Starting phenix.real_space_refine on Tue Feb 13 20:28:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nnt_12483/02_2024/7nnt_12483.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nnt_12483/02_2024/7nnt_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nnt_12483/02_2024/7nnt_12483.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nnt_12483/02_2024/7nnt_12483.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nnt_12483/02_2024/7nnt_12483.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nnt_12483/02_2024/7nnt_12483.pdb" } 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 Residue "A PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 17": "OD1" <-> "OD2" Residue "A ASP 25": "OD1" <-> "OD2" Residue "A PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 84": "OE1" <-> "OE2" Residue "A ASP 104": "OD1" <-> "OD2" Residue "A TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 138": "OD1" <-> "OD2" Residue "A GLU 177": "OE1" <-> "OE2" Residue "A ASP 217": "OD1" <-> "OD2" Residue "A ASP 223": "OD1" <-> "OD2" Residue "A TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 256": "OE1" <-> "OE2" Residue "A GLU 264": "OE1" <-> "OE2" Residue "A ASP 268": "OD1" <-> "OD2" Residue "A GLU 269": "OE1" <-> "OE2" Residue "B ASP 24": "OD1" <-> "OD2" Residue "B PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 32": "OE1" <-> "OE2" Residue "B PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 170": "OD1" <-> "OD2" Residue "B GLU 183": "OE1" <-> "OE2" Residue "B TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 206": "OD1" <-> "OD2" Residue "B TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 231": "OE1" <-> "OE2" Residue "C ARG 14": "NH1" <-> "NH2" Residue "C PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 68": "OD1" <-> "OD2" Residue "C PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 145": "NH1" <-> "NH2" Residue "C GLU 149": "OE1" <-> "OE2" Residue "C GLU 165": "OE1" <-> "OE2" Residue "D TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 115": "NH1" <-> "NH2" Residue "D PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 196": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 4.53, per 1000 atoms: 0.59 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 - 3.50 Amino acid : False - 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: 2.92 Conformation dependent library (CDL) restraints added in 1.4 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: 0.64 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: 1.65 Time building geometry restraints manager: 3.17 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: 100.13 - 106.93: 221 106.93 - 113.73: 4465 113.73 - 120.54: 3228 120.54 - 127.34: 2596 127.34 - 134.14: 89 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 2.520 nonbonded pdb=" OH TYR D 30 " pdb=" OG1 THR D 256 " model vdw 2.228 2.440 nonbonded pdb=" O MET C 133 " pdb=" NH1 ARG D 115 " model vdw 2.344 2.520 nonbonded pdb=" OG1 THR A 12 " pdb=" OD2 ASP A 60 " model vdw 2.346 2.440 nonbonded pdb=" O PRO B 164 " pdb=" OH TYR B 191 " model vdw 2.357 2.440 ... (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 ========== 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: 0.890 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: 4.030 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 23.100 Find NCS groups from input model: 0.240 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: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.240 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 0.742 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: 0.2373 time to fit residues: 33.2559 Evaluate side-chains 92 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.901 ------------------------------------------------------------------------------- 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: 1.9990 chunk 39 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 38 optimal weight: 0.2980 chunk 74 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 ASN B 41 HIS ** C 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.0537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7827 Z= 0.163 Angle : 0.478 5.450 10599 Z= 0.243 Chirality : 0.040 0.136 1223 Planarity : 0.004 0.043 1325 Dihedral : 4.159 15.177 1035 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.84 % Allowed : 6.63 % Favored : 92.52 % 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: -0.15 (0.27), residues: 967 helix: 0.82 (0.22), residues: 567 sheet: -1.79 (0.72), residues: 63 loop : -1.26 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 66 HIS 0.003 0.001 HIS B 41 PHE 0.010 0.001 PHE C 61 TYR 