Starting phenix.real_space_refine (version: 1.21rc1) on Tue Jul 4 11:12:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e7z_31005/07_2023/7e7z_31005.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e7z_31005/07_2023/7e7z_31005.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e7z_31005/07_2023/7e7z_31005.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e7z_31005/07_2023/7e7z_31005.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e7z_31005/07_2023/7e7z_31005.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e7z_31005/07_2023/7e7z_31005.pdb" } resolution = 3.2 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= 0.007 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 56 5.16 5 C 5152 2.51 5 N 1264 2.21 5 O 1336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 323": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 7808 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1952 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 8, 'TRANS': 239} Chain breaks: 1 Chain: "B" Number of atoms: 1952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1952 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 8, 'TRANS': 239} Chain breaks: 1 Chain: "C" Number of atoms: 1952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1952 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 8, 'TRANS': 239} Chain breaks: 1 Chain: "D" Number of atoms: 1952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1952 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 8, 'TRANS': 239} Chain breaks: 1 Time building chain proxies: 4.35, per 1000 atoms: 0.56 Number of scatterers: 7808 At special positions: 0 Unit cell: (111.251, 111.251, 78.1763, 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 56 16.00 O 1336 8.00 N 1264 7.00 C 5152 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.37 Conformation dependent library (CDL) restraints added in 1.1 seconds 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1880 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 0 sheets defined 82.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 166 through 177 removed outlier: 4.277A pdb=" N ARG A 170 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ALA A 174 " --> pdb=" O ARG A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 207 Processing helix chain 'A' and resid 227 through 249 Processing helix chain 'A' and resid 253 through 260 Processing helix chain 'A' and resid 260 through 282 Proline residue: A 272 - end of helix removed outlier: 3.769A pdb=" N ASN A 282 " --> pdb=" O VAL A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 296 removed outlier: 4.115A pdb=" N VAL A 290 " --> pdb=" O SER A 286 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N THR A 291 " --> pdb=" O GLY A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 305 removed outlier: 3.735A pdb=" N ARG A 305 " --> pdb=" O LYS A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 320 removed outlier: 3.850A pdb=" N ARG A 311 " --> pdb=" O SER A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 346 Processing helix chain 'A' and resid 356 through 369 removed outlier: 4.249A pdb=" N TRP A 362 " --> pdb=" O PRO A 358 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N TYR A 363 " --> pdb=" O ALA A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 399 removed outlier: 4.040A pdb=" N SER A 391 " --> pdb=" O GLY A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 417 removed outlier: 4.610A pdb=" N VAL A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN A 417 " --> pdb=" O TYR A 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 177 removed outlier: 4.266A pdb=" N ARG B 170 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ALA B 174 " --> pdb=" O ARG B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 207 Processing helix chain 'B' and resid 227 through 249 Processing helix chain 'B' and resid 253 through 260 Processing helix chain 'B' and resid 260 through 282 Proline residue: B 272 - end of helix removed outlier: 3.759A pdb=" N ASN B 282 " --> pdb=" O VAL B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 296 removed outlier: 4.138A pdb=" N VAL B 290 " --> pdb=" O SER B 286 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N THR B 291 " --> pdb=" O GLY B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 305 removed outlier: 3.739A pdb=" N ARG B 305 " --> pdb=" O LYS B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 320 removed outlier: 3.830A pdb=" N ARG B 311 " --> pdb=" O SER B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 346 Processing helix chain 'B' and resid 356 through 369 removed outlier: 4.230A pdb=" N TRP B 362 " --> pdb=" O PRO B 358 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N TYR B 363 " --> pdb=" O ALA B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 399 removed outlier: 4.020A pdb=" N SER B 391 " --> pdb=" O GLY B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 417 removed outlier: 4.666A pdb=" N VAL B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN B 417 " --> pdb=" O TYR B 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 177 removed outlier: 4.315A pdb=" N ARG C 170 " --> pdb=" O THR C 166 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ALA C 174 " --> pdb=" O ARG C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 205 Processing helix chain 'C' and resid 227 through 249 removed outlier: 3.784A pdb=" N CYS C 231 " --> pdb=" O VAL C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 260 removed outlier: 3.619A pdb=" N ARG C 259 " --> pdb=" O TYR C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 282 Proline residue: C 272 - end of helix removed outlier: 3.816A pdb=" N ASN C 282 " --> pdb=" O VAL C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 296 Processing helix chain 'C' and resid 297 through 305 removed outlier: 3.743A pdb=" N ARG C 305 " --> pdb=" O LYS C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 320 removed outlier: 3.799A pdb=" N ARG C 311 " --> pdb=" O SER C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 346 Processing helix chain 'C' and resid 356 through 369 removed outlier: 4.158A pdb=" N TRP C 362 " --> pdb=" O PRO C 358 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N TYR C 363 " --> pdb=" O ALA C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 399 removed outlier: 4.024A pdb=" N SER C 391 " --> pdb=" O GLY C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 417 removed outlier: 4.594A pdb=" N VAL C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN C 417 " --> pdb=" O TYR C 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 177 removed outlier: 4.275A pdb=" N ARG D 170 " --> pdb=" O THR D 166 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ALA D 174 " --> pdb=" O ARG D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 207 Processing helix chain 'D' and resid 227 through 249 Processing helix chain 'D' and resid 253 through 260 Processing helix chain 'D' and resid 260 through 282 Proline residue: D 272 - end of helix removed outlier: 3.768A pdb=" N ASN D 282 " --> pdb=" O VAL D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 296 removed outlier: 4.129A pdb=" N VAL D 290 " --> pdb=" O SER D 286 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N THR D 291 " --> pdb=" O GLY D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 305 removed outlier: 3.565A pdb=" N PHE D 301 " --> pdb=" O PHE D 298 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG D 305 " --> pdb=" O LYS D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 320 removed outlier: 3.840A pdb=" N ARG D 311 " --> pdb=" O SER D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 346 Processing helix chain 'D' and resid 356 through 369 removed outlier: 4.260A pdb=" N TRP D 362 " --> pdb=" O PRO D 358 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N TYR D 363 " --> pdb=" O ALA D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 399 removed outlier: 4.016A pdb=" N SER D 391 " --> pdb=" O GLY D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 417 removed outlier: 4.618A pdb=" N VAL D 404 " --> pdb=" O LEU D 400 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN D 417 " --> pdb=" O TYR D 413 " (cutoff:3.500A) 567 hydrogen bonds defined for protein. 1644 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: 1.96 Time building geometry restraints manager: 3.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2351 1.35 - 1.46: 2134 1.46 - 1.58: 3423 1.58 - 1.70: 0 1.70 - 1.82: 92 Bond restraints: 8000 Sorted by residual: bond pdb=" C LEU A 271 " pdb=" N PRO A 272 " ideal model delta sigma weight residual 1.334 1.364 -0.030 1.51e-02 4.39e+03 3.82e+00 bond pdb=" C LEU C 400 " pdb=" N PRO C 401 " ideal model delta sigma weight residual 1.332 1.340 -0.008 8.90e-03 1.26e+04 7.70e-01 bond pdb=" C LEU D 400 " pdb=" N PRO D 401 " ideal model delta sigma weight residual 1.332 1.340 -0.008 8.90e-03 1.26e+04 7.45e-01 bond pdb=" C LEU B 400 " pdb=" N PRO B 401 " ideal model delta sigma weight residual 1.332 1.340 -0.008 8.90e-03 1.26e+04 7.33e-01 bond pdb=" C LEU A 400 " pdb=" N PRO A 401 " ideal model delta sigma weight residual 1.332 1.340 -0.007 8.90e-03 1.26e+04 6.56e-01 ... (remaining 7995 not shown) Histogram of bond angle deviations from ideal: 99.72 - 106.58: 199 106.58 - 113.44: 4382 113.44 - 120.30: 2991 120.30 - 127.16: 3230 127.16 - 134.02: 62 Bond angle restraints: 10864 Sorted by residual: angle pdb=" N VAL C 171 " pdb=" CA VAL C 171 " pdb=" C VAL C 171 " ideal model delta sigma weight residual 113.39 108.45 4.94 1.47e+00 4.63e-01 1.13e+01 angle pdb=" CB MET D 262 " pdb=" CG MET D 262 " pdb=" SD MET D 262 " ideal model delta sigma weight residual 112.70 121.33 -8.63 3.00e+00 1.11e-01 8.27e+00 angle pdb=" CB MET C 262 " pdb=" CG MET C 262 " pdb=" SD MET C 262 " ideal model delta sigma weight residual 112.70 121.11 -8.41 3.00e+00 1.11e-01 7.86e+00 angle pdb=" CB MET B 262 " pdb=" CG MET B 262 " pdb=" SD MET B 262 " ideal model delta sigma weight residual 112.70 121.02 -8.32 3.00e+00 1.11e-01 