Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 02:50:35 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ms1_3562/04_2023/5ms1_3562.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ms1_3562/04_2023/5ms1_3562.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ms1_3562/04_2023/5ms1_3562.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ms1_3562/04_2023/5ms1_3562.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ms1_3562/04_2023/5ms1_3562.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ms1_3562/04_2023/5ms1_3562.pdb" } resolution = 4.25 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= 0.001 sd= 0.028 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 30 5.16 5 C 2774 2.51 5 N 732 2.21 5 O 814 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 4350 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1501 Classifications: {'peptide': 189} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 170} Chain breaks: 1 Chain: "B" Number of atoms: 2849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2849 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 14, 'TRANS': 352} Time building chain proxies: 2.80, per 1000 atoms: 0.64 Number of scatterers: 4350 At special positions: 0 Unit cell: (89.1, 85.8, 91.3, 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 30 16.00 O 814 8.00 N 732 7.00 C 2774 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: 1.82 Conformation dependent library (CDL) restraints added in 684.3 milliseconds 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1034 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 9 sheets defined 12.9% alpha, 46.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 54 through 61 Processing helix chain 'A' and resid 82 through 86 Processing helix chain 'A' and resid 137 through 141 Processing helix chain 'B' and resid 4 through 8 Processing helix chain 'B' and resid 48 through 52 Processing helix chain 'B' and resid 58 through 63 Processing helix chain 'B' and resid 103 through 108 Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 230 through 237 Processing helix chain 'B' and resid 277 through 281 Processing helix chain 'B' and resid 300 through 304 Processing helix chain 'B' and resid 317 through 321 removed outlier: 3.522A pdb=" N ASP B 321 " --> pdb=" O LEU B 318 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 51 removed outlier: 6.226A pdb=" N MET A 163 " --> pdb=" O PRO A 13 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 51 removed outlier: 6.226A pdb=" N MET A 163 " --> pdb=" O PRO A 13 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ALA A 63 " --> pdb=" O ASN A 174 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ASN A 174 " --> pdb=" O ALA A 63 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 38 through 41 removed outlier: 3.734A pdb=" N ARG A 106 " --> pdb=" O LEU A 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 180 through 181 Processing sheet with id=AA5, first strand: chain 'B' and resid 24 through 32 removed outlier: 6.017A pdb=" N LYS B 24 " --> pdb=" O ILE B 172 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE B 172 " --> pdb=" O LYS B 24 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 40 through 46 removed outlier: 5.691A pdb=" N VAL B 41 " --> pdb=" O CYS B 152 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N CYS B 152 " --> pdb=" O VAL B 41 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N CYS B 87 " --> pdb=" O VAL B 153 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASP B 111 " --> pdb=" O ILE B 92 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 202 removed outlier: 7.015A pdb=" N CYS B 187 " --> pdb=" O CYS B 355 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N CYS B 355 " --> pdb=" O CYS B 187 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASN B 189 " --> pdb=" O ASP B 353 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL B 349 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ARG B 195 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LYS B 347 " --> pdb=" O ARG B 195 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N MET B 197 " --> pdb=" O GLY B 345 " (cutoff:3.500A) removed outlier: 9.575A pdb=" N GLY B 345 " --> pdb=" O MET B 197 " (cutoff:3.500A) removed outlier: 8.912A pdb=" N LYS B 199 " --> pdb=" O ASN B 343 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N ASN B 343 " --> pdb=" O LYS B 199 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N VAL B 346 " --> pdb=" O THR B 251 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N THR B 251 " --> pdb=" O VAL B 346 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N LEU B 348 " --> pdb=" O GLU B 249 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N GLU B 249 " --> pdb=" O LEU B 348 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N PHE B 354 " --> pdb=" O ARG B 243 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ARG B 243 " --> pdb=" O PHE B 354 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N GLY B 356 " --> pdb=" O TYR B 241 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N TYR B 241 " --> pdb=" O GLY B 356 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 202 removed outlier: 7.015A pdb=" N CYS B 187 " --> pdb=" O CYS B 355 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N CYS B 355 " --> pdb=" O CYS B 187 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASN B 189 " --> pdb=" O ASP B 353 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL B 349 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ARG B 195 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LYS B 347 " --> pdb=" O ARG B 195 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N MET B 197 " --> pdb=" O GLY B 345 " (cutoff:3.500A) removed outlier: 9.575A pdb=" N GLY B 345 " --> pdb=" O MET B 197 " (cutoff:3.500A) removed outlier: 8.912A pdb=" N LYS B 199 " --> pdb=" O ASN B 343 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N ASN B 343 " --> pdb=" O LYS B 199 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N VAL B 346 " --> pdb=" O THR B 251 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N THR B 251 " --> pdb=" O VAL B 346 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N LEU B 348 " --> pdb=" O GLU B 249 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N GLU B 249 " --> pdb=" O LEU B 348 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N PHE B 354 " --> pdb=" O ARG B 243 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ARG B 243 " --> pdb=" O PHE B 354 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N GLY B 356 " --> pdb=" O TYR B 241 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N TYR B 241 " --> pdb=" O GLY B 356 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 210 through 214 179 hydrogen bonds defined for protein. 447 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: 1.31 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1009 1.32 - 1.45: 1181 1.45 - 1.57: 2226 1.57 - 1.69: 0 1.69 - 1.82: 47 Bond restraints: 4463 Sorted by residual: bond pdb=" N PRO B 282 " pdb=" CA PRO B 282 " ideal model delta sigma weight residual 1.467 1.415 0.052 1.21e-02 6.83e+03 1.83e+01 bond pdb=" N PRO A 181 " pdb=" CA PRO A 181 " ideal model delta sigma weight residual 1.466 1.418 0.048 1.19e-02 7.06e+03 1.59e+01 bond pdb=" N PRO A 41 " pdb=" CA PRO A 41 " ideal model delta sigma weight residual 1.466 1.420 0.045 1.19e-02 7.06e+03 1.44e+01 bond pdb=" N PRO A 13 " pdb=" CA PRO A 13 " ideal model delta sigma weight residual 1.467 1.421 0.046 1.21e-02 6.83e+03 1.44e+01 bond pdb=" N PRO B 214 " pdb=" CA PRO B 214 " ideal model delta sigma weight residual 1.467 1.423 0.044 1.21e-02 6.83e+03 1.34e+01 ... (remaining 4458 not shown) Histogram of bond angle deviations from ideal: 98.25 - 105.38: 119 105.38 - 112.51: 2197 112.51 - 119.64: 1503 119.64 - 126.77: 2200 126.77 - 133.90: 55 Bond angle restraints: 6074 Sorted by residual: angle pdb=" CA ARG A 77 " pdb=" C ARG A 77 " pdb=" O ARG A 77 " ideal model delta sigma weight residual 120.71 113.89 6.82 1.06e+00 8.90e-01 4.15e+01 angle pdb=" C PRO A 20 " pdb=" N PRO A 21 " pdb=" CA PRO A 21 " ideal model delta sigma weight residual 120.03 126.37 -6.34 9.90e-01 1.02e+00 4.10e+01 angle pdb=" C GLY A 126 " pdb=" N PRO A 127 " pdb=" CA PRO A 127 " ideal model delta sigma weight residual 119.64 125.65 -6.01 1.01e+00 9.80e-01 3.54e+01 angle pdb=" C PRO A 54 " pdb=" N PRO A 55 " pdb=" CA PRO A 55 " ideal model delta sigma weight residual 119.32 125.73 -6.41 1.14e+00 7.69e-01 3.17e+01 angle pdb=" C THR A 19 " pdb=" N PRO A 20 " pdb=" CA PRO A 20 " ideal model delta sigma weight residual 119.66 123.52 -3.86 7.30e-01 1.88e+00 2.79e+01 ... (remaining 6069 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.74: 2555 16.74 - 33.48: 41 33.48 - 50.22: 15 50.22 - 66.96: 9 66.96 - 83.70: 4 Dihedral angle restraints: 2624 sinusoidal: 1022 harmonic: 1602 Sorted by residual: dihedral pdb=" CA ARG A 77 " pdb=" C ARG A 77 " pdb=" N GLY A 78 " pdb=" CA GLY A 78 " ideal model delta harmonic sigma weight residual 0.00 37.92 -37.92 0 5.00e+00 4.00e-02 5.75e+01 dihedral pdb=" CG ARG A 154 " pdb=" CD ARG A 154 " pdb=" NE ARG A 154 " pdb=" CZ ARG A 154 " ideal model delta sinusoidal sigma weight residual -90.00 -130.34 40.34 2 1.50e+01 4.44e-03 8.94e+00 dihedral pdb=" CA ASP A 166 " pdb=" CB ASP A 166 " pdb=" CG ASP A 166 " pdb=" OD1 ASP A 166 " ideal model delta sinusoidal sigma weight residual -30.00 -80.90 50.90 1 2.00e+01 2.50e-03 8.86e+00 ... (remaining 2621 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 410 0.058 - 0.117: 199 0.117 - 0.175: 51 0.175 - 0.234: 12 0.234 - 0.292: 1 Chirality restraints: 673 Sorted by residual: chirality pdb=" CA MET B 231 " pdb=" N MET B 231 " pdb=" C MET B 231 " pdb=" CB MET B 231 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CA SER B 309 " pdb=" N SER B 309 " pdb=" C SER B 309 " pdb=" CB SER B 309 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA LEU B 184 " pdb=" N LEU B 184 " pdb=" C LEU B 184 " pdb=" CB LEU B 184 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.74e-01 ... (remaining 670 not shown) Planarity restraints: 782 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 77 " 0.059 2.00e-02 2.50e+03 1.20e-01 1.43e+02 pdb=" C ARG A 77 " -0.207 2.00e-02 2.50e+03 pdb=" O ARG A 77 " 0.077 2.00e-02 2.50e+03 pdb=" N GLY A 78 " 0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 47 " -0.036 2.00e-02 2.50e+03 1.74e-02 7.60e+00 pdb=" CG TRP A 47 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TRP A 47 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP A 47 " 0.018 2.00e-02 2.50e+03 pdb=" NE1 TRP A 47 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A 47 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 47 " 0.017 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 47 " -0.020 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 47 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 47 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN B 130 " 0.036 5.00e-02 4.00e+02 5.84e-02 5.46e+00 pdb=" N PRO B 131 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO B 131 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 131 " 0.031 5.00e-02 4.00e+02 ... (remaining 779 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 1966 2.91 - 3.41: 3911 3.41 - 3.91: 7317 3.91 - 4.40: 8459 4.40 - 4.90: 13903 Nonbonded interactions: 35556 Sorted by model distance: nonbonded pdb=" N GLU B 279 " pdb=" OE1 