Starting phenix.real_space_refine on Wed Aug 5 02:49:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9s6y_54633/08_2026/9s6y_54633.cif Found real_map, /net/cci-nas-00/data/ceres_data/9s6y_54633/08_2026/9s6y_54633.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9s6y_54633/08_2026/9s6y_54633.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9s6y_54633/08_2026/9s6y_54633.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9s6y_54633/08_2026/9s6y_54633.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9s6y_54633/08_2026/9s6y_54633.map" } resolution = 3.98 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 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= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 5071 2.51 5 N 1331 2.21 5 O 1550 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7988 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1694 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 206} Chain: "B" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1768 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 14, 'TRANS': 222} Chain: "C" Number of atoms: 4442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 558, 4442 Classifications: {'peptide': 558} Link IDs: {'PTRANS': 38, 'TRANS': 519} Chain breaks: 1 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 1.83, per 1000 atoms: 0.23 Number of scatterers: 7988 At special positions: 0 Unit cell: (76, 83.6, 186.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 1550 8.00 N 1331 7.00 C 5071 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 24 " - pdb=" SG CYS A 94 " distance=2.03 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 200 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 104 " - pdb=" SG CYS B 109 " distance=2.03 Simple disulfide: pdb=" SG CYS B 164 " - pdb=" SG CYS B 220 " distance=2.03 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS C 134 " distance=2.03 Simple disulfide: pdb=" SG CYS C 279 " - pdb=" SG CYS C 289 " distance=2.03 Simple disulfide: pdb=" SG CYS C 324 " - pdb=" SG CYS C 349 " distance=2.03 Simple disulfide: pdb=" SG CYS C 367 " - pdb=" SG CYS C 420 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 512 " distance=2.03 Simple disulfide: pdb=" SG CYS C 468 " - pdb=" SG CYS C 475 " distance=2.03 Simple disulfide: pdb=" SG CYS C 525 " - pdb=" SG CYS C 577 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Links applied NAG-ASN " NAG C1301 " - " ASN C 110 " " NAG C1302 " - " ASN C 120 " " NAG C1303 " - " ASN C 145 " " NAG C1304 " - " ASN C 228 " " NAG C1305 " - " ASN C 270 " " NAG C1306 " - " ASN C 319 " Time building additional restraints: 0.62 Conformation dependent library (CDL) restraints added in 480.2 milliseconds 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1886 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 18 sheets defined 9.8% alpha, 28.4% 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 127 through 132 Processing helix chain 'A' and resid 188 through 195 removed outlier: 3.597A pdb=" N HIS A 195 " --> pdb=" O ASP A 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 30 No H-bonds generated for 'chain 'B' and resid 28 through 30' Processing helix chain 'B' and resid 62 through 65 removed outlier: 3.555A pdb=" N GLN B 65 " --> pdb=" O GLN B 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 62 through 65' Processing helix chain 'B' and resid 87 through 91 removed outlier: 3.563A pdb=" N ASP B 90 " --> pdb=" O ARG B 87 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N THR B 91 " --> pdb=" O SER B 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 87 through 91' Processing helix chain 'B' and resid 105 through 110 removed outlier: 4.326A pdb=" N SER B 108 " --> pdb=" O SER B 105 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR B 110 " --> pdb=" O THR B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 213 No H-bonds generated for 'chain 'B' and resid 211 through 213' Processing helix chain 'C' and resid 282 through 292 Processing helix chain 'C' and resid 325 through 332 removed outlier: 4.046A pdb=" N VAL C 329 " --> pdb=" O PRO C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 341 Processing helix chain 'C' and resid 352 through 354 No H-bonds generated for 'chain 'C' and resid 352 through 354' Processing helix chain 'C' and resid 355 through 360 removed outlier: 3.633A pdb=" N THR C 360 " --> pdb=" O LEU C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 376 Processing helix chain 'C' and resid 391 through 398 removed outlier: 4.414A pdb=" N ARG C 396 " --> pdb=" O ASP C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 Processing helix chain 'C' and resid 426 through 431 removed outlier: 3.664A pdb=" N ASP C 430 " --> pdb=" O THR C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 493 removed outlier: 3.565A pdb=" N GLN C 493 " --> pdb=" O ILE C 490 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 8 Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 13 removed outlier: 3.653A pdb=" N GLU A 111 " --> pdb=" O SER A 12 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N GLN A 43 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N LEU