7.69e+00 angle pdb=" CB MET A 262 " pdb=" CG MET A 262 " pdb=" SD MET A 262 " ideal model delta sigma weight residual 112.70 121.02 -8.32 3.00e+00 1.11e-01 7.69e+00 ... (remaining 10859 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.05: 4150 16.05 - 32.10: 412 32.10 - 48.15: 94 48.15 - 64.20: 9 64.20 - 80.25: 7 Dihedral angle restraints: 4672 sinusoidal: 1760 harmonic: 2912 Sorted by residual: dihedral pdb=" CA ALA B 226 " pdb=" C ALA B 226 " pdb=" N VAL B 227 " pdb=" CA VAL B 227 " ideal model delta harmonic sigma weight residual 180.00 154.90 25.10 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA ALA A 226 " pdb=" C ALA A 226 " pdb=" N VAL A 227 " pdb=" CA VAL A 227 " ideal model delta harmonic sigma weight residual 180.00 155.93 24.07 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA ALA D 226 " pdb=" C ALA D 226 " pdb=" N VAL D 227 " pdb=" CA VAL D 227 " ideal model delta harmonic sigma weight residual 180.00 156.75 23.25 0 5.00e+00 4.00e-02 2.16e+01 ... (remaining 4669 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 749 0.026 - 0.052: 321 0.052 - 0.078: 167 0.078 - 0.104: 43 0.104 - 0.130: 12 Chirality restraints: 1292 Sorted by residual: chirality pdb=" CA VAL D 227 " pdb=" N VAL D 227 " pdb=" C VAL D 227 " pdb=" CB VAL D 227 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.22e-01 chirality pdb=" CA VAL A 227 " pdb=" N VAL A 227 " pdb=" C VAL A 227 " pdb=" CB VAL A 227 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.09e-01 chirality pdb=" CB VAL A 297 " pdb=" CA VAL A 297 " pdb=" CG1 VAL A 297 " pdb=" CG2 VAL A 297 " both_signs ideal model delta sigma weight residual False -2.63 -2.51 -0.12 2.00e-01 2.50e+01 3.53e-01 ... (remaining 1289 not shown) Planarity restraints: 1316 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 271 " 0.043 5.00e-02 4.00e+02 6.39e-02 6.53e+00 pdb=" N PRO B 272 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO B 272 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 272 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 271 " -0.040 5.00e-02 4.00e+02 6.02e-02 5.80e+00 pdb=" N PRO D 272 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO D 272 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 272 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 240 " -0.010 2.00e-02 2.50e+03 1.94e-02 3.77e+00 pdb=" C PHE D 240 " 0.034 2.00e-02 2.50e+03 pdb=" O PHE D 240 " -0.013 2.00e-02 2.50e+03 pdb=" N THR D 241 " -0.011 2.00e-02 2.50e+03 ... (remaining 1313 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1619 2.77 - 3.30: 8082 3.30 - 3.84: 12863 3.84 - 4.37: 14658 4.37 - 4.90: 25308 Nonbonded interactions: 62530 Sorted by model distance: nonbonded pdb=" O MET D 238 " pdb=" OG1 THR D 241 " model vdw 2.240 2.440 nonbonded pdb=" O MET B 238 " pdb=" OG1 THR B 241 " model vdw 2.242 2.440 nonbonded pdb=" O MET A 238 " pdb=" OG1 THR A 241 " model vdw 2.242 2.440 nonbonded pdb=" OE2 GLU C 205 " pdb=" NH2 ARG C 296 " model vdw 2.254 2.520 nonbonded pdb=" OG SER C 181 " pdb=" N THR C 182 " model vdw 2.289 2.520 ... (remaining 62525 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 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.430 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: 2.720 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 23.000 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.040 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 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 : 0.002 0.030 8000 Z= 0.131 Angle : 0.511 8.627 10864 Z= 0.274 Chirality : 0.037 0.130 1292 Planarity : 0.005 0.064 1316 Dihedral : 13.400 80.246 2792 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.26), residues: 976 helix: 0.79 (0.19), residues: 732 sheet: None (None), residues: 0 loop : -2.76 (0.34), residues: 244 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.2291 time to fit residues: 40.7469 Evaluate side-chains 101 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.922 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 4.9990 chunk 72 optimal weight: 20.0000 chunk 40 optimal weight: 0.6980 chunk 24 optimal weight: 20.0000 chunk 49 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 29 optimal weight: 0.0370 chunk 45 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 overall best weight: 1.7464 ------------------------------------------------------------------------------- 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: 0.7911 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.035 8000 Z= 0.301 Angle : 0.579 6.659 10864 Z= 0.310 Chirality : 0.044 0.153 1292 Planarity : 0.005 0.053 1316 Dihedral : 4.216 29.068 1088 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer Outliers : 1.64 % 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: 0.58 (0.27), residues: 976 helix: 1.32 (0.19), residues: 744 sheet: None (None), residues: 0 loop : -2.78 (0.33), residues: 232 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 123 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 132 