Starting phenix.real_space_refine (version: dev) on Tue Nov 29 13:38:26 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0y_26953/11_2022/7v0y_26953.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0y_26953/11_2022/7v0y_26953.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0y_26953/11_2022/7v0y_26953.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0y_26953/11_2022/7v0y_26953.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0y_26953/11_2022/7v0y_26953.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0y_26953/11_2022/7v0y_26953.pdb" } resolution = 3.0 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= 0.239 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "E TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 109": "OE1" <-> "OE2" Residue "E GLU 152": "OE1" <-> "OE2" Residue "E PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 277": "OD1" <-> "OD2" Residue "E TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 297": "OD1" <-> "OD2" Residue "E GLU 341": "OE1" <-> "OE2" Residue "C GLU 63": "OE1" <-> "OE2" Residue "C GLU 90": "OE1" <-> "OE2" Residue "C GLU 125": "OE1" <-> "OE2" Residue "C GLU 238": "OE1" <-> "OE2" Residue "C GLU 249": "OE1" <-> "OE2" Residue "C PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 297": "OD1" <-> "OD2" Residue "C GLU 306": "OE1" <-> "OE2" Residue "C ASP 316": "OD1" <-> "OD2" Residue "C GLU 341": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 4454 Number of models: 1 Model: "" Number of chains: 3 Chain: "E" Number of atoms: 2270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2270 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 267} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 2183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2183 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 258} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 2.97, per 1000 atoms: 0.67 Number of scatterers: 4454 At special positions: 0 Unit cell: (93.375, 75.53, 64.325, 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 12 16.00 O 825 8.00 N 777 7.00 C 2840 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: 1.81 Conformation dependent library (CDL) restraints added in 659.2 milliseconds 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1056 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 6 sheets defined 40.9% alpha, 26.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'E' and resid 104 through 116 removed outlier: 3.765A pdb=" N LYS E 116 " --> pdb=" O ARG E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 142 Processing helix chain 'E' and resid 146 through 148 No H-bonds generated for 'chain 'E' and resid 146 through 148' Processing helix chain 'E' and resid 149 through 158 Processing helix chain 'E' and resid 165 through 170 removed outlier: 4.262A pdb=" N ALA E 169 " --> pdb=" O GLY E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 200 Processing helix chain 'E' and resid 277 through 291 Processing helix chain 'E' and resid 291 through 301 Processing helix chain 'E' and resid 303 through 317 removed outlier: 3.765A pdb=" N LEU E 307 " --> pdb=" O SER E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 334 No H-bonds generated for 'chain 'E' and resid 332 through 334' Processing helix chain 'E' and resid 335 through 349 Processing helix chain 'C' and resid 103 through 116 removed outlier: 3.668A pdb=" N LYS C 116 " --> pdb=" O ARG C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 142 Processing helix chain 'C' and resid 146 through 148 No H-bonds generated for 'chain 'C' and resid 146 through 148' Processing helix chain 'C' and resid 149 through 158 Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 194 through 201 Processing helix chain 'C' and resid 277 through 291 Processing helix chain 'C' and resid 291 through 300 Processing helix chain 'C' and resid 303 through 317 removed outlier: 3.748A pdb=" N LEU C 307 " --> pdb=" O SER C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 334 Processing helix chain 'C' and resid 334 through 343 removed outlier: 4.439A pdb=" N VAL C 338 " --> pdb=" O SER C 334 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 85 through 87 removed outlier: 6.737A pdb=" N LEU E 61 " --> pdb=" O ALA E 78 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ARG E 80 " --> pdb=" O VAL E 59 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL E 59 " --> pdb=" O ARG E 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 118 through 123 removed outlier: 6.423A pdb=" N THR E 118 " --> pdb=" O PHE E 244 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N ARG E 246 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU E 120 " --> pdb=" O ARG E 246 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N GLN E 248 " --> pdb=" O LEU E 120 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ASP E 122 " --> pdb=" O GLN E 248 " (cutoff:3.500A) removed outlier: 10.053A pdb=" N ALA E 250 " --> pdb=" O ASP E 122 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ARG E 263 " --> pdb=" O LEU E 247 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ALA E 226 " --> pdb=" O ILE E 262 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE E 264 " --> pdb=" O ALA E 226 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N TYR E 58 " --> pdb=" O THR E 227 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N VAL E 229 " --> pdb=" O TYR E 58 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N GLU E 60 " --> pdb=" O VAL E 229 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N VAL E 231 " --> pdb=" O GLU E 60 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N GLN E 62 " --> pdb=" O VAL E 231 " (cutoff:3.500A) removed outlier: 8.525A pdb=" N ARG E 233 " --> pdb=" O GLN E 62 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N LEU E 64 " --> pdb=" O ARG E 233 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL E 59 " --> pdb=" O ARG E 80 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ARG E 80 " --> pdb=" O VAL E 59 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU E 61 " --> pdb=" O ALA E 78 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 102 through 103 Processing sheet with id=AA4, first strand: chain 'E' and resid 177 through 178 Processing sheet with id=AA5, first strand: chain 'C' and resid 85 through 87 removed outlier: 6.862A pdb=" N LEU C 61 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ARG C 80 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VAL C 59 " --> pdb=" O ARG C 80 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N LYS C 56 " --> pdb=" O GLU C 225 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N THR C 227 " --> pdb=" O LYS C 56 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N TYR C 58 " --> pdb=" O THR C 227 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N VAL C 229 " --> pdb=" O TYR C 58 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLU C 60 " --> pdb=" O VAL C 229 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N VAL C 231 " --> pdb=" O GLU C 60 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N GLN C 62 " --> pdb=" O VAL C 231 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ILE C 262 " --> pdb=" O SER C 224 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ALA C 226 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE C 264 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ARG C 263 " --> pdb=" O LEU C 247 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLN C 248 " --> pdb=" O ASP C 122 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 85 through 87 removed outlier: 6.862A pdb=" N LEU C 61 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ARG C 80 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VAL C 59 " --> pdb=" O ARG C 80 " (cutoff:3.500A) 203 hydrogen bonds defined for protein. 582 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: 1.18 Time building geometry restraints manager: 1.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1517 1.34 - 1.46: 832 1.46 - 1.58: 2173 1.58 - 1.69: 0 1.69 - 1.81: 20 Bond restraints: 4542 Sorted by residual: bond pdb=" C VAL E 336 " pdb=" N PRO E 337 " ideal model delta sigma weight residual 1.335 1.366 -0.032 1.28e-02 6.10e+03 6.13e+00 bond pdb=" CB GLN E 302 " pdb=" CG GLN E 302 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.48e+00 bond pdb=" CB ASN C 91 " pdb=" CG ASN C 91 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.13e+00 bond pdb=" CG GLN E 302 " pdb=" CD GLN E 302 " ideal model delta sigma weight residual 1.516 1.540 -0.024 2.50e-02 1.60e+03 9.39e-01 bond pdb=" N ASN C 91 " pdb=" CA ASN C 91 " ideal model delta sigma weight residual 1.458 1.474 -0.016 1.77e-02 3.19e+03 7.74e-01 ... (remaining 4537 not shown) Histogram of bond angle deviations from ideal: 99.89 - 106.71: 153 106.71 - 113.53: 2508 113.53 - 120.35: 1620 120.35 - 127.17: 1824 127.17 - 133.99: 59 Bond angle restraints: 6164 Sorted by residual: angle pdb=" C SER E 328 " pdb=" N GLU E 329 " pdb=" CA GLU E 329 " ideal model delta sigma weight residual 121.54 128.45 -6.91 1.91e+00 2.74e-01 1.31e+01 angle pdb=" C GLU C 90 " pdb=" N ASN C 91 " pdb=" CA ASN C 91 " ideal model delta sigma weight residual 125.66 131.25 -5.59 1.85e+00 2.92e-01 9.12e+00 angle pdb=" CB GLN E 302 " pdb=" CG GLN E 302 " pdb=" CD GLN E 302 " ideal model delta sigma weight residual 112.60 117.33 -4.73 1.70e+00 3.46e-01 7.73e+00 angle pdb=" C VAL E 82 " pdb=" N GLN E 83 " pdb=" CA GLN E 83 " ideal model delta sigma weight residual 121.54 126.39 -4.85 1.91e+00 2.74e-01 6.45e+00 angle pdb=" N ASP E 277 " pdb=" CA ASP E 277 " pdb=" C ASP E 277 " ideal model delta sigma weight residual 108.52 104.93 3.59 1.63e+00 3.76e-01 4.85e+00 ... (remaining 6159 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.85: 2332 16.85 - 33.71: 262 33.71 - 50.56: 116 50.56 - 67.42: 42 67.42 - 84.27: 15 Dihedral angle restraints: 2767 sinusoidal: 1150 harmonic: 1617 Sorted by residual: dihedral pdb=" CG ARG E 304 " pdb=" CD ARG E 304 " pdb=" NE ARG E 304 " pdb=" CZ ARG E 304 " ideal model delta sinusoidal sigma weight residual 180.00 136.41 43.59 2 1.50e+01 4.44e-03 1.01e+01 dihedral pdb=" CA ASP C 137 " pdb=" CB ASP C 137 " pdb=" CG ASP C 137 " pdb=" OD1 ASP C 137 " ideal model delta sinusoidal sigma weight residual -30.00 -83.50 53.50 1 2.00e+01 2.50e-03 9.72e+00 dihedral pdb=" CB GLU C 60 " pdb=" CG GLU C 60 " pdb=" CD GLU C 60 " pdb=" OE1 GLU C 60 " ideal model delta sinusoidal sigma weight residual 0.00 84.07 -84.07 1 3.00e+01 1.11e-03 9.56e+00 ... (remaining 2764 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 