0.008 0.001 TYR C 134 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 109 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 102 time to evaluate : 0.873 Fit side-chains REVERT: A 140 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.8094 (mp0) REVERT: B 41 HIS cc_start: 0.3715 (m90) cc_final: 0.3187 (m170) REVERT: C 87 LEU cc_start: 0.8492 (tp) cc_final: 0.8187 (tp) REVERT: C 175 LYS cc_start: 0.8103 (mmmm) cc_final: 0.7793 (mmtt) outliers start: 7 outliers final: 4 residues processed: 106 average time/residue: 0.2286 time to fit residues: 32.0509 Evaluate side-chains 97 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 92 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 144 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 47 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.0751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7827 Z= 0.166 Angle : 0.463 5.144 10599 Z= 0.236 Chirality : 0.040 0.130 1223 Planarity : 0.004 0.041 1325 Dihedral : 3.909 14.649 1035 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.21 % Allowed : 9.29 % Favored : 89.51 % 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: 0.19 (0.28), residues: 967 helix: 1.10 (0.22), residues: 567 sheet: -1.75 (0.73), residues: 63 loop : -1.10 (0.33), 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 0.009 0.001 PHE C 61 TYR 0.008 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 fitting. rotamer outliers: 10 poor density : 99 time to evaluate : 0.865 Fit side-chains REVERT: B 41 HIS cc_start: 0.3634 (m90) cc_final: 0.3313 (m170) REVERT: C 175 LYS cc_start: 0.8129 (mmmm) cc_final: 0.7802 (mmtt) outliers start: 10 outliers final: 8 residues processed: 104 average time/residue: 0.2334 time to fit residues: 33.1833 Evaluate side-chains 99 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 91 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain C residue 108 TRP Chi-restraints excluded: chain C residue 113 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 85 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 GLN ** C 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.0792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 7827 Z= 0.295 Angle : 0.526 6.269 10599 Z= 0.268 Chirality : 0.043 0.131 1223 Planarity : 0.004 0.042 1325 Dihedral : 4.088 14.409 1035 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.81 % Allowed : 11.70 % Favored : 86.49 % 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: 0.07 (0.28), residues: 967 helix: 0.99 (0.22), residues: 567 sheet: -1.86 (0.72), residues: 63 loop : -1.12 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 94 HIS 0.004 0.001 HIS D 95 PHE 0.012 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 107 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 92 time to evaluate : 0.938 Fit side-chains REVERT: A 183 LEU cc_start: 0.8504 (mt) cc_final: 0.8175 (mt) REVERT: C 175 LYS cc_start: 0.8233 (mmmm) cc_final: 0.7867 (mmtt) outliers start: 15 outliers final: 13 residues processed: 100 average time/residue: 0.2153 time to fit residues: 29.0666 Evaluate side-chains 103 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 90 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 192 GLN Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain C residue 108 TRP Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 190 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 76 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 1 optimal weight: 0.0170 chunk 68 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 78 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 overall best weight: 1.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.0869 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= 0.272 Angle : 0.511 6.196 10599 Z= 0.261 Chirality : 0.042 0.128 1223 Planarity : 0.004 0.041 1325 Dihedral : 4.073 14.206 1035 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.41 % Allowed : 12.91 % Favored : 84.68 % 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: 0.08 (0.28), residues: 967 helix: 1.02 (0.22), residues: 567 sheet: -1.95 (0.72), residues: 63 loop : -1.12 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 94 HIS 0.003 0.001 HIS D 95 PHE 0.012 0.001 PHE A 28 TYR 0.010 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 fitting. rotamer outliers: 20 poor density : 91 time to evaluate : 0.808 Fit side-chains REVERT: A 13 PHE cc_start: 0.8093 (OUTLIER) cc_final: 0.7457 (m-10) REVERT: A 183 LEU cc_start: 0.8559 (mt) cc_final: 0.8224 (mt) REVERT: C 87 LEU cc_start: 0.8507 (tp) cc_final: 0.8171 (tp) REVERT: C 175 LYS cc_start: 0.8272 (mmmm) cc_final: 0.7871 (mmtt) outliers start: 20 outliers final: 14 residues processed: 104 average time/residue: 0.2150 time to fit residues: 30.2315 Evaluate side-chains 104 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 89 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 177 ASP 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 113 SER Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 123 SER 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 30 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 42 optimal weight: 0.3980 chunk 7 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 88 optimal weight: 3.