A 52 " --> pdb=" O GLN A 43 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 136 through 145 removed outlier: 6.050A pdb=" N TYR A 179 " --> pdb=" O ASN A 144 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 151 through 156 Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 6 Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 12 removed outlier: 5.699A pdb=" N GLY B 33 " --> pdb=" O GLY B 99 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE B 34 " --> pdb=" O TRP B 50 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N TRP B 50 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N TRP B 36 " --> pdb=" O MET B 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 17 through 19 Processing sheet with id=AA8, first strand: chain 'B' and resid 72 through 73 Processing sheet with id=AA9, first strand: chain 'B' and resid 144 through 148 removed outlier: 4.376A pdb=" N GLY B 163 " --> pdb=" O LEU B 148 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N TYR B 200 " --> pdb=" O ASP B 168 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 144 through 148 removed outlier: 4.376A pdb=" N GLY B 163 " --> pdb=" O LEU B 148 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N TYR B 200 " --> pdb=" O ASP B 168 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 175 through 178 removed outlier: 4.780A pdb=" N TYR B 218 " --> pdb=" O VAL B 235 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 33 through 34 removed outlier: 3.521A pdb=" N VAL C 67 " --> pdb=" O PHE C 34 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU C 195 " --> pdb=" O LYS C 222 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N LYS C 222 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N VAL C 197 " --> pdb=" O ILE C 220 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 53 through 60 Processing sheet with id=AB5, first strand: chain 'C' and resid 82 through 83 removed outlier: 3.527A pdb=" N PHE C 232 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN C 231 " --> pdb=" O GLY C 105 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY C 101 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE C 162 " --> pdb=" O ALA C 128 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 147 through 149 removed outlier: 4.283A pdb=" N VAL C 140 " --> pdb=" O ILE C 149 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N PHE C 139 " --> pdb=" O ALA C 238 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 313 through 316 removed outlier: 7.130A pdb=" N VAL C 314 " --> pdb=" O ASN C 529 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N SER C 562 " --> pdb=" O GLY C 553 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 343 through 346 Processing sheet with id=AB9, first strand: chain 'C' and resid 440 through 442 224 hydrogen bonds defined for protein. 558 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: 1.34 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2542 1.34 - 1.46: 1977 1.46 - 1.58: 3637 1.58 - 1.70: 0 1.70 - 1.82: 45 Bond restraints: 8201 Sorted by residual: bond pdb=" CA SER B 139 " pdb=" C SER B 139 " ideal model delta sigma weight residual 1.523 1.532 -0.010 1.10e-02 8.26e+03 8.08e-01 bond pdb=" CA SER A 69 " pdb=" CB SER A 69 " ideal model delta sigma weight residual 1.534 1.518 0.015 1.72e-02 3.38e+03 7.99e-01 bond pdb=" CB PRO B 171 " pdb=" CG PRO B 171 " ideal model delta sigma weight residual 1.492 1.535 -0.043 5.00e-02 4.00e+02 7.38e-01 bond pdb=" CA VAL B 133 " pdb=" CB VAL B 133 " ideal model delta sigma weight residual 1.537 1.527 0.011 1.26e-02 6.30e+03 7.17e-01 bond pdb=" C THR C 534 " pdb=" N GLY C 535 " ideal model delta sigma weight residual 1.331 1.319 0.012 1.46e-02 4.69e+03 6.68e-01 ... (remaining 8196 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.19: 10808 1.19 - 2.39: 269 2.39 - 3.58: 81 3.58 - 4.78: 6 4.78 - 5.97: 4 Bond angle restraints: 11168 Sorted by residual: angle pdb=" N ILE C 153 " pdb=" CA ILE C 153 " pdb=" C ILE C 153 " ideal model delta sigma weight residual 111.48 108.91 2.57 9.40e-01 1.13e+00 7.48e+00 angle pdb=" C ASN C 120 " pdb=" N SER C 121 " pdb=" CA SER C 121 " ideal model delta sigma weight residual 121.54 126.53 -4.99 1.91e+00 2.74e-01 6.83e+00 angle pdb=" CA GLY C 404 " pdb=" C GLY C 404 " pdb=" N VAL C 405 " ideal model delta sigma weight residual 115.62 117.25 -1.63 7.60e-01 1.73e+00 4.63e+00 angle pdb=" N GLY B 99 " pdb=" CA GLY B 99 " pdb=" C GLY B 99 " ideal model delta sigma weight residual 112.34 116.54 -4.20 2.04e+00 2.40e-01 4.24e+00 angle pdb=" CA GLY C 404 " pdb=" C GLY C 404 " pdb=" O GLY C 404 " ideal model delta sigma weight residual 121.66 119.90 1.76 8.80e-01 1.29e+00 4.02e+00 ... (remaining 11163 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.65: 4470 11.65 - 23.30: 351 23.30 - 34.95: 91 34.95 - 46.60: 30 46.60 - 58.25: 11 Dihedral angle restraints: 4953 sinusoidal: 2009 harmonic: 2944 Sorted by residual: dihedral pdb=" CA ARG B 98 " pdb=" C ARG B 98 " pdb=" N GLY B 99 " pdb=" CA GLY B 99 " ideal model delta harmonic sigma weight residual -180.00 -160.21 -19.79 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA LEU C 449 " pdb=" C LEU C 449 " pdb=" N ARG C 450 " pdb=" CA ARG C 450 " ideal model delta harmonic sigma weight residual 180.00 163.76 16.24 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" N CYS C 468 " pdb=" CA CYS C 468 " pdb=" CB CYS C 468 " pdb=" SG CYS C 468 " ideal model delta sinusoidal sigma weight residual -180.00 -121.75 -58.25 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 4950 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 905 0.041 - 0.082: 225 0.082 - 0.123: 100 0.123 - 0.164: 8 0.164 - 0.204: 1 Chirality restraints: 1239 Sorted by residual: chirality pdb=" C1 NAG C1302 " pdb=" ND2 ASN C 120 " pdb=" C2 NAG C1302 " pdb=" O5 NAG C1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA ILE C 117 " pdb=" N ILE C 117 " pdb=" C ILE C 117 " pdb=" CB ILE C 117 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.94e-01 chirality pdb=" C1 NAG C1305 " pdb=" ND2 ASN C 270 " pdb=" C2 NAG C1305 " pdb=" O5 NAG C1305 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 4.87e-01 ... (remaining 1236 not shown) Planarity restraints: 1452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 172 " -0.023 5.00e-02 4.00e+02 3.51e-02 1.97e+00 pdb=" N PRO B 173 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 173 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 173 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 469 " 0.020 5.00e-02 4.00e+02 3.06e-02 1.50e+00 pdb=" N PRO C 470 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO C 470 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 470 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 470 " -0.018 5.00e-02 4.00e+02 2.73e-02 1.19e+00 pdb=" N PRO C 471 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO C 471 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 471 " -0.016 5.00e-02 4.00e+02 ... (remaining 1449 not shown) Histogram of nonbonded interaction distances: 2.56 - 3.02: 4650 3.02 - 3.49: 7523 3.49 - 3.96: 11990 3.96 - 4.43: 13228 4.43 - 4.90: 22404 Nonbonded interactions: 59795 Sorted by model distance: nonbonded pdb=" CA ASN C 51 " pdb=" O TYR C 267 " model vdw 2.556 3.470 nonbonded pdb=" N THR C 248 " pdb=" OG1 THR C 248 " model vdw 2.559 2.496 nonbonded pdb=" N SER C 121 " pdb=" N THR C 122 " model vdw 2.609 2.560 nonbonded pdb=" N SER B 136 " pdb=" O SER B 136 " model vdw 2.622 2.496 nonbonded pdb=" N THR B 58 " pdb=" OG1 THR B 58 " model vdw 2.626 2.496 ... (remaining 59790 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 8.580 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8219 Z= 0.124 Angle : 0.515 5.970 11210 Z= 0.274 Chirality : 0.043 0.204 1239 Planarity : 0.004 0.035 1446 Dihedral : 9.776 58.248 3031 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.80 % Allowed : 6.86 % Favored : 91.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.26), residues: 1007 helix: -1.34 (0.69), residues: 58 sheet: -0.31 (0.28), residues: 367 loop : -1.22 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 98 TYR 0.012 0.001 TYR C 253 PHE 0.010 0.001 PHE C 84 TRP 0.008 0.001 TRP C 424 HIS 0.003 0.001 HIS A 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 8201) covalent geometry : angle 0.51098 / 0.27 (11168) SS BOND : bond 0.00215 / 0.14 ( 12) SS BOND : angle 0.57432 / 0.30 ( 24) hydrogen bonds : bond 0.13321 / 9.40 ( 210) hydrogen bonds : angle 6.37854 / 4.62 ( 558) link_NAG-ASN : bond 0.00327 / 0.20 ( 6) link_NAG-ASN : angle 1.57602 / 1.00 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 183 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 VAL cc_start: 0.7494 (m) cc_final: 0.6346 (t) REVERT: A 111 GLU cc_start: 0.7481 (mt-10) cc_final: 0.6551 (mt-10) REVERT: A 122 PHE cc_start: 0.8229 (m-80) cc_final: 0.7800 (m-80) REVERT: A 179 TYR cc_start: 0.8051 (m-80) cc_final: 0.7807 (m-80) REVERT: A 202 VAL cc_start: 0.8567 (t) cc_final: 0.8006 (p) REVERT: B 13 LYS cc_start: 0.8930 (mmmt) cc_final: 0.8612 (mmmt) REVERT: B 23 LYS cc_start: 0.8015 (tttp) cc_final: 0.7615 (ttmt) REVERT: B 178 TRP cc_start: 0.7648 (m100) cc_final: 0.7385 (m100) REVERT: B 224 HIS cc_start: 0.8716 (t-90) cc_final: 0.8345 (t-90) REVERT: C 55 LEU cc_start: 0.8171 (tp) cc_final: 0.7816 (mm) REVERT: C 70 PHE cc_start: 0.9114 (m-80) cc_final: 0.8813 (m-10) REVERT: C 86 ASP cc_start: 0.8168 (OUTLIER) cc_final: 0.7660 (t0) REVERT: C 154 PHE cc_start: 0.7677 (p90) cc_final: 0.7251 (p90) REVERT: C 169 PHE cc_start: 0.8566 (p90) cc_final: 0.8310 (p90) REVERT: C 233 ARG cc_start: 0.8741 (ttm-80) cc_final: 0.8386 (tpp80) REVERT: C 253 TYR cc_start: 0.8710 (p90) cc_final: 0.8390 (p90) REVERT: C 380 PHE cc_start: 0.8718 (m-80) cc_final: 0.8462 (m-10) REVERT: C 454 ARG cc_start: 0.9007 (OUTLIER) cc_final: 0.8725 (ttt180) outliers start: 16 outliers final: 7 residues processed: 197 average time/residue: 0.0878 time to fit residues: 23.2085 Evaluate side-chains 123 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 468 CYS Chi-restraints excluded: chain C residue 482 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.1980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 547 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.180359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 99)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.125856 restraints weight = 12112.