Starting phenix.real_space_refine on Tue Mar 3 20:54:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wz7_32905/03_2026/7wz7_32905_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wz7_32905/03_2026/7wz7_32905.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wz7_32905/03_2026/7wz7_32905.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wz7_32905/03_2026/7wz7_32905.map" model { file = "/net/cci-nas-00/data/ceres_data/7wz7_32905/03_2026/7wz7_32905_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wz7_32905/03_2026/7wz7_32905_neut.cif" } resolution = 2.83 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= 0.019 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 57 5.16 5 C 5553 2.51 5 N 1487 2.21 5 O 1579 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8676 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1734 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 205} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "C" Number of atoms: 1776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1776 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "E" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "R" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2130 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 9, 'TRANS': 262} Chain breaks: 2 Time building chain proxies: 2.02, per 1000 atoms: 0.23 Number of scatterers: 8676 At special positions: 0 Unit cell: (93.96, 117.72, 131.76, 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 57 16.00 O 1579 8.00 N 1487 7.00 C 5553 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 147 " - pdb=" SG CYS C 217 " distance=2.05 Simple disulfide: pdb=" SG CYS R 657 " - pdb=" SG CYS R 733 " distance=2.04 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 Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 294.7 milliseconds 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2070 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 12 sheets defined 38.7% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 15 through 38 Processing helix chain 'A' and resid 49 through 66 removed outlier: 3.673A pdb=" N ASN A 66 " --> pdb=" O ILE A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 238 Processing helix chain 'A' and resid 265 through 278 removed outlier: 3.863A pdb=" N ASN A 278 " --> pdb=" O GLU A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 283 Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 319 through 333 removed outlier: 3.767A pdb=" N VAL A 323 " --> pdb=" O ARG A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 375 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 53 through 56 removed outlier: 4.168A pdb=" N GLY C 56 " --> pdb=" O SER C 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 53 through 56' Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.923A pdb=" N THR C 91 " --> pdb=" O SER C 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 24 removed outlier: 3.624A pdb=" N ASN E 24 " --> pdb=" O LYS E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 44 Processing helix chain 'E' and resid 45 through 48 removed outlier: 3.574A pdb=" N ASP E 48 " --> pdb=" O ALA E 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 45 through 48' Processing helix chain 'E' and resid 55 through 59 Processing helix chain 'R' and resid 568 through 573 Processing helix chain 'R' and resid 578 through 580 No H-bonds generated for 'chain 'R' and resid 578 through 580' Processing helix chain 'R' and resid 581 through 611 removed outlier: 4.495A pdb=" N TRP R 587 " --> pdb=" O PRO R 583 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA R 608 " --> pdb=" O LEU R 604 " (cutoff:3.500A) Processing helix chain 'R' and resid 617 through 646 removed outlier: 3.740A pdb=" N THR R 646 " --> pdb=" O ILE R 642 " (cutoff:3.500A) Processing helix chain 'R' and resid 655 through 688 Processing helix chain 'R' and resid 694 through 707 Processing helix chain 'R' and resid 707 through 722 Processing helix chain 'R' and resid 744 through 768 Proline residue: R 750 - end of helix Processing helix chain 'R' and resid 785 through 801 Proline residue: R 798 - end of helix Processing helix chain 'R' and resid 802 through 805 Processing helix chain 'R' and resid 806 through 813 Processing helix chain 'R' and resid 814 through 817 removed outlier: 3.962A pdb=" N LEU R 817 " --> pdb=" O SER R 814 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 814 through 817' Processing helix chain 'R' and resid 818 through 828 Processing helix chain 'R' and resid 829 through 837 Processing helix chain 'R' and resid 842 through 854 Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 213 removed outlier: 6.632A pdb=" N LYS A 42 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N LEU A 245 " --> pdb=" O LYS A 42 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU A 44 " --> pdb=" O LEU A 245 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N MET A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N LEU A 46 " --> pdb=" O MET A 247 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N HIS A 345 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU A 289 " --> pdb=" O HIS A 345 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.522A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.652A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.039A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.594A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 6.630A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.614A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.620A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.181A pdb=" N GLY C 10 " --> pdb=" O THR C 118 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N MET C 34 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N TYR C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 128 through 130 Processing sheet with id=AB3, first strand: chain 'C' and resid 134 through 136 removed outlier: 3.652A pdb=" N GLU C 234 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N LEU C 166 " --> pdb=" O LEU C 175 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N LEU C 175 " --> pdb=" O LEU C 166 " (cutoff:3.500A) 443 hydrogen bonds defined for protein. 1239 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: 1.12 Time building geometry restraints manager: 1.16 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: 2793 1.34 - 1.46: 2168 1.46 - 1.59: 3808 1.59 - 1.71: 0 1.71 - 1.83: 86 Bond restraints: 8855 Sorted by residual: bond pdb=" N TYR C 223 " pdb=" CA TYR C 223 " ideal model delta sigma weight residual 1.454 1.492 -0.038 1.14e-02 7.69e+03 1.11e+01 bond pdb=" CA ALA B 309 " pdb=" C ALA B 309 " ideal model delta sigma weight residual 1.524 1.485 0.039 1.31e-02 5.83e+03 8.72e+00 bond pdb=" N LYS R 728 " pdb=" CA LYS R 728 " ideal model delta sigma weight residual 1.454 1.485 -0.031 1.15e-02 7.56e+03 7.32e+00 bond pdb=" N SER C 52 " pdb=" CA SER C 52 " ideal model delta sigma weight residual 1.454 1.424 0.030 1.16e-02 7.43e+03 6.72e+00 bond pdb=" CA LYS R 728 " pdb=" C LYS R 728 " ideal model delta sigma weight residual 1.524 1.491 0.033 1.