10 residues processed: 99 average time/residue: 0.1970 time to fit residues: 26.7083 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 : 0.883 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 1 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 88 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 67 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.134205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.116350 restraints weight = 10411.849| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.70 r_work: 0.3195 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7827 Z= 0.177 Angle : 0.466 5.420 10599 Z= 0.239 Chirality : 0.041 0.127 1223 Planarity : 0.004 0.039 1325 Dihedral : 3.820 13.615 1035 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.69 % Allowed : 14.60 % Favored : 83.72 % 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: 0.40 (0.28), residues: 967 helix: 1.31 (0.22), residues: 567 sheet: -1.86 (0.79), residues: 53 loop : -1.09 (0.33), 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 52 PHE 0.009 0.001 PHE A 28 TYR 0.009 0.001 TYR D 251 ARG 0.005 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 107 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.853 Fit side-chains REVERT: A 119 GLU cc_start: 0.8307 (tp30) cc_final: 0.8099 (mp0) REVERT: A 140 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8431 (mp0) REVERT: B 192 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8420 (tt0) REVERT: C 87 LEU cc_start: 0.8522 (tp) cc_final: 0.8183 (tp) REVERT: C 175 LYS cc_start: 0.8237 (mmmm) cc_final: 0.7703 (mmtt) outliers start: 14 outliers final: 9 residues processed: 99 average time/residue: 0.1979 time to fit residues: 27.1860 Evaluate side-chains 100 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 26 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 33 optimal weight: 0.4980 chunk 80 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 94 optimal weight: 0.0670 chunk 19 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 overall best weight: 0.7118 ------------------------------------------------------------------------------- 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 = 0.3524 r_free = 0.3524 target = 0.134832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.116818 restraints weight = 10489.024| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.71 r_work: 0.3204 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7827 Z= 0.162 Angle : 0.458 5.312 10599 Z= 0.234 Chirality : 0.040 0.125 1223 Planarity : 0.004 0.039 1325 Dihedral : 3.743 13.605 1035 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.05 % Allowed : 14.96 % Favored : 82.99 % 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 (0.28), residues: 967 helix: 1.40 (0.23), residues: 565 sheet: -1.76 (0.80), residues: 53 loop : -0.99 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 128 HIS 0.002 0.001 HIS B 52 PHE 0.008 0.001 PHE C 61 TYR 0.009 0.001 TYR D 251 ARG 0.005 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 110 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.865 Fit side-chains REVERT: A 140 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8420 (mp0) REVERT: A 183 LEU cc_start: 0.8510 (mt) cc_final: 0.8206 (mt) REVERT: A 263 ASP cc_start: 0.7135 (m-30) cc_final: 0.6615 (t0) REVERT: B 192 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.8413 (tt0) REVERT: C 87 LEU cc_start: 0.8502 (tp) cc_final: 0.8164 (tp) REVERT: C 175 LYS cc_start: 0.8243 (mmmm) cc_final: 0.7706 (mmtt) outliers start: 17 outliers final: 11 residues processed: 101 average time/residue: 0.1888 time to fit residues: 26.2908 Evaluate side-chains 102 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.917 ------------------------------------------------------------------------------- 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 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 78 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 6 optimal weight: 7.9990 chunk 40 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 33 optimal weight: 0.0980 chunk 13 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.135547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.117594 restraints weight = 10594.339| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.72 r_work: 0.3201 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1367 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= 0.160 Angle : 0.457 5.350 10599 Z= 0.236 Chirality : 0.040 0.125 1223 Planarity : 0.004 0.037 1325 Dihedral : 3.688 13.667 1035 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.93 % Allowed : 15.20 % Favored : 82.87 % 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: 0.65 (0.28), residues: 967 helix: 1.47 (0.23), residues: 564 sheet: -1.73 (0.79), residues: 53 loop : -0.89 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 108 HIS 0.002 0.000 HIS B 226 PHE 0.010 0.001 PHE C 61 TYR 0.009 0.001 TYR D 251 ARG 0.004 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 110 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.817 Fit side-chains REVERT: A 13 PHE cc_start: 0.8305 (OUTLIER) cc_final: 0.7370 (m-10) REVERT: A 140 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8388 (mp0) REVERT: A 183 LEU cc_start: 0.8469 (mt) cc_final: 0.8141 (mt) REVERT: A 263 ASP cc_start: 0.7120 (m-30) cc_final: 0.6583 (t0) REVERT: B 192 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.8358 (tt0) REVERT: C 87 LEU cc_start: 0.8482 (tp) cc_final: 0.8153 (tp) REVERT: C 175 LYS cc_start: 0.8246 (mmmm) cc_final: 0.7705 (mmtt) REVERT: D 75 MET cc_start: 