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.121172 restraints weight = 11144.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.122160 restraints weight = 10612.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.122394 restraints weight = 9808.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.122918 restraints weight = 8544.689| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8219 Z= 0.135 Angle : 0.578 6.986 11210 Z= 0.296 Chirality : 0.046 0.283 1239 Planarity : 0.004 0.041 1446 Dihedral : 5.669 58.675 1240 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.92 % Allowed : 10.35 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.26), residues: 1007 helix: -1.22 (0.72), residues: 52 sheet: -0.27 (0.28), residues: 373 loop : -1.25 (0.24), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 554 TYR 0.012 0.001 TYR B 54 PHE 0.028 0.002 PHE B 146 TRP 0.018 0.001 TRP C 246 HIS 0.002 0.001 HIS B 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 8201) covalent geometry : angle 0.57422 / 0.30 (11168) SS BOND : bond 0.00503 / 0.35 ( 12) SS BOND : angle 0.81090 / 0.45 ( 24) hydrogen bonds : bond 0.03284 / 2.36 ( 210) hydrogen bonds : angle 5.64865 / 4.08 ( 558) link_NAG-ASN : bond 0.00325 / 0.19 ( 6) link_NAG-ASN : angle 1.54371 / 1.02 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 VAL cc_start: 0.7788 (m) cc_final: 0.6710 (t) REVERT: A 122 PHE cc_start: 0.8058 (m-80) cc_final: 0.7851 (m-80) REVERT: A 124 PHE cc_start: 0.7817 (m-10) cc_final: 0.7564 (m-10) REVERT: A 144 ASN cc_start: 0.8789 (m-40) cc_final: 0.8575 (m-40) REVERT: A 216 ASN cc_start: 0.8762 (m-40) cc_final: 0.8245 (t0) REVERT: B 13 LYS cc_start: 0.8873 (mmmt) cc_final: 0.8640 (mmmt) REVERT: B 23 LYS cc_start: 0.8018 (tttp) cc_final: 0.7640 (ttmt) REVERT: B 57 ASN cc_start: 0.7892 (m110) cc_final: 0.7621 (m110) REVERT: B 104 CYS cc_start: 0.5161 (p) cc_final: 0.4798 (p) REVERT: B 126 VAL cc_start: 0.8739 (OUTLIER) cc_final: 0.8444 (p) REVERT: B 141 LYS cc_start: 0.9160 (tppt) cc_final: 0.8750 (tppt) REVERT: B 224 HIS cc_start: 0.8224 (t-90) cc_final: 0.7965 (t70) REVERT: C 86 ASP cc_start: 0.8104 (OUTLIER) cc_final: 0.7484 (t0) REVERT: C 154 PHE cc_start: 0.7198 (p90) cc_final: 0.6897 (p90) REVERT: C 201 TYR cc_start: 0.6644 (t80) cc_final: 0.6381 (t80) REVERT: C 253 TYR cc_start: 0.8385 (p90) cc_final: 0.7970 (p90) REVERT: C 380 PHE cc_start: 0.8742 (m-80) cc_final: 0.8531 (m-10) REVERT: C 454 ARG cc_start: 0.8988 (OUTLIER) cc_final: 0.8631 (ttt180) outliers start: 26 outliers final: 13 residues processed: 143 average time/residue: 0.0798 time to fit residues: 15.5936 Evaluate side-chains 122 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 468 CYS Chi-restraints excluded: chain C residue 482 TYR Chi-restraints excluded: chain C residue 557 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 53 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 3 optimal weight: 0.1980 chunk 34 optimal weight: 0.9990 chunk 98 optimal weight: 0.0270 chunk 77 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 overall best weight: 0.5642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 7 GLN A 28 GLN ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.181473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.142107 restraints weight = 11988.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.131764 restraints weight = 18448.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.130971 restraints weight = 15518.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.130489 restraints weight = 12903.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.130861 restraints weight = 10987.924| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8219 Z= 0.120 Angle : 0.561 6.780 11210 Z= 0.285 Chirality : 0.045 0.202 1239 Planarity : 0.004 0.042 1446 Dihedral : 5.605 58.685 1239 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.36 % Allowed : 11.81 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.26), residues: 1007 helix: -1.27 (0.71), residues: 52 sheet: -0.15 (0.28), residues: 377 loop : -1.26 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 217 TYR 0.018 0.001 TYR C 253 PHE 0.026 0.001 PHE B 146 TRP 0.008 0.001 TRP C 102 HIS 0.002 0.001 HIS A 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 8201) covalent geometry : angle 0.55829 / 0.28 (11168) SS BOND : bond 0.00183 / 0.12 ( 12) SS BOND : angle 0.64231 / 0.47 ( 24) hydrogen bonds : bond 0.02954 / 2.10 ( 210) hydrogen bonds : angle 5.46346 / 3.92 ( 558) link_NAG-ASN : bond 0.00334 / 0.20 ( 6) link_NAG-ASN : angle 1.48557 / 0.99 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 ASN cc_start: 0.8800 (m-40) cc_final: 0.8513 (m-40) REVERT: A 216 ASN cc_start: 0.8651 (m-40) cc_final: 0.8092 (t0) REVERT: B 13 LYS cc_start: 0.8859 (mmmt) cc_final: 0.8596 (mmmt) REVERT: B 23 LYS cc_start: 0.8067 (tttp) cc_final: 0.7722 (ttmt) REVERT: B 141 LYS cc_start: 0.9096 (tppt) cc_final: 0.8768 (tppt) REVERT: C 169 PHE cc_start: 0.7801 (p90) cc_final: 0.7442 (p90) REVERT: C 201 TYR cc_start: 0.6479 (t80) cc_final: 0.6238 (t80) REVERT: C 380 PHE cc_start: 0.8734 (m-80) cc_final: 0.8517 (m-10) outliers start: 21 outliers final: 18 residues processed: 133 average time/residue: 0.0882 time to fit residues: 16.2670 Evaluate side-chains 125 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 468 CYS Chi-restraints excluded: chain C residue 482 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 25 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 27 optimal weight: 0.1980 chunk 70 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 48 optimal weight: 8.9990 chunk 24 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.179841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.136900 restraints weight = 12227.