Starting phenix.real_space_refine on Sat Apr 6 09:00:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e7z_31005/04_2024/7e7z_31005.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e7z_31005/04_2024/7e7z_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_31005/04_2024/7e7z_31005.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e7z_31005/04_2024/7e7z_31005.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e7z_31005/04_2024/7e7z_31005.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e7z_31005/04_2024/7e7z_31005.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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-dev-5288/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: 4.54, per 1000 atoms: 0.58 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: 3.10 Conformation dependent library (CDL) restraints added in 1.5 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: 0.67 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: 2.15 Time building geometry restraints manager: 3.29 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: 0.740 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: 2.340 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 23.830 Find NCS groups from input model: 0.480 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: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.220 ------------------------------------------------------------------------------- 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 % Allowed : 0.23 % Favored : 99.77 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 362 HIS 0.001 0.000 HIS C 414 PHE 0.006 0.001 PHE B 343 TYR 0.014 0.001 TYR D 188 ARG 0.002 0.000 ARG A 170 *********************** 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 : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 379 LYS cc_start: 0.8468 (mtmt) cc_final: 0.8113 (mttp) REVERT: B 379 LYS cc_start: 0.8460 (mtmt) cc_final: 0.7860 (mttm) REVERT: C 318 LYS cc_start: 0.8522 (ttpp) cc_final: 0.8229 (ttpp) REVERT: C 333 MET cc_start: 0.8069 (ttm) cc_final: 0.7660 (ttt) REVERT: C 379 LYS cc_start: 0.8608 (mtmt) cc_final: 0.8077 (mttm) REVERT: D 318 LYS cc_start: 0.8583 (ttpp) cc_final: 0.8297 (ttpp) REVERT: D 379 LYS cc_start: 0.8420 (mtmt) cc_final: 0.8057 (mttp) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.2257 time to fit residues: 40.0739 Evaluate side-chains 103 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.806 ------------------------------------------------------------------------------- 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: 0.3980 chunk 56 optimal weight: 7.9990 chunk 87 optimal weight: 2.9990 overall best weight: 1.0262 ------------------------------------------------------------------------------- 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: 0.7850 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8000 Z= 0.216 Angle : 0.534 5.038 10864 Z= 0.286 Chirality : 0.041 0.152 1292 Planarity : 0.005 0.053 1316 Dihedral : 4.054 26.457 1088 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 1.17 % Allowed : 10.33 % Favored : 88.50 % 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: 0.72 (0.27), residues: 976 helix: 1.43 (0.19), residues: 744 sheet: None (None), residues: 0 loop : -2.75 (0.34), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 362 HIS 0.002 0.001 HIS A 414 PHE 0.013 0.001 PHE B 289 TYR 0.016 0.001 TYR A 188 ARG 0.006 0.000 ARG C 293 *********************** 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 131 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 121 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 379 LYS cc_start: 0.8565 (mtmt) cc_final: 0.8310 (mttm) REVERT: B 379 LYS cc_start: 0.8427 (mtmt) cc_final: 0.8092 (mttm) REVERT: C 318 LYS cc_start: 0.8626 (ttpp) cc_final: 0.8289 (ttpp) REVERT: C 333 MET cc_start: 0.8440 (ttm) cc_final: 0.8152 (mtp) REVERT: C 379 LYS cc_start: 0.8634 (mtmt) cc_final: 0.8375 (mttp) REVERT: C 396 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7444 (tp) REVERT: D 318 LYS cc_start: 0.8600 (ttpp) cc_final: 0.8248 (ttpp) REVERT: D 379 LYS cc_start: 0.8515 (mtmt) cc_final: 0.8268 (mttm) outliers start: 10 outliers final: 7 residues processed: 127 average time/residue: 0.2149 time to fit residues: 36.6190 Evaluate side-chains 128 