475 0.034 - 0.068: 158 0.068 - 0.102: 47 0.102 - 0.136: 22 0.136 - 0.170: 2 Chirality restraints: 704 Sorted by residual: chirality pdb=" CG LEU E 158 " pdb=" CB LEU E 158 " pdb=" CD1 LEU E 158 " pdb=" CD2 LEU E 158 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.21e-01 chirality pdb=" CA VAL E 82 " pdb=" N VAL E 82 " pdb=" C VAL E 82 " pdb=" CB VAL E 82 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.14 2.00e-01 2.50e+01 5.19e-01 chirality pdb=" CG LEU E 108 " pdb=" CB LEU E 108 " pdb=" CD1 LEU E 108 " pdb=" CD2 LEU E 108 " both_signs ideal model delta sigma weight residual False -2.59 -2.46 -0.13 2.00e-01 2.50e+01 4.41e-01 ... (remaining 701 not shown) Planarity restraints: 805 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN E 302 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.21e+00 pdb=" CD GLN E 302 " -0.035 2.00e-02 2.50e+03 pdb=" OE1 GLN E 302 " 0.013 2.00e-02 2.50e+03 pdb=" NE2 GLN E 302 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG E 146 " 0.023 5.00e-02 4.00e+02 3.42e-02 1.87e+00 pdb=" N PRO E 147 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO E 147 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO E 147 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 340 " -0.100 9.50e-02 1.11e+02 4.52e-02 1.59e+00 pdb=" NE ARG E 340 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG E 340 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG E 340 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG E 340 " -0.000 2.00e-02 2.50e+03 ... (remaining 802 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 350 2.74 - 3.28: 4143 3.28 - 3.82: 7834 3.82 - 4.36: 9191 4.36 - 4.90: 15677 Nonbonded interactions: 37195 Sorted by model distance: nonbonded pdb=" OG1 THR E 179 " pdb=" O ASP E 183 " model vdw 2.203 2.440 nonbonded pdb=" OD1 ASP E 316 " pdb=" NE1 TRP C 105 " model vdw 2.265 2.520 nonbonded pdb=" OD1 ASN C 133 " pdb=" NH2 ARG C 150 " model vdw 2.275 2.520 nonbonded pdb=" O PRO E 221 " pdb=" OG SER E 224 " model vdw 2.313 2.440 nonbonded pdb=" OE2 GLU C 109 " pdb=" NH1 ARG C 112 " model vdw 2.341 2.520 ... (remaining 37190 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'C' and (resid 54 through 203 or resid 217 through 348)) selection = (chain 'E' and ((resid 54 and (name N or name CA or name C or name O or name CB \ )) or resid 55 or (resid 56 and (name N or name CA or name C or name O or name C \ B )) or resid 57 through 181 or resid 192 through 348)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 12 5.16 5 C 2840 2.51 5 N 777 2.21 5 O 825 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.880 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: 0.000 Extract box with map and model: 5.170 Check model and map are aligned: 0.070 Convert atoms to be neutral: 0.040 Process input model: 16.430 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:11.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 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 : 0.003 0.037 4542 Z= 0.201 Angle : 0.626 7.556 6164 Z= 0.339 Chirality : 0.041 0.170 704 Planarity : 0.005 0.045 805 Dihedral : 19.396 84.270 1711 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer Outliers : 1.46 % 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: 0.80 (0.35), residues: 548 helix: 0.77 (0.37), residues: 211 sheet: 1.11 (0.50), residues: 105 loop : 0.19 (0.37), residues: 232 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 54 time to evaluate : 0.518 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 60 average time/residue: 1.4515 time to fit residues: 89.9615 Evaluate side-chains 53 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 48 time to evaluate : 0.398 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 1 average time/residue: 1.3019 time to fit residues: 1.8925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 46 optimal weight: 0.0070 chunk 41 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 14 optimal weight: 0.0000 chunk 28 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.7604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 302 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.0606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 4542 Z= 0.145 Angle : 0.488 5.833 6164 Z= 0.249 Chirality : 0.038 0.124 704 Planarity : 0.004 0.027 805 Dihedral : 4.056 13.785 603 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer Outliers : 4.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.36), residues: 548 helix: 1.22 (0.38), residues: 214 sheet: 1.10 (0.49), residues: 105 loop : 0.36 (0.38), residues: 229 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 57 time to evaluate : 0.526 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 8 residues processed: 74 average time/residue: 1.2313 time to fit residues: 94.6330 Evaluate side-chains 65 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 57 time to evaluate : 0.466 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 0.6616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 27 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 13 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 44 optimal weight: 6.9990 chunk 49 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 302 