0.6933 (tmm) cc_final: 0.6666 (tmm) outliers start: 16 outliers final: 12 residues processed: 100 average time/residue: 0.2010 time to fit residues: 27.8886 Evaluate side-chains 105 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.897 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain D residue 190 ASP 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: 5.9990 chunk 81 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.3513 r_free = 0.3513 target = 0.133863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.115871 restraints weight = 10623.814| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.71 r_work: 0.3178 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 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 : 0.003 0.038 7827 Z= 0.216 Angle : 0.489 6.627 10599 Z= 0.250 Chirality : 0.041 0.128 1223 Planarity : 0.004 0.036 1325 Dihedral : 3.767 13.278 1035 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.05 % Allowed : 15.20 % Favored : 82.75 % 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: 0.60 (0.28), residues: 967 helix: 1.42 (0.23), residues: 564 sheet: -1.76 (0.79), residues: 53 loop : -0.89 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 128 HIS 0.002 0.001 HIS B 52 PHE 0.011 0.001 PHE C 61 TYR 0.012 0.001 TYR B 12 ARG 0.004 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 111 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.861 Fit side-chains REVERT: A 13 PHE cc_start: 0.8378 (OUTLIER) cc_final: 0.7477 (m-10) REVERT: A 140 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8415 (mp0) REVERT: A 183 LEU cc_start: 0.8534 (mt) cc_final: 0.8207 (mt) REVERT: A 263 ASP cc_start: 0.7107 (m-30) cc_final: 0.6623 (t0) REVERT: B 192 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.8413 (tt0) REVERT: C 175 LYS cc_start: 0.8273 (mmmm) cc_final: 0.7707 (mmtt) outliers start: 17 outliers final: 12 residues processed: 100 average time/residue: 0.1892 time to fit residues: 26.3771 Evaluate side-chains 107 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.889 ------------------------------------------------------------------------------- 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 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 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 74 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 88 optimal weight: 0.1980 chunk 17 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3518 r_free = 0.3518 target = 0.134409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.116310 restraints weight = 10528.134| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.72 r_work: 0.3202 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7827 Z= 0.167 Angle : 0.471 7.566 10599 Z= 0.240 Chirality : 0.040 0.126 1223 Planarity : 0.004 0.036 1325 Dihedral : 3.686 16.157 1035 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.81 % Allowed : 15.92 % 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 (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: 0.68 (0.28), residues: 967 helix: 1.49 (0.23), residues: 565 sheet: -1.71 (0.79), residues: 53 loop : -0.88 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 128 HIS 0.002 0.000 HIS B 52 PHE 0.011 0.001 PHE C 61 TYR 0.023 0.001 TYR D 9 ARG 0.004 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 110 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.834 Fit side-chains REVERT: A 13 PHE cc_start: 0.8380 (OUTLIER) cc_final: 0.7530 (m-10) REVERT: A 140 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8418 (mp0) REVERT: A 183 LEU cc_start: 0.8502 (mt) cc_final: 0.8174 (mt) REVERT: A 263 ASP cc_start: 0.7117 (m-30) cc_final: 0.6629 (t0) REVERT: B 192 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.8403 (tt0) REVERT: C 87 LEU cc_start: 0.8543 (tp) cc_final: 0.8207 (tp) REVERT: C 175 LYS cc_start: 0.8270 (mmmm) cc_final: 0.7710 (mmtt) outliers start: 15 outliers final: 12 residues processed: 101 average time/residue: 0.1853 time to fit residues: 26.1901 Evaluate side-chains 108 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.851 ------------------------------------------------------------------------------- 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 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 35 ILE 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 3 optimal weight: 2.9990 chunk 86 optimal weight: 0.0570 chunk 53 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 90 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 overall best weight: 0.5898 ------------------------------------------------------------------------------- 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 = 0.3540 r_free = 0.3540 target = 0.136246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.118311 restraints weight = 10513.984| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.71 r_work: 0.3209 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 7827 Z= 0.154 Angle : 0.463 8.025 10599 Z= 0.235 Chirality : 0.040 0.124 1223 Planarity : 0.004 0.037 1325 Dihedral : 3.591 14.883 1035 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.81 % Allowed : 16.16 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.28), residues: 967 helix: 1.63 (0.23), residues: 554 sheet: -1.63 (0.80), residues: 53 loop : -0.66 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 128 HIS 0.002 0.000 HIS B 226 PHE 0.011 0.001 PHE C 61 TYR 0.013 0.001 TYR B 12 ARG 0.004 0.000 ARG B 153 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3479.22 seconds wall clock time: 62 minutes 33.35 seconds (3753.35 seconds total)