GLU B 279 " model vdw 2.413 2.520 nonbonded pdb=" OG SER B 366 " pdb=" N ARG B 367 " model vdw 2.438 2.520 nonbonded pdb=" O SER A 183 " pdb=" OG1 THR A 184 " model vdw 2.439 2.440 nonbonded pdb=" N GLU A 101 " pdb=" OE1 GLU A 101 " model vdw 2.442 2.520 nonbonded pdb=" OG1 THR B 224 " pdb=" N GLN B 225 " model vdw 2.474 2.520 ... (remaining 35551 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 group one per residue 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: 3.870 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: 19.580 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 16.630 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 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 : 0.014 0.058 4463 Z= 0.906 Angle : 1.510 8.431 6074 Z= 1.007 Chirality : 0.071 0.292 673 Planarity : 0.008 0.120 782 Dihedral : 9.301 83.699 1590 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 1.09 % Allowed : 5.45 % Favored : 93.45 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.81 (0.34), residues: 550 helix: -3.05 (0.45), residues: 53 sheet: 1.15 (0.36), residues: 192 loop : -1.24 (0.33), residues: 305 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 0.596 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.1852 time to fit residues: 38.8763 Evaluate side-chains 91 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.518 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 22 optimal weight: 9.9990 chunk 13 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 119 ASN A 157 GLN B 287 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 4463 Z= 0.218 Angle : 0.606 7.281 6074 Z= 0.328 Chirality : 0.046 0.169 673 Planarity : 0.005 0.040 782 Dihedral : 4.680 19.777 594 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.00 % Favored : 97.82 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.19 % 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: -0.26 (0.34), residues: 550 helix: -1.55 (0.69), residues: 48 sheet: 0.99 (0.37), residues: 197 loop : -0.73 (0.32), residues: 305 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 0.518 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.1322 time to fit residues: 23.2620 Evaluate side-chains 101 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.529 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 49 optimal weight: 9.9990 chunk 53 optimal weight: 4.9990 chunk 43 optimal weight: 0.4980 chunk 48 optimal weight: 0.3980 chunk 16 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN B 27 GLN B 343 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 4463 Z= 0.227 Angle : 0.582 6.890 6074 Z= 0.314 Chirality : 0.045 0.155 673 Planarity : 0.005 0.040 782 Dihedral : 4.374 16.117 594 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.91 % Favored : 96.91 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.19 % 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: -0.29 (0.35), residues: 550 helix: -1.11 (0.71), residues: 48 sheet: 0.82 (0.38), residues: 202 loop : -0.74 (0.34), residues: 300 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 0.530 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.1302 time to fit residues: 21.1967 Evaluate side-chains 96 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.531 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 0.8980 chunk 36 optimal weight: 9.9990 chunk 25 optimal weight: 0.9990 chunk 5 optimal weight: 7.9990 chunk 23 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 52 optimal weight: 10.0000 chunk 46 optimal weight: 0.6980 chunk 14 optimal weight: 0.0030 chunk 43 optimal weight: 0.8980 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.4357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 4463 Z= 0.156 Angle : 0.555 6.422 6074 Z= 0.288 Chirality : 0.045 0.142 673 Planarity : 0.004 0.035 782 Dihedral : 4.180 16.456 594 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.55 % Favored : 97.27 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.19 % 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 (0.35), residues: 550 helix: -0.98 (0.72), residues: 48 sheet: 0.86 (0.38), residues: 194 loop : -0.61 (0.33), residues: 308 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.558 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.1408 time to fit residues: 21.8821 Evaluate side-chains 95 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.476 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 38 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 44 optimal weight: 8.9990 chunk 36 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 ASN ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.5640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.048 4463 Z= 0.450 Angle : 0.731 9.993 6074 Z= 0.382 Chirality : 0.049 0.156 673 Planarity : 0.005 0.035 782 Dihedral : 4.778 16.841 594 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.82 % Favored : 96.00 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.19 % 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: -0.66 (0.34), residues: 550 helix: -1.55 (0.65), residues: 54 sheet: 0.78 (0.37), residues: 201 loop : -1.11 (0.33), residues: 295 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 121 time to evaluate : 0.478 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 122 average time/residue: 0.1477 time to fit residues: 23.3369 Evaluate side-chains 91 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.487 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 52 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 4 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 GLN ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.5921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 