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.0831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 4542 Z= 0.159 Angle : 0.480 5.769 6164 Z= 0.243 Chirality : 0.039 0.138 704 Planarity : 0.004 0.026 805 Dihedral : 4.006 13.895 603 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer Outliers : 3.74 % 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: 1.33 (0.36), residues: 548 helix: 1.35 (0.38), residues: 214 sheet: 1.22 (0.50), residues: 105 loop : 0.41 (0.38), residues: 229 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 64 time to evaluate : 0.476 Fit side-chains outliers start: 18 outliers final: 9 residues processed: 79 average time/residue: 1.1949 time to fit residues: 98.0378 Evaluate side-chains 74 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 65 time to evaluate : 0.489 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 1 average time/residue: 0.0484 time to fit residues: 0.8335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 49 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 47 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 62 GLN E 198 GLN E 302 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 4542 Z= 0.282 Angle : 0.569 6.868 6164 Z= 0.287 Chirality : 0.041 0.127 704 Planarity : 0.004 0.027 805 Dihedral : 4.443 15.549 603 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer Outliers : 5.82 % 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: 1.15 (0.35), residues: 548 helix: 1.20 (0.37), residues: 213 sheet: 0.90 (0.47), residues: 122 loop : 0.41 (0.39), residues: 213 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 66 time to evaluate : 0.584 Fit side-chains outliers start: 28 outliers final: 12 residues processed: 86 average time/residue: 1.4522 time to fit residues: 129.2214 Evaluate side-chains 73 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 61 time to evaluate : 0.529 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 8 residues processed: 4 average time/residue: 0.4348 time to fit residues: 2.6237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 44 optimal weight: 3.9990 chunk 30 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 39 optimal weight: 0.0000 chunk 21 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 overall best weight: 2.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 134 GLN E 191 GLN E 198 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.037 4542 Z= 0.297 Angle : 0.565 6.848 6164 Z= 0.285 Chirality : 0.041 0.127 704 Planarity : 0.004 0.027 805 Dihedral : 4.585 16.448 603 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer Outliers : 4.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.35), residues: 548 helix: 1.13 (0.37), residues: 212 sheet: 0.74 (0.49), residues: 110 loop : 0.40 (0.39), residues: 226 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 67 time to evaluate : 0.554 Fit side-chains outliers start: 24 outliers final: 13 residues processed: 84 average time/residue: 1.3635 time to fit residues: 118.4262 Evaluate side-chains 74 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 61 time to evaluate : 0.540 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 9 residues processed: 4 average time/residue: 0.0699 time to fit residues: 1.1926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 47 optimal weight: 8.9990 chunk 10 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 13 optimal weight: 20.0000 chunk 53 optimal weight: 2.9990 chunk 44 optimal weight: 0.0570 chunk 24 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 overall best weight: 2.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 198 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 4542 Z= 0.263 Angle : 0.547 6.601 6164 Z= 0.276 Chirality : 0.041 0.126 704 Planarity : 0.004 0.029 805 Dihedral : 4.520 16.684 603 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer Outliers : 5.41 % 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: 1.05 (0.36), residues: 548 helix: 1.22 (0.37), residues: 212 sheet: 0.79 (0.49), residues: 108 loop : 0.30 (0.39), residues: 228 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 66 time to evaluate : 0.531 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 11 residues processed: 83 average time/residue: 1.3468 time to fit residues: 115.6417 Evaluate side-chains 73 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 62 time to evaluate : 0.530 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 1 average time/residue: 0.0933 time to fit residues: 0.8775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 5 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 44 optimal weight: 0.0470 chunk 29 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 overall best weight: 1.5682 ------------------------------------------------------------------------------- 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: 0.8564 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 4542 Z= 0.204 Angle : 0.518 5.974 6164 Z= 0.262 Chirality : 0.039 0.125 704 Planarity : 0.004 0.041 805 Dihedral : 4.400 15.792 603 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer Outliers : 3.74 % 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: 1.15 (0.36), residues: 548 helix: 1.35 (0.38), residues: 212 sheet: 0.83 (0.49), residues: 