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 120 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 CYS Chi-restraints excluded: chain B residue 221 CYS Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain D residue 221 CYS Chi-restraints excluded: chain D residue 300 ILE 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: 0.7980 chunk 72 optimal weight: 20.0000 chunk 59 optimal weight: 10.0000 chunk 24 optimal weight: 20.0000 chunk 87 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 29 optimal weight: 0.0970 chunk 70 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 ASN C 416 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1826 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= 0.162 Angle : 0.484 5.081 10864 Z= 0.261 Chirality : 0.039 0.133 1292 Planarity : 0.005 0.053 1316 Dihedral : 3.931 26.119 1088 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.11 % Allowed : 12.44 % Favored : 85.45 % 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: 1.08 (0.27), residues: 976 helix: 1.73 (0.19), residues: 744 sheet: None (None), residues: 0 loop : -2.82 (0.33), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 362 HIS 0.001 0.000 HIS C 414 PHE 0.009 0.001 PHE D 289 TYR 0.015 0.001 TYR A 188 ARG 0.004 0.000 ARG C 293 *********************** 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 127 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 109 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 379 LYS cc_start: 0.8573 (mtmt) cc_final: 0.8249 (mttm) REVERT: B 379 LYS cc_start: 0.8424 (mtmt) cc_final: 0.8113 (mttm) REVERT: C 318 LYS cc_start: 0.8620 (ttpp) cc_final: 0.8263 (ttpp) REVERT: C 353 LYS cc_start: 0.8800 (mttt) cc_final: 0.8542 (mttt) REVERT: C 379 LYS cc_start: 0.8605 (mtmt) cc_final: 0.8246 (mttm) REVERT: D 318 LYS cc_start: 0.8596 (ttpp) cc_final: 0.8238 (ttpp) REVERT: D 379 LYS cc_start: 0.8530 (mtmt) cc_final: 0.8206 (mttm) outliers start: 18 outliers final: 7 residues processed: 115 average time/residue: 0.2062 time to fit residues: 31.7165 Evaluate side-chains 112 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 105 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 300 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.1980 chunk 65 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 77 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 416 ASN D 416 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2023 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= 0.158 Angle : 0.474 4.608 10864 Z= 0.256 Chirality : 0.039 0.136 1292 Planarity : 0.004 0.051 1316 Dihedral : 3.868 25.884 1088 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.00 % Allowed : 13.97 % Favored : 84.04 % 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: 1.26 (0.27), residues: 976 helix: 1.87 (0.19), residues: 744 sheet: None (None), residues: 0 loop : -2.77 (0.33), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 362 HIS 0.001 0.000 HIS C 414 PHE 0.008 0.001 PHE A 289 TYR 0.015 0.001 TYR B 188 ARG 0.002 0.000 ARG C 293 *********************** 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 138 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 121 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 379 LYS cc_start: 0.8567 (mtmt) cc_final: 0.8204 (mttm) REVERT: B 353 LYS cc_start: 0.8748 (mttt) cc_final: 0.8541 (mttt) REVERT: B 379 LYS cc_start: 0.8404 (mtmt) cc_final: 0.8086 (mttm) REVERT: C 318 LYS cc_start: 0.8614 (ttpp) cc_final: 0.8266 (ttpp) REVERT: C 379 LYS cc_start: 0.8608 (mtmt) cc_final: 0.8235 (mttm) REVERT: D 318 LYS cc_start: 0.8578 (ttpp) cc_final: 0.8226 (ttpp) REVERT: D 379 LYS cc_start: 0.8516 (mtmt) cc_final: 0.8168 (mttm) outliers start: 17 outliers final: 15 residues processed: 122 average time/residue: 0.2262 time to fit residues: 36.8316 Evaluate side-chains 132 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 117 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 333 MET Chi-restraints excluded: chain D residue 396 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 47 optimal weight: 0.0570 chunk 83 optimal weight: 2.9990 chunk 23 optimal weight: 0.0770 chunk 31 optimal weight: 0.9980 overall best weight: 0.5256 ------------------------------------------------------------------------------- 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: 