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.132430 restraints weight = 17725.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.127714 restraints weight = 14325.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.127401 restraints weight = 13074.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.127674 restraints weight = 11632.047| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8219 Z= 0.137 Angle : 0.569 7.991 11210 Z= 0.287 Chirality : 0.045 0.197 1239 Planarity : 0.004 0.039 1446 Dihedral : 5.349 58.425 1233 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.92 % Allowed : 12.82 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.26), residues: 1007 helix: -1.36 (0.70), residues: 52 sheet: -0.01 (0.28), residues: 367 loop : -1.29 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 233 TYR 0.035 0.001 TYR C 253 PHE 0.019 0.001 PHE B 146 TRP 0.008 0.001 TRP A 154 HIS 0.005 0.001 HIS B 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 8201) covalent geometry : angle 0.56564 / 0.29 (11168) SS BOND : bond 0.00203 / 0.14 ( 12) SS BOND : angle 0.99729 / 0.83 ( 24) hydrogen bonds : bond 0.02984 / 2.08 ( 210) hydrogen bonds : angle 5.42108 / 3.90 ( 558) link_NAG-ASN : bond 0.00316 / 0.19 ( 6) link_NAG-ASN : angle 1.43463 / 0.97 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 PHE cc_start: 0.7298 (p90) cc_final: 0.7084 (p90) REVERT: A 216 ASN cc_start: 0.8626 (m-40) cc_final: 0.8162 (t0) REVERT: B 13 LYS cc_start: 0.8858 (mmmt) cc_final: 0.8555 (mmmt) REVERT: B 23 LYS cc_start: 0.8113 (tttp) cc_final: 0.7738 (ttmt) REVERT: B 126 VAL cc_start: 0.8766 (OUTLIER) cc_final: 0.8488 (p) REVERT: B 141 LYS cc_start: 0.9043 (tppt) cc_final: 0.8803 (tppt) REVERT: B 146 PHE cc_start: 0.7051 (m-80) cc_final: 0.6787 (m-80) REVERT: C 86 ASP cc_start: 0.8001 (OUTLIER) cc_final: 0.7352 (t0) REVERT: C 169 PHE cc_start: 0.7719 (p90) cc_final: 0.7374 (p90) REVERT: C 201 TYR cc_start: 0.6564 (t80) cc_final: 0.6320 (t80) REVERT: C 380 PHE cc_start: 0.8786 (m-80) cc_final: 0.8577 (m-10) outliers start: 26 outliers final: 19 residues processed: 130 average time/residue: 0.0859 time to fit residues: 15.3295 Evaluate side-chains 124 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 468 CYS Chi-restraints excluded: chain C residue 482 TYR Chi-restraints excluded: chain C residue 557 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 60 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 chunk 12 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 98 optimal weight: 0.0770 chunk 8 optimal weight: 5.9990 chunk 71 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.179425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 125)---------------| | r_work = 0.3405 r_free = 0.3405 target = 0.120368 restraints weight = 12164.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.117738 restraints weight = 9300.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.118359 restraints weight = 9329.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.118562 restraints weight = 8455.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.118854 restraints weight = 7784.869| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8219 Z= 0.150 Angle : 0.561 6.604 11210 Z= 0.285 Chirality : 0.045 0.193 1239 Planarity : 0.004 0.041 1446 Dihedral : 5.368 58.053 1233 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.04 % Allowed : 13.50 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.26), residues: 1007 helix: -1.22 (0.74), residues: 51 sheet: 0.01 (0.28), residues: 367 loop : -1.35 (0.24), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 233 TYR 0.032 0.001 TYR C 253 PHE 0.023 0.002 PHE C 70 TRP 0.006 0.001 TRP C 424 HIS 0.003 0.001 HIS A 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 8201) covalent geometry : angle 0.55747 / 0.28 (11168) SS BOND : bond 0.00325 / 0.23 ( 12) SS BOND : angle 1.03005 / 0.85 ( 24) hydrogen bonds : bond 0.03008 / 2.10 ( 210) hydrogen bonds : angle 5.41902 / 3.90 ( 558) link_NAG-ASN : bond 0.00292 / 0.18 ( 6) link_NAG-ASN : angle 1.43456 / 0.98 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 GLU cc_start: 0.7573 (tp30) cc_final: 0.7195 (tp30) REVERT: A 216 ASN cc_start: 0.9021 (m-40) cc_final: 0.8606 (t0) REVERT: B 13 LYS cc_start: 0.8920 (mmmt) cc_final: 0.8652 (mmmt) REVERT: B 23 LYS cc_start: 0.8102 (tttp) cc_final: 0.7717 (ttmt) REVERT: B 126 VAL cc_start: 0.8761 (OUTLIER) cc_final: 0.8479 (p) REVERT: B 141 