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.0940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7827 Z= 0.225 Angle : 0.489 5.697 10599 Z= 0.250 Chirality : 0.041 0.126 1223 Planarity : 0.004 0.042 1325 Dihedral : 3.987 13.726 1035 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.53 % Allowed : 12.79 % Favored : 84.68 % 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: 0.20 (0.28), residues: 967 helix: 1.12 (0.22), residues: 567 sheet: -1.97 (0.72), residues: 63 loop : -1.08 (0.33), residues: 337 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 A 28 TYR 0.010 0.001 TYR D 251 ARG 0.009 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 116 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 95 time to evaluate : 0.978 Fit side-chains REVERT: A 13 PHE cc_start: 0.8096 (OUTLIER) cc_final: 0.7459 (m-10) REVERT: A 183 LEU cc_start: 0.8508 (mt) cc_final: 0.8168 (mt) REVERT: C 175 LYS cc_start: 0.8268 (mmmm) cc_final: 0.7856 (mmtt) outliers start: 21 outliers final: 13 residues processed: 108 average time/residue: 0.2008 time to fit residues: 29.8579 Evaluate side-chains 103 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 89 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 177 ASP 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 113 SER Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 190 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 10 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 77 optimal weight: 7.9990 chunk 51 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 39 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 7827 Z= 0.293 Angle : 0.535 8.242 10599 Z= 0.271 Chirality : 0.043 0.130 1223 Planarity : 0.004 0.043 1325 Dihedral : 4.103 15.589 1035 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.53 % Allowed : 13.87 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.15 (0.28), residues: 967 helix: 1.05 (0.22), residues: 565 sheet: -2.00 (0.72), residues: 63 loop : -1.03 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 94 HIS 0.003 0.001 HIS D 95 PHE 0.012 0.001 PHE A 28 TYR 0.011 0.001 TYR D 251 ARG 0.009 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 117 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 96 time to evaluate : 0.949 Fit side-chains REVERT: A 13 PHE cc_start: 0.8173 (OUTLIER) cc_final: 0.7636 (m-10) REVERT: A 183 LEU cc_start: 0.8530 (mt) cc_final: 0.8185 (mt) REVERT: B 224 ILE cc_start: 0.8924 (pt) cc_final: 0.8716 (mt) REVERT: C 175 LYS cc_start: 0.8299 (mmmm) cc_final: 0.7887 (mmtt) outliers start: 21 outliers final: 16 residues processed: 107 average time/residue: 0.1967 time to fit residues: 28.8260 Evaluate side-chains 108 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 91 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 192 GLN Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 108 TRP Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 144 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 54 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 71 optimal weight: 0.0270 chunk 83 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7827 Z= 0.162 Angle : 0.483 8.349 10599 Z= 0.244 Chirality : 0.040 0.134 1223 Planarity : 0.004 0.042 1325 Dihedral : 3.871 16.396 1035 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.81 % Allowed : 14.48 % 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: 1.26 (0.23), residues: 569 sheet: -1.93 (0.73), residues: 63 loop : -0.96 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 128 HIS 0.002 0.000 HIS B 52 PHE 0.008 0.001 PHE C 61 TYR 0.012 0.001 TYR B 12 ARG 0.009 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 109 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 94 time to evaluate : 0.912 Fit side-chains REVERT: A 13 PHE cc_start: 0.8137 (OUTLIER) cc_final: 0.7501 (m-10) REVERT: A 183 LEU cc_start: 0.8443 (mt) cc_final: 0.8107 (mt) REVERT: C 87 LEU cc_start: 0.8458 (tp) cc_final: 0.8137 (tp) REVERT: C 175 LYS cc_start: 0.8250 (mmmm) cc_final: 0.7824 (mmtt) REVERT: D 126 MET