average time/residue: 0.2079 time to fit residues: 37.1794 Evaluate side-chains 129 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 120 time to evaluate : 0.901 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0736 time to fit residues: 2.4678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 20.0000 chunk 27 optimal weight: 1.9990 chunk 72 optimal weight: 20.0000 chunk 59 optimal weight: 8.9990 chunk 24 optimal weight: 20.0000 chunk 87 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 77 optimal weight: 7.9990 chunk 86 optimal weight: 0.7980 chunk 29 optimal weight: 7.9990 chunk 70 optimal weight: 0.4980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 416 ASN D 416 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.028 8000 Z= 0.225 Angle : 0.519 4.765 10864 Z= 0.280 Chirality : 0.041 0.140 1292 Planarity : 0.005 0.053 1316 Dihedral : 4.149 29.653 1088 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer Outliers : 2.35 % 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: 0.84 (0.27), residues: 976 helix: 1.38 (0.19), residues: 768 sheet: None (None), residues: 0 loop : -2.61 (0.35), residues: 208 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 111 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 9 residues processed: 123 average time/residue: 0.2120 time to fit residues: 35.2293 Evaluate side-chains 115 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 106 time to evaluate : 0.854 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1537 time to fit residues: 3.1558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 83 optimal weight: 7.9990 chunk 25 optimal weight: 9.9990 chunk 77 optimal weight: 7.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 ASN B 416 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 8000 Z= 0.182 Angle : 0.494 4.573 10864 Z= 0.267 Chirality : 0.040 0.138 1292 Planarity : 0.004 0.052 1316 Dihedral : 4.025 28.221 1088 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer Outliers : 1.29 % 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: 1.09 (0.27), residues: 976 helix: 1.74 (0.19), residues: 744 sheet: None (None), residues: 0 loop : -2.83 (0.33), residues: 232 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 117 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 10 residues processed: 126 average time/residue: 0.2110 time to fit residues: 35.7760 Evaluate side-chains 121 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 111 time to evaluate : 0.875 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0774 time to fit residues: 2.6021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 0.9980 chunk 1 optimal weight: 7.9990 chunk 69 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 79 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 83 optimal weight: 9.9990 chunk 23 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.7867 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 8000 Z= 0.176 Angle : 0.481 4.546 10864 Z= 0.259 Chirality : 0.040 0.141 1292 Planarity : 0.004 0.051 1316 Dihedral : 4.002 28.348 1088 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer Outliers : 1.17 % 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: 1.22 (0.27), residues: 976 helix: 1.65 (0.19), residues: 768 sheet: None (None), residues: 0 loop : -2.49 (0.36), residues: 208 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 114 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 10 residues processed: 118 average time/residue: 0.2082 time to fit residues: 33.0509 Evaluate side-chains 120 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 110 time to evaluate : 0.839 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1416 time to fit residues: 3.1564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 9.9990 chunk 18 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 48 optimal weight: 20.0000 chunk 89 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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: 0.7877 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 8000 Z= 0.190 Angle : 0.491 4.569 10864 Z= 0.264 Chirality : 0.040 0.139 1292 Planarity : 0.004 0.051 1316 Dihedral : 3.985 28.451 1088 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer Outliers : 0.94 % 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: 1.29 (0.27), residues: 976 helix: 1.70 (0.19), residues: 768 sheet: None (None), residues: 0 loop : -2.45 (0.36), residues: 208 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 110 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 8 residues processed: 116 average time/residue: 0.2022 time to fit residues: 31.9553 Evaluate side-chains 113 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 105 time to evaluate : 0.871 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0967 time to fit residues: 2.5650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 4.9990 chunk 52 optimal weight: 0.1980 chunk 67 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 42 optimal weight: 