LYS cc_start: 0.9178 (tppt) cc_final: 0.8745 (tppt) REVERT: B 146 PHE cc_start: 0.7370 (m-80) cc_final: 0.7100 (m-10) REVERT: C 86 ASP cc_start: 0.8201 (OUTLIER) cc_final: 0.7312 (t0) REVERT: C 169 PHE cc_start: 0.8493 (p90) cc_final: 0.8075 (p90) REVERT: C 264 MET cc_start: 0.7961 (mmm) cc_final: 0.7655 (mmm) outliers start: 27 outliers final: 19 residues processed: 132 average time/residue: 0.0905 time to fit residues: 16.2847 Evaluate side-chains 126 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 468 CYS Chi-restraints excluded: chain C residue 482 TYR Chi-restraints excluded: chain C residue 557 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 63 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 49 optimal weight: 0.0770 chunk 50 optimal weight: 5.9990 overall best weight: 0.7142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 28 GLN ** A 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.179366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.137579 restraints weight = 12023.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.129239 restraints weight = 16301.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.124838 restraints weight = 13121.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.124507 restraints weight = 12899.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.125363 restraints weight = 10346.672| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8219 Z= 0.130 Angle : 0.560 6.629 11210 Z= 0.283 Chirality : 0.044 0.194 1239 Planarity : 0.004 0.046 1446 Dihedral : 5.247 58.110 1231 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.47 % Allowed : 14.85 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.26), residues: 1007 helix: -1.13 (0.74), residues: 51 sheet: 0.03 (0.28), residues: 367 loop : -1.31 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 217 TYR 0.031 0.001 TYR C 253 PHE 0.018 0.001 PHE C 502 TRP 0.008 0.001 TRP C 424 HIS 0.004 0.001 HIS A 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 ( 8201) covalent geometry : angle 0.55741 / 0.28 (11168) SS BOND : bond 0.00213 / 0.14 ( 12) SS BOND : angle 0.80060 / 0.65 ( 24) hydrogen bonds : bond 0.02866 / 1.99 ( 210) hydrogen bonds : angle 5.38918 / 3.88 ( 558) link_NAG-ASN : bond 0.00310 / 0.19 ( 6) link_NAG-ASN : angle 1.39097 / 0.95 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 ASN cc_start: 0.8657 (m-40) cc_final: 0.8250 (t0) REVERT: B 13 LYS cc_start: 0.8914 (mmmt) cc_final: 0.8675 (mmmt) REVERT: B 23 LYS cc_start: 0.8096 (tttp) cc_final: 0.7714 (ttmt) REVERT: B 70 MET cc_start: 0.8320 (mtm) cc_final: 0.7977 (mtm) REVERT: B 126 VAL cc_start: 0.8665 (OUTLIER) cc_final: 0.8375 (p) REVERT: B 141 LYS cc_start: 0.9048 (tppt) cc_final: 0.8752 (tppt) REVERT: C 86 ASP cc_start: 0.8026 (OUTLIER) cc_final: 0.7314 (t0) REVERT: C 169 PHE cc_start: 0.7962 (p90) cc_final: 0.7706 (p90) REVERT: C 264 MET cc_start: 0.7835 (mmm) cc_final: 0.7629 (mmm) outliers start: 22 outliers final: 18 residues processed: 122 average time/residue: 0.0965 time to fit residues: 15.9990 Evaluate side-chains 123 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 468 CYS Chi-restraints excluded: chain C residue 482 TYR Chi-restraints excluded: chain C residue 557 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 81 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 37 optimal weight: 20.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.174077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.131204 restraints weight = 12206.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.127334 restraints weight = 18267.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.123123 restraints weight = 12396.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.123236 restraints weight = 13149.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.123808 restraints weight = 9346.884| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 8219 Z= 0.291 Angle : 0.670 7.017 11210 Z= 0.349 Chirality : 0.047 0.182 1239 Planarity : 0.005 0.047 1446 Dihedral : 5.818 58.517 1231 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 3.04 % Allowed : 15.30 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.26), residues: 1007 helix: -1.09 (0.77), residues: 51 sheet: -0.14 (0.28), residues: 360 loop : -1.54 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 217 TYR 0.030 0.002 TYR C 253 PHE 0.030 0.002 PHE B 146 TRP 0.013 0.002 TRP A 154 HIS 0.005 0.002 HIS A 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00673 / 0.29 ( 8201) covalent geometry : angle 0.66632 / 0.35 (11168) SS BOND : bond 0.00399 / 0.28 ( 12) SS BOND : angle 1.30743 / 1.03 ( 24) hydrogen bonds : bond 0.03777 / 2.68 ( 210) hydrogen bonds : angle 5.74663 / 4.17 ( 558) link_NAG-ASN : bond 0.00261 / 0.16 ( 6) link_NAG-ASN : angle 1.39790 / 0.96 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 GLU cc_start: 0.7462 (pp20) cc_final: 0.7078 (pp20) REVERT: A 201 GLU cc_start: 0.7479 (tp30) cc_final: 0.6885 (tp30) REVERT: A 216 ASN cc_start: 0.8532 (m-40) cc_final: 0.8231 (t0) REVERT: B 13 LYS cc_start: 0.8958 (mmmt) cc_final: 0.8729 (mmmt) REVERT: B 23 LYS cc_start: 0.8142 (tttp) cc_final: 