cc_start: 0.7594 (tpp) cc_final: 0.7337 (tpt) outliers start: 15 outliers final: 12 residues processed: 103 average time/residue: 0.1893 time to fit residues: 27.1638 Evaluate side-chains 102 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 89 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain C residue 108 TRP Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 144 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 0.6980 chunk 87 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 67 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 90 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 39 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7827 Z= 0.228 Angle : 0.515 8.082 10599 Z= 0.259 Chirality : 0.041 0.131 1223 Planarity : 0.004 0.041 1325 Dihedral : 3.918 16.283 1035 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.69 % Allowed : 15.20 % 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: 0.37 (0.28), residues: 967 helix: 1.24 (0.22), residues: 569 sheet: -1.93 (0.73), residues: 63 loop : -0.97 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 128 HIS 0.002 0.000 HIS B 52 PHE 0.011 0.001 PHE C 61 TYR 0.010 0.001 TYR B 12 ARG 0.009 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 110 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 96 time to evaluate : 0.950 Fit side-chains REVERT: A 13 PHE cc_start: 0.8199 (OUTLIER) cc_final: 0.7668 (m-10) REVERT: A 183 LEU cc_start: 0.8473 (mt) cc_final: 0.8124 (mt) REVERT: C 175 LYS cc_start: 0.8277 (mmmm) cc_final: 0.7862 (mmtt) outliers start: 14 outliers final: 12 residues processed: 104 average time/residue: 0.1999 time to fit residues: 28.5379 Evaluate side-chains 103 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 90 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain C residue 108 TRP Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 123 SER 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 42 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 46 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 39 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7827 Z= 0.206 Angle : 0.508 8.142 10599 Z= 0.254 Chirality : 0.041 0.130 1223 Planarity : 0.004 0.042 1325 Dihedral : 3.898 16.399 1035 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.69 % Allowed : 15.80 % Favored : 82.51 % 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: 0.43 (0.28), residues: 967 helix: 1.28 (0.22), residues: 569 sheet: -1.91 (0.72), residues: 63 loop : -0.94 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 128 HIS 0.002 0.000 HIS B 52 PHE 0.011 0.001 PHE C 61 TYR 0.011 0.001 TYR B 12 ARG 0.010 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 108 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 94 time to evaluate : 0.897 Fit side-chains REVERT: A 13 PHE cc_start: 0.8225 (OUTLIER) cc_final: 0.7687 (m-10) REVERT: A 183 LEU cc_start: 0.8446 (mt) cc_final: 0.8100 (mt) REVERT: A 195 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8505 (pp) REVERT: C 31 GLN cc_start: 0.8228 (mm-40) cc_final: 0.7777 (mt0) REVERT: C 175 LYS cc_start: 0.8270 (mmmm) cc_final: 0.7852 (mmtt) outliers start: 14 outliers final: 12 residues processed: 101 average time/residue: 0.1978 time to fit residues: 27.3345 Evaluate side-chains 107 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 93 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain C residue 108 TRP Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 123 SER 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 69 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 20 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 77 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 39 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.130839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.113154 restraints weight = 10522.071| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.68 r_work: 0.3149 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 7827 Z= 0.331 Angle : 0.570 7.750 10599 Z= 0.287 Chirality : 0.043 0.133 1223 Planarity : 0.004 0.047 1325 Dihedral : 4.132 16.291 1035 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.05 % Allowed : 15.68 % 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: 0.24 (0.28), residues: 967 helix: 1.11 (0.22), residues: 567 sheet: -2.04 (0.71), residues: 63 loop : -0.97 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 128 HIS 0.003 0.001 HIS D 95 PHE 0.013 0.001 PHE A 28 TYR 0.012 0.001 TYR D 251 ARG 0.011 0.000 ARG B 153 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1690.09 seconds wall clock time: 31 minutes 24.69 seconds (1884.69 seconds total)