Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 14:34:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nnt_12483/04_2023/7nnt_12483.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nnt_12483/04_2023/7nnt_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_12483/04_2023/7nnt_12483.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nnt_12483/04_2023/7nnt_12483.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nnt_12483/04_2023/7nnt_12483.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nnt_12483/04_2023/7nnt_12483.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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-1.21rc1-4938/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: 4.59, per 1000 atoms: 0.60 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: 3.13 Conformation dependent library (CDL) restraints added in 1.2 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: 0.24 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: 1.64 Time building geometry restraints manager: 3.39 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: 0.700 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: 4.230 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 22.670 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.680 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 0.940 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.2359 time to fit residues: 33.0583 Evaluate side-chains 92 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.946 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3133 ------------------------------------------------------------------------------- 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 ** 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: 0.7885 moved from start: 0.0555 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= 0.163 Angle : 0.477 5.294 10599 Z= 0.243 Chirality : 0.040 0.135 1223 Planarity : 0.004 0.043 1325 Dihedral : 4.145 15.125 1035 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer Outliers : 0.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.27), residues: 967 helix: 0.83 (0.22), residues: 567 sheet: -1.80 (0.71), residues: 63 loop : -1.25 (0.32), residues: 337 *********************** 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: 8 poor density : 101 time to evaluate : 0.980 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 105 average time/residue: 0.2242 time to fit residues: 31.5315 Evaluate side-chains 95 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 90 time to evaluate : 0.931 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0720 time to fit residues: 1.9588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 47 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 86 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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: 0.7883 moved from start: 0.0740 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= 0.165 Angle : 0.465 5.113 10599 Z= 0.237 Chirality : 0.040 0.132 1223 Planarity : 0.004 0.041 1325 Dihedral : 3.941 14.835 1035 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer Outliers : 0.48 % 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: 0.16 (0.28), residues: 967 helix: 1.08 (0.22), residues: 567 sheet: -1.78 (0.72), residues: 63 loop : -1.12 (0.32), residues: 337 *********************** 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 101 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 97 time to evaluate : 0.937 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 99 average time/residue: 0.2177 time to fit residues: 29.0213 Evaluate side-chains 91 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 88 time to evaluate : 0.931 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0918 time to fit residues: 1.7477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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: 0.7938 moved from start: 0.0761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 7827 Z= 0.298 Angle : 0.522 6.005 10599 Z= 0.266 Chirality : 0.043 0.130 1223 Planarity : 0.004 0.042 1325 Dihedral : 4.092 14.555 1035 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer Outliers : 1.33 % 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: 1.02 (0.22), residues: 565 sheet: -1.87 (0.72), residues: 63 loop : -1.07 (0.33), residues: 339 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 94 time to evaluate : 0.959 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 101 average time/residue: 0.2236 time to fit residues: 30.6405 Evaluate side-chains 97 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 89 time to evaluate : 1.001 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0750 time to fit residues: 2.3844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.4980 chunk 68 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 78 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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: 0.7920 moved from start: 0.0856 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= 0.224 Angle : 0.486 5.252 10599 Z= 0.248 Chirality : 0.041 0.127 1223 Planarity : 0.004 0.041 1325 Dihedral : 3.998 14.108 1035 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer Outliers : 1.09 % 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: 0.15 (0.28), residues: 967 helix: 1.07 (0.22), residues: 567 sheet: -1.94 (0.72), residues: 63 loop : -1.09 (0.33), residues: 337 *********************** 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 100 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 91 time to evaluate : 0.949 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 96 average time/residue: 0.2079 time to fit residues: 27.4816 Evaluate side-chains 93 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 88 time to evaluate : 0.915 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0768 time to fit residues: 2.0014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 30 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.076 7827 Z= 0.471 Angle : 0.634 7.965 10599 Z= 0.323 Chirality : 0.047 0.220 1223 Planarity : 0.005 0.045 1325 Dihedral : 4.476 16.677 1035 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer Outliers : 1.21 % 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: -0.27 (0.27), residues: 967 helix: 0.69 (0.22), residues: 563 sheet: -2.14 (0.71), residues: 63 loop : -1.15 (0.33), residues: 341 *********************** 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 103 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 93 time to evaluate : 0.987 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 100 average time/residue: 0.2169 time to fit residues: 29.0849 Evaluate side-chains 95 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 90 time to evaluate : 0.860 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0744 time to fit residues: 1.8406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 10 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.7913 moved from start: 0.0984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 7827 Z= 0.181 Angle : 0.480 6.019 10599 Z= 0.245 Chirality : 0.040 0.128 1223 Planarity : 0.004 0.043 1325 Dihedral : 4.051 14.774 1035 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer Outliers : 0.97 % 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: 1.09 (0.23), residues: 565 sheet: -2.04 (0.72), residues: 63 loop : -1.09 (0.33), residues: 339 *********************** 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 106 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 98 time to evaluate : 0.935 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 100 average time/residue: 0.2166 time to fit residues: 29.3371 Evaluate side-chains 93 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 89 time to evaluate : 0.915 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0755 time to fit residues: 1.7925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 17 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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: 0.7968 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.060 7827 Z= 0.359 Angle : 0.579 8.671 10599 Z= 0.293 Chirality : 0.045 0.214 1223 Planarity : 0.005 0.045 1325 Dihedral : 4.293 15.818 1035 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer Outliers : 0.72 % 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: -0.06 (0.28), residues: 967 helix: 0.90 (0.22), residues: 564 sheet: -2.18 (0.70), residues: 63 loop : -1.13 (0.33), residues: 340 *********************** 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 100 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 94 time to evaluate : 0.998 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 96 average time/residue: 0.2121 time to fit residues: 27.7493 Evaluate side-chains 94 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 90 time to evaluate : 0.920 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1081 time to fit residues: 2.0374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 80 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.7916 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 7827 Z= 0.207 Angle : 0.515 8.635 10599 Z= 0.259 Chirality : 0.041 0.132 1223 Planarity : 0.004 0.052 1325 Dihedral : 4.119 15.770 1035 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer Outliers : 0.24 % 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: 1.09 (0.22), residues: 567 sheet: -2.05 (0.72), residues: 63 loop : -1.10 (0.33), residues: 337 *********************** 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 98 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 96 time to evaluate : 0.963 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 96 average time/residue: 0.2225 time to fit residues: 29.0820 Evaluate side-chains 89 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 88 time to evaluate : 0.969 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0770 time to fit residues: 1.4566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 42 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.7897 moved from start: 0.1212 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= 0.189 Angle : 0.507 8.786 10599 Z= 0.256 Chirality : 0.041 0.202 1223 Planarity : 0.004 0.047 1325 Dihedral : 3.984 15.257 1035 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer Outliers : 0.36 % 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: 0.30 (0.28), residues: 967 helix: 1.22 (0.23), residues: 567 sheet: -1.98 (0.73), residues: 63 loop : -1.05 (0.33), residues: 337 ********************** 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 99 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 96 time to evaluate : 0.875 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 97 average time/residue: 0.2423 time to fit residues: 32.7939 Evaluate side-chains 92 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 91 time to evaluate : 1.380 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1117 time to fit residues: 2.0111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 69 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 20 optimal weight: 8.9990 chunk 75 optimal weight: 2.9990 chunk 31 optimal weight: 0.1980 chunk 77 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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** D 39 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.131310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.113588 restraints weight = 10477.242| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.69 r_work: 0.3183 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 7827 Z= 0.225 Angle : 0.522 8.606 10599 Z= 0.261 Chirality : 0.041 0.129 1223 Planarity : 0.004 0.055 1325 Dihedral : 3.996 15.579 1035 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer Outliers : 0.36 % 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: 0.34 (0.28), residues: 967 helix: 1.25 (0.23), residues: 567 sheet: -1.99 (0.73), residues: 63 loop : -1.04 (0.33), residues: 337 =============================================================================== Job complete usr+sys time: 1658.42 seconds wall clock time: 30 minutes 51.21 seconds (1851.21 seconds total)