108 loop : 0.31 (0.39), residues: 228 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 65 time to evaluate : 0.521 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 11 residues processed: 79 average time/residue: 1.2650 time to fit residues: 103.6456 Evaluate side-chains 75 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 64 time to evaluate : 0.539 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 1 average time/residue: 0.1022 time to fit residues: 0.9044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 15 optimal weight: 0.0970 chunk 10 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 41 optimal weight: 10.0000 chunk 48 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 198 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 4542 Z= 0.213 Angle : 0.530 6.043 6164 Z= 0.266 Chirality : 0.040 0.125 704 Planarity : 0.004 0.034 805 Dihedral : 4.387 16.154 603 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer Outliers : 4.57 % 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: 1.12 (0.36), residues: 548 helix: 1.35 (0.38), residues: 212 sheet: 0.75 (0.49), residues: 108 loop : 0.32 (0.39), residues: 228 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 66 time to evaluate : 0.526 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 12 residues processed: 82 average time/residue: 1.2343 time to fit residues: 105.0179 Evaluate side-chains 76 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 64 time to evaluate : 0.515 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 11 residues processed: 1 average time/residue: 0.1175 time to fit residues: 0.8964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 50 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 38 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 46 optimal weight: 0.1980 chunk 49 optimal weight: 0.7980 chunk 32 optimal weight: 8.9990 chunk 52 optimal weight: 0.7980 chunk 31 optimal weight: 7.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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: 0.8544 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 4542 Z= 0.171 Angle : 0.505 5.327 6164 Z= 0.254 Chirality : 0.039 0.125 704 Planarity : 0.004 0.042 805 Dihedral : 4.272 16.784 603 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer Outliers : 2.70 % 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: 1.24 (0.36), residues: 548 helix: 1.47 (0.38), residues: 212 sheet: 0.79 (0.49), residues: 108 loop : 0.36 (0.39), residues: 228 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 66 time to evaluate : 0.528 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 11 residues processed: 78 average time/residue: 1.1927 time to fit residues: 96.6937 Evaluate side-chains 73 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 62 time to evaluate : 0.547 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 11 residues processed: 0 time to fit residues: 0.7221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 24 optimal weight: 0.7980 chunk 36 optimal weight: 10.0000 chunk 54 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 55 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 4542 Z= 0.294 Angle : 0.586 6.424 6164 Z= 0.292 Chirality : 0.042 0.179 704 Planarity : 0.004 0.038 805 Dihedral : 4.609 19.756 603 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer Outliers : 3.74 % 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: 1.00 (0.36), residues: 548 helix: 1.25 (0.38), residues: 212 sheet: 0.57 (0.48), residues: 110 loop : 0.31 (0.39), residues: 226 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 68 time to evaluate : 0.562 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 11 residues processed: 82 average time/residue: 1.2812 time to fit residues: 108.8826 Evaluate side-chains 79 residues out of total 484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 68 time to evaluate : 0.542 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 1 average time/residue: 0.0952 time to fit residues: 0.8626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 40 optimal weight: 0.2980 chunk 6 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 302 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.163479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.128011 restraints weight = 4630.161| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.11 r_work: 0.3243 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 1.97 restraints_weight: 0.2500 r_work: 0.3178 rms_B_bonded: 2.25 restraints_weight: 0.1250 r_work: 0.3125 rms_B_bonded: 2.83 restraints_weight: 0.0625 r_work: 0.3042 rms_B_bonded: 3.91 restraints_weight: 0.0312 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 4542 Z= 0.225 Angle : 0.555 6.258 6164 Z= 0.276 Chirality : 0.041 0.169 704 Planarity : 0.004 0.036 805 Dihedral : 4.502 19.907 603 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer Outliers : 2.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.36), residues: 548 helix: 1.32 (0.38), residues: 212 sheet: 0.67 (0.49), residues: 106 loop : 0.30 (0.38), residues: 230 =============================================================================== Job complete usr+sys time: 2101.73 seconds wall clock time: 38 minutes 16.97 seconds (2296.97 seconds total)