0.7760 (ttmt) REVERT: B 141 LYS cc_start: 0.8928 (tppt) cc_final: 0.8576 (tppt) REVERT: B 146 PHE cc_start: 0.6922 (OUTLIER) cc_final: 0.6308 (m-80) REVERT: C 86 ASP cc_start: 0.8085 (OUTLIER) cc_final: 0.7309 (t0) REVERT: C 169 PHE cc_start: 0.7820 (p90) cc_final: 0.7258 (p90) outliers start: 27 outliers final: 20 residues processed: 121 average time/residue: 0.0976 time to fit residues: 15.9482 Evaluate side-chains 120 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 146 PHE Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 135 ASP Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 468 CYS Chi-restraints excluded: chain C residue 482 TYR Chi-restraints excluded: chain C residue 557 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 65 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 17 optimal weight: 0.0040 chunk 73 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 25 optimal weight: 0.2980 chunk 82 optimal weight: 0.6980 chunk 87 optimal weight: 0.8980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.178888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.137592 restraints weight = 12082.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.127357 restraints weight = 17844.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.124235 restraints weight = 14605.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.123702 restraints weight = 13296.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.124986 restraints weight = 11117.049| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8219 Z= 0.126 Angle : 0.582 8.118 11210 Z= 0.296 Chirality : 0.044 0.190 1239 Planarity : 0.004 0.051 1446 Dihedral : 5.437 58.105 1231 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.47 % Allowed : 16.31 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.26), residues: 1007 helix: -0.87 (0.79), residues: 51 sheet: 0.05 (0.28), residues: 361 loop : -1.35 (0.24), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 217 TYR 0.029 0.001 TYR C 253 PHE 0.030 0.002 PHE A 124 TRP 0.013 0.001 TRP C 424 HIS 0.004 0.001 HIS B 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 8201) covalent geometry : angle 0.57910 / 0.30 (11168) SS BOND : bond 0.00193 / 0.13 ( 12) SS BOND : angle 0.72683 / 0.60 ( 24) hydrogen bonds : bond 0.02940 / 2.04 ( 210) hydrogen bonds : angle 5.52998 / 3.97 ( 558) link_NAG-ASN : bond 0.00307 / 0.19 ( 6) link_NAG-ASN : angle 1.36608 / 0.92 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 GLU cc_start: 0.7475 (tp30) cc_final: 0.6839 (tp30) REVERT: A 216 ASN cc_start: 0.8842 (m-40) cc_final: 0.8092 (t0) REVERT: B 13 LYS cc_start: 0.8960 (mmmt) cc_final: 0.8731 (mmmt) REVERT: B 23 LYS cc_start: 0.8074 (tttp) cc_final: 0.7654 (ttmt) REVERT: B 70 MET cc_start: 0.8285 (mtm) cc_final: 0.7973 (mtm) REVERT: B 141 LYS cc_start: 0.8945 (tppt) cc_final: 0.8665 (tppt) REVERT: C 169 PHE cc_start: 0.8067 (p90) cc_final: 0.7669 (p90) REVERT: C 264 MET cc_start: 0.7824 (mmm) cc_final: 0.7500 (mmm) outliers start: 22 outliers final: 20 residues processed: 125 average time/residue: 0.1047 time to fit residues: 17.9911 Evaluate side-chains 123 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 468 CYS Chi-restraints excluded: chain C residue 482 TYR Chi-restraints excluded: chain C residue 557 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 70 optimal weight: 7.9990 chunk 32 optimal weight: 0.0030 chunk 84 optimal weight: 0.0670 chunk 36 optimal weight: 7.9990 chunk 8 optimal weight: 0.5980 chunk 61 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 overall best weight: 0.4728 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.180144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.132946 restraints weight = 11887.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.126536 restraints weight = 15082.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.122197 restraints weight = 10424.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.123232 restraints weight = 9686.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.123061 restraints weight = 9041.525| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8219 Z= 0.114 Angle : 0.573 9.305 11210 Z= 0.291 Chirality : 0.044 0.192 1239 Planarity : 0.004 0.042 1446 Dihedral : 5.256 58.434 1231 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.25 % Allowed : 16.54 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.27), residues: 1007 helix: -0.54 (0.84), residues: 43 sheet: 0.07 (0.28), residues: 364 loop : -1.24 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 67 TYR 0.029 0.001 TYR C 253 PHE 0.024 0.002 PHE B 170 TRP 0.009 0.001 TRP C 424 HIS 0.006 0.001 HIS A 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.11 ( 8201) covalent geometry : angle 0.57083 / 0.29 (11168) SS BOND : bond 0.00189 / 0.13 ( 12) SS BOND : angle 0.75704 / 0.62 ( 24) hydrogen bonds : bond 0.02817 / 1.95 ( 210) hydrogen bonds : angle 5.42317 / 3.90 ( 558) link_NAG-ASN : bond 0.00315 / 0.19 ( 6) link_NAG-ASN : angle 1.36103 / 0.91 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 ARG cc_start: 0.8131 (mmm-85) cc_final: 0.7888 (mmm-85) REVERT: A 201 GLU cc_start: 0.7630 (tp30) cc_final: 0.7008 (tp30) REVERT: A 216 ASN cc_start: 0.8741 (m-40) cc_final: 0.7991 (t0) REVERT: B 13 LYS cc_start: 0.8961 (mmmt) cc_final: 0.8757 (mmmt) REVERT: B 23 LYS cc_start: 0.8073 (tttp) cc_final: 0.7665 (ttmt) REVERT: B 70 MET cc_start: 0.8364 (mtm) cc_final: 0.8109 (mtm) REVERT: B 141 LYS cc_start: 0.8997 (tppt) cc_final: 0.8674 (tppt) REVERT: C 264 MET cc_start: 0.7817 (mmm) cc_final: 0.7505 (mmm) outliers start: 20 outliers final: 19 residues processed: 126 average time/residue: 0.0947 time to fit residues: 16.2470 Evaluate side-chains 126 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 468 CYS Chi-restraints excluded: chain C residue 482 TYR Chi-restraints excluded: chain C residue 557 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 51 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 34 optimal weight: 0.0870 chunk 55 optimal weight: 6.9990 chunk 49 optimal weight: 0.0980 chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 35 optimal weight: 0.0870 chunk 5 optimal weight: 0.4980 chunk 66 optimal weight: 0.6980 overall best weight: 0.2936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.182141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.134831 restraints weight = 12125.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.129690 restraints weight = 14890.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.121519 restraints weight = 9901.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.122685 restraints weight = 11197.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.123233 restraints weight = 9077.463| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8219 Z= 0.102 Angle : 0.573 9.743 11210 Z= 0.290 Chirality : 0.044 0.196 1239 Planarity : 0.004 0.042 1446 Dihedral : 5.146 58.368 1231 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.80 % Allowed : 17.44 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.26), residues: 1007 helix: -0.50 (0.83), residues: 43 sheet: 0.08 (0.28), residues: 369 loop : -1.24 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 67 TYR 0.027 0.001 TYR C 253 PHE 0.028 0.001 PHE A 124 TRP 0.008 0.001 TRP B 50 HIS 0.005 0.001 HIS B 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.10 ( 8201) covalent geometry : angle 0.57048 / 0.29 (11168) SS BOND : bond 0.00174 / 0.11 ( 12) SS BOND : angle 0.67204 / 0.52 ( 24) hydrogen bonds : bond 0.02656 / 1.82 ( 210) hydrogen bonds : angle 5.39048 / 3.87 ( 558) link_NAG-ASN : bond 0.00321 / 0.20 ( 6) link_NAG-ASN : angle 1.35599 / 0.91 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 GLU cc_start: 0.7750 (tp30) cc_final: 0.7136 (tp30) REVERT: A 216 ASN cc_start: 0.8726 (m-40) cc_final: 0.8094 (t0) REVERT: B 23 LYS cc_start: 0.8054 (tttp) cc_final: 0.7630 (ttmt) REVERT: B 70 MET cc_start: 0.8242 (mtm) cc_final: 0.7971 (mtm) REVERT: B 141 LYS cc_start: 0.8976 (tppt) cc_final: 0.8684 (tppt) REVERT: C 264 MET cc_start: 0.7743 (mmm) cc_final: 0.7450 (mmm) outliers start: 16 outliers final: 16 residues processed: 122 average time/residue: 0.0950 time to fit residues: 15.8167 Evaluate side-chains 122 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 468 CYS Chi-restraints excluded: chain C residue 482 TYR Chi-restraints excluded: chain C residue 557 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 44 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 49 optimal weight: 0.0970 chunk 11 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 46 optimal weight: 0.0670 chunk 74 optimal weight: 0.4980 chunk 12 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 70 optimal weight: 9.9990 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.181542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.140735 restraints weight = 12022.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.135220 restraints weight = 17143.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.128041 restraints weight = 15483.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.127857 restraints weight = 16013.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.129661 restraints weight = 11671.249| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8219 Z= 0.109 Angle : 0.571 9.856 11210 Z= 0.291 Chirality : 0.044 0.194 1239 Planarity : 0.005 0.084 1446 Dihedral : 5.133 58.303 1231 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.91 % Allowed : 17.44 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.26), residues: 1007 helix: -0.68 (0.81), residues: 43 sheet: 0.12 (0.28), residues: 369 loop : -1.21 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 67 TYR 0.027 0.001 TYR C 253 PHE 0.033 0.001 PHE A 124 TRP 0.007 0.001 TRP C 424 HIS 0.003 0.001 HIS B 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 8201) covalent geometry : angle 0.56860 / 0.29 (11168) SS BOND : bond 0.00180 / 0.11 ( 12) SS BOND : angle 0.73507 / 0.57 ( 24) hydrogen bonds : bond 0.02719 / 1.87 ( 210) hydrogen bonds : angle 5.36203 / 3.84 ( 558) link_NAG-ASN : bond 0.00317 / 0.20 ( 6) link_NAG-ASN : angle 1.34017 / 0.90 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1522.62 seconds wall clock time: 27 minutes 2.52 seconds (1622.52 seconds total)