0.2980 chunk 36 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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: 0.7835 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 8000 Z= 0.147 Angle : 0.463 4.556 10864 Z= 0.250 Chirality : 0.039 0.140 1292 Planarity : 0.004 0.051 1316 Dihedral : 3.907 27.271 1088 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer Outliers : 0.94 % 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: 1.47 (0.27), residues: 976 helix: 2.05 (0.19), residues: 744 sheet: None (None), residues: 0 loop : -2.80 (0.33), residues: 232 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 117 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 120 average time/residue: 0.2009 time to fit residues: 32.5123 Evaluate side-chains 119 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 113 time to evaluate : 0.880 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1388 time to fit residues: 2.4648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 72 optimal weight: 20.0000 chunk 84 optimal weight: 0.9980 chunk 88 optimal weight: 0.5980 chunk 80 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.7856 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 8000 Z= 0.181 Angle : 0.485 4.569 10864 Z= 0.260 Chirality : 0.039 0.138 1292 Planarity : 0.004 0.050 1316 Dihedral : 3.913 27.558 1088 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer Outliers : 0.82 % 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: 1.50 (0.27), residues: 976 helix: 1.87 (0.19), residues: 768 sheet: None (None), residues: 0 loop : -2.50 (0.35), residues: 208 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 123 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 126 average time/residue: 0.1946 time to fit residues: 33.6640 Evaluate side-chains 128 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 122 time to evaluate : 0.848 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2022 time to fit residues: 2.8297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 56 optimal weight: 0.2980 chunk 91 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.7832 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 8000 Z= 0.154 Angle : 0.467 4.558 10864 Z= 0.251 Chirality : 0.039 0.138 1292 Planarity : 0.004 0.050 1316 Dihedral : 3.857 26.847 1088 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer Outliers : 0.23 % 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: 1.59 (0.27), residues: 976 helix: 1.95 (0.19), residues: 768 sheet: None (None), residues: 0 loop : -2.53 (0.34), residues: 208 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 116 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 118 average time/residue: 0.1968 time to fit residues: 31.8561 Evaluate side-chains 116 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 115 time to evaluate : 0.897 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3650 time to fit residues: 1.6953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 76 optimal weight: 0.0470 chunk 7 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 overall best weight: 0.7680 ------------------------------------------------------------------------------- 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: 0.7848 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 8000 Z= 0.172 Angle : 0.480 4.570 10864 Z= 0.257 Chirality : 0.039 0.143 1292 Planarity : 0.004 0.050 1316 Dihedral : 3.849 27.485 1088 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer Outliers : 0.35 % 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: 1.62 (0.27), residues: 976 helix: 1.97 (0.19), residues: 768 sheet: None (None), residues: 0 loop : -2.51 (0.34), residues: 208 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 123 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 123 average time/residue: 0.1937 time to fit residues: 32.9485 Evaluate side-chains 125 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 122 time to evaluate : 0.799 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0858 time to fit residues: 1.5441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 11 optimal weight: 10.0000 chunk 21 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.190722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.124949 restraints weight = 7710.698| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.75 r_work: 0.3070 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 8000 Z= 0.188 Angle : 0.487 4.585 10864 Z= 0.261 Chirality : 0.040 0.139 1292 Planarity : 0.004 0.050 1316 Dihedral : 3.891 27.311 1088 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer Outliers : 0.47 % 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: 1.58 (0.27), residues: 976 helix: 1.93 (0.19), residues: 768 sheet: None (None), residues: 0 loop : -2.50 (0.35), residues: 208 =============================================================================== Job complete usr+sys time: 1752.30 seconds wall clock time: 32 minutes 46.78 seconds (1966.78 seconds total)