0.7806 moved from start: 0.2142 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= 0.145 Angle : 0.465 4.780 10864 Z= 0.251 Chirality : 0.039 0.135 1292 Planarity : 0.004 0.050 1316 Dihedral : 3.798 24.839 1088 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.35 % Allowed : 13.38 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.27), residues: 976 helix: 1.99 (0.19), residues: 744 sheet: None (None), residues: 0 loop : -2.73 (0.33), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 362 HIS 0.001 0.000 HIS B 414 PHE 0.007 0.001 PHE C 326 TYR 0.014 0.001 TYR B 188 ARG 0.002 0.000 ARG C 293 *********************** 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 126 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 106 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 379 LYS cc_start: 0.8566 (mtmt) cc_final: 0.8216 (mttm) REVERT: B 318 LYS cc_start: 0.8526 (tttp) cc_final: 0.8211 (ttpp) REVERT: B 379 LYS cc_start: 0.8447 (mtmt) cc_final: 0.8108 (mttm) REVERT: C 318 LYS cc_start: 0.8563 (ttpp) cc_final: 0.8215 (ttpp) REVERT: C 353 LYS cc_start: 0.8687 (mttt) cc_final: 0.8485 (mttt) REVERT: C 379 LYS cc_start: 0.8583 (mtmt) cc_final: 0.8210 (mttm) REVERT: D 318 LYS cc_start: 0.8563 (ttpp) cc_final: 0.8214 (ttpp) REVERT: D 379 LYS cc_start: 0.8522 (mtmt) cc_final: 0.8191 (mttm) outliers start: 20 outliers final: 19 residues processed: 113 average time/residue: 0.2333 time to fit residues: 34.6755 Evaluate side-chains 123 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 104 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 221 CYS Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 333 MET Chi-restraints excluded: chain D residue 347 LYS Chi-restraints excluded: chain D residue 396 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 10.0000 chunk 18 optimal weight: 0.0050 chunk 54 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 77 optimal weight: 0.0670 chunk 43 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 20.0000 chunk 89 optimal weight: 1.9990 overall best weight: 0.5132 ------------------------------------------------------------------------------- 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: 0.7808 moved from start: 0.2189 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= 0.142 Angle : 0.457 4.706 10864 Z= 0.247 Chirality : 0.038 0.135 1292 Planarity : 0.004 0.050 1316 Dihedral : 3.763 24.847 1088 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.46 % Allowed : 14.44 % Favored : 83.10 % 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: 2.10 (0.19), residues: 744 sheet: None (None), residues: 0 loop : -2.68 (0.33), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 362 HIS 0.001 0.000 HIS C 414 PHE 0.018 0.001 PHE C 289 TYR 0.014 0.001 TYR B 188 ARG 0.002 0.000 ARG C 293 *********************** 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 129 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 108 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 LYS cc_start: 0.8497 (tttp) cc_final: 0.8184 (ttpp) REVERT: A 379 LYS cc_start: 0.8569 (mtmt) cc_final: 0.8212 (mttm) REVERT: B 318 LYS cc_start: 0.8510 (tttp) cc_final: 0.8211 (ttpp) REVERT: B 379 LYS cc_start: 0.8480 (mtmt) cc_final: 0.8127 (mttm) REVERT: C 318 LYS cc_start: 0.8553 (ttpp) cc_final: 0.8242 (ttpp) REVERT: C 379 LYS cc_start: 0.8606 (mtmt) cc_final: 0.8196 (mttm) REVERT: D 318 LYS cc_start: 0.8558 (ttpp) cc_final: 0.8218 (ttpp) REVERT: D 379 LYS cc_start: 0.8531 (mtmt) cc_final: 0.8189 (mttm) outliers start: 21 outliers final: 21 residues processed: 115 average time/residue: 0.2228 time to fit residues: 34.1613 Evaluate side-chains 126 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 105 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 221 CYS Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 221 CYS Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 333 MET Chi-restraints excluded: chain D residue 347 LYS Chi-restraints excluded: chain D residue 396 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 6.9990 chunk 52 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 92 optimal weight: 0.6980 chunk 57 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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: 0.7849 moved from start: 0.2323 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= 0.184 Angle : 0.487 4.642 10864 Z= 0.261 Chirality : 0.040 0.137 1292 Planarity : 0.004 0.049 1316 Dihedral : 3.860 26.396 1088 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.82 % Allowed : 13.73 % Favored : 83.45 % 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: 1.56 (0.27), residues: 976 helix: 2.09 (0.19), residues: 744 sheet: None (None), residues: 0 loop : -2.69 (0.34), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 362 HIS 0.001 0.001 HIS C 414 PHE 0.007 0.001 PHE C 326 TYR 0.016 0.001 TYR B 188 ARG 0.002 0.000 ARG C 293 *********************** 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 142 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 118 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 379 LYS cc_start: 0.8627 (mtmt) cc_final: 0.8215 (mttm) REVERT: B 318 LYS cc_start: 0.8519 (tttp) cc_final: 0.8212 (ttpp) REVERT: B 379 LYS cc_start: 0.8484 (mtmt) cc_final: 0.8137 (mttm) REVERT: C 318 LYS cc_start: 0.8567 (ttpp) cc_final: 0.8214 (ttpp) REVERT: C 379 LYS cc_start: 0.8613 (mtmt) cc_final: 0.8289 (mttp) REVERT: D 318 LYS cc_start: 0.8577 (ttpp) cc_final: 0.8201 (ttpp) REVERT: D 379 LYS cc_start: 0.8538 (mtmt) cc_final: 0.8184 (mttm) outliers start: 24 outliers final: 21 residues processed: 129 average time/residue: 0.2211 time to fit residues: 38.5413 Evaluate side-chains 136 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 115 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 221 CYS Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 221 CYS Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 333 MET Chi-restraints excluded: chain D residue 347 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 72 optimal weight: 20.0000 chunk 84 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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: 0.7860 moved from start: 0.2434 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= 0.186 Angle : 0.485 4.634 10864 Z= 0.261 Chirality : 0.040 0.139 1292 Planarity : 0.004 0.048 1316 Dihedral : 3.890 27.290 1088 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.58 % Allowed : 13.85 % Favored : 83.57 % 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: 1.55 (0.27), residues: 976 helix: 2.08 (0.19), residues: 744 sheet: None (None), residues: 0 loop : -2.69 (0.34), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 362 HIS 0.001 0.001 HIS C 414 PHE 0.008 0.001 PHE A 289 TYR 0.017 0.001 TYR D 188 ARG 0.002 0.000 ARG C 293 *********************** 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 138 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 116 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 CYS cc_start: 0.7695 (m) cc_final: 0.7417 (m) REVERT: A 379 LYS cc_start: 0.8557 (mtmt) cc_final: 0.8149 (mttm) REVERT: B 379 LYS cc_start: 0.8475 (mtmt) cc_final: 0.8100 (mttm) REVERT: C 318 LYS cc_start: 0.8544 (ttpp) cc_final: 0.8192 (ttpp) REVERT: C 379 LYS cc_start: 0.8611 (mtmt) cc_final: 0.8212 (mttm) REVERT: D 231 CYS cc_start: 0.7639 (m) cc_final: 0.7383 (m) REVERT: D 318 LYS cc_start: 0.8572 (ttpp) cc_final: 0.8201 (ttpp) REVERT: D 379 LYS cc_start: 0.8525 (mtmt) cc_final: 0.8242 (mttp) outliers start: 22 outliers final: 22 residues processed: 128 average time/residue: 0.2027 time to fit residues: 35.1158 Evaluate side-chains 137 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 115 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 221 CYS Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 221 CYS Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 333 MET Chi-restraints excluded: chain D residue 396 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.6980 chunk 88 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.7847 moved from start: 0.2461 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= 0.170 Angle : 0.481 4.599 10864 Z= 0.258 Chirality : 0.039 0.138 1292 Planarity : 0.004 0.048 1316 Dihedral : 3.879 27.081 1088 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.70 % Allowed : 13.73 % Favored : 83.57 % 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: 1.58 (0.27), residues: 976 helix: 2.11 (0.19), residues: 744 sheet: None (None), residues: 0 loop : -2.70 (0.34), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 362 HIS 0.001 0.000 HIS C 414 PHE 0.007 0.001 PHE C 326 TYR 0.016 0.001 TYR D 188 ARG 0.002 0.000 ARG C 293 *********************** 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 139 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 116 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 CYS cc_start: 0.7668 (m) cc_final: 0.7382 (m) REVERT: A 379 LYS cc_start: 0.8591 (mtmt) cc_final: 0.8147 (mttm) REVERT: B 379 LYS cc_start: 0.8481 (mtmt) cc_final: 0.8112 (mttm) REVERT: C 318 LYS cc_start: 0.8535 (ttpp) cc_final: 0.8185 (ttpp) REVERT: C 379 LYS cc_start: 0.8620 (mtmt) cc_final: 0.8219 (mttm) REVERT: D 231 CYS cc_start: 0.7636 (m) cc_final: 0.7363 (m) REVERT: D 318 LYS cc_start: 0.8567 (ttpp) cc_final: 0.8188 (ttpp) REVERT: D 379 LYS cc_start: 0.8532 (mtmt) cc_final: 0.8260 (mttp) outliers start: 23 outliers final: 23 residues processed: 128 average time/residue: 0.1890 time to fit residues: 33.0128 Evaluate side-chains 139 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 116 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 221 CYS Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 221 CYS Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 333 MET Chi-restraints excluded: chain D residue 396 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.7855 moved from start: 0.2514 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= 0.173 Angle : 0.480 4.613 10864 Z= 0.258 Chirality : 0.040 0.143 1292 Planarity : 0.004 0.048 1316 Dihedral : 3.874 27.102 1088 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.93 % Allowed : 14.08 % Favored : 82.98 % 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: 1.60 (0.27), residues: 976 helix: 2.12 (0.19), residues: 744 sheet: None (None), residues: 0 loop : -2.68 (0.34), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 362 HIS 0.001 0.000 HIS C 414 PHE 0.010 0.001 PHE A 289 TYR 0.016 0.001 TYR D 188 ARG 0.002 0.000 ARG C 293 ********************** 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 137 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 112 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 CYS cc_start: 0.7663 (m) cc_final: 0.7385 (m) REVERT: A 379 LYS cc_start: 0.8597 (mtmt) cc_final: 0.8269 (mttp) REVERT: B 379 LYS cc_start: 0.8498 (mtmt) cc_final: 0.8130 (mttm) REVERT: C 318 LYS cc_start: 0.8533 (ttpp) cc_final: 0.8190 (ttpp) REVERT: C 379 LYS cc_start: 0.8633 (mtmt) cc_final: 0.8230 (mttm) REVERT: D 231 CYS cc_start: 0.7630 (m) cc_final: 0.7367 (m) REVERT: D 318 LYS cc_start: 0.8567 (ttpp) cc_final: 0.8197 (ttpp) REVERT: D 379 LYS cc_start: 0.8575 (mtmt) cc_final: 0.8277 (mttp) outliers start: 25 outliers final: 25 residues processed: 126 average time/residue: 0.2116 time to fit residues: 35.7850 Evaluate side-chains 137 residues out of total 852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 112 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 221 CYS Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 221 CYS Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain D residue 243 GLU Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 333 MET Chi-restraints excluded: chain D residue 396 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 11 optimal weight: 9.9990 chunk 21 optimal weight: 0.7980 chunk 76 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4087 r_free = 0.4087 target = 0.196446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 130)---------------| | r_work = 0.3431 r_free = 0.3431 target = 0.134080 restraints weight = 7730.417| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.36 r_work: 0.3033 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2535 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= 0.171 Angle : 0.484 4.604 10864 Z= 0.260 Chirality : 0.039 0.144 1292 Planarity : 0.004 0.048 1316 Dihedral : 3.863 27.059 1088 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 3.05 % Allowed : 13.50 % Favored : 83.45 % 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: 2.15 (0.19), residues: 744 sheet: None (None), residues: 0 loop : -2.71 (0.34), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 362 HIS 0.001 0.000 HIS C 414 PHE 0.007 0.001 PHE C 326 TYR 0.016 0.001 TYR D 188 ARG 0.002 0.000 ARG C 293 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1848.87 seconds wall clock time: 34 minutes 28.82 seconds (2068.82 seconds total)