4463 Z= 0.205 Angle : 0.581 6.392 6074 Z= 0.305 Chirality : 0.045 0.142 673 Planarity : 0.004 0.038 782 Dihedral : 4.370 15.911 594 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.55 % Favored : 97.27 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.35), residues: 550 helix: -1.37 (0.67), residues: 54 sheet: 1.05 (0.39), residues: 181 loop : -0.94 (0.33), residues: 315 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.535 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.1467 time to fit residues: 19.1695 Evaluate side-chains 82 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.537 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 3.9990 chunk 38 optimal weight: 8.9990 chunk 43 optimal weight: 0.9990 chunk 52 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 chunk 24 optimal weight: 0.8980 chunk 20 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 33 optimal weight: 0.0670 overall best weight: 1.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 GLN ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.6272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.027 4463 Z= 0.234 Angle : 0.580 7.381 6074 Z= 0.303 Chirality : 0.045 0.137 673 Planarity : 0.004 0.036 782 Dihedral : 4.338 15.653 594 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.19 % 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: -0.52 (0.35), residues: 550 helix: -1.49 (0.66), residues: 53 sheet: 0.99 (0.40), residues: 183 loop : -0.98 (0.33), residues: 314 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.555 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.1518 time to fit residues: 19.0661 Evaluate side-chains 80 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.654 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 45 optimal weight: 0.0000 chunk 48 optimal weight: 0.4980 chunk 29 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 GLN ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.6417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 4463 Z= 0.179 Angle : 0.559 8.584 6074 Z= 0.291 Chirality : 0.045 0.169 673 Planarity : 0.004 0.041 782 Dihedral : 4.176 14.198 594 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.19 % 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: -0.51 (0.36), residues: 550 helix: -1.54 (0.65), residues: 53 sheet: 1.00 (0.39), residues: 185 loop : -0.98 (0.34), residues: 312 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.528 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.1627 time to fit residues: 20.6351 Evaluate side-chains 82 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.480 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 0.8980 chunk 43 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 31 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 GLN ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.6607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 4463 Z= 0.221 Angle : 0.586 8.673 6074 Z= 0.302 Chirality : 0.045 0.161 673 Planarity : 0.004 0.041 782 Dihedral : 4.198 14.188 594 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.19 % 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: -0.50 (0.36), residues: 550 helix: -1.59 (0.65), residues: 53 sheet: 1.09 (0.40), residues: 184 loop : -1.02 (0.34), residues: 313 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.555 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1657 time to fit residues: 20.7369 Evaluate side-chains 78 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.558 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 chunk 45 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 GLN ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.6798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 4463 Z= 0.206 Angle : 0.557 6.870 6074 Z= 0.291 Chirality : 0.045 0.157 673 Planarity : 0.004 0.045 782 Dihedral : 4.120 14.659 594 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.19 % 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: -0.52 (0.36), residues: 550 helix: -1.71 (0.64), residues: 53 sheet: 1.07 (0.40), residues: 186 loop : -1.02 (0.35), residues: 311 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.530 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.1564 time to fit residues: 19.1448 Evaluate side-chains 78 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.485 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 49 optimal weight: 0.1980 chunk 28 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 1 optimal weight: 0.2980 chunk 34 optimal weight: 10.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 GLN ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.108544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.097384 restraints weight = 6650.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.098532 restraints weight = 5103.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.099436 restraints weight = 4200.592| |-----------------------------------------------------------------------------| r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.6891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 4463 Z= 0.175 Angle : 0.570 8.076 6074 Z= 0.290 Chirality : 0.045 0.155 673 Planarity : 0.004 0.044 782 Dihedral : 4.071 15.065 594 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.19 % 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: -0.38 (0.36), residues: 550 helix: -1.49 (0.67), residues: 53 sheet: 1.02 (0.39), residues: 193 loop : -0.89 (0.36), residues: 304 =============================================================================== Job complete usr+sys time: 1425.55 seconds wall clock time: 26 minutes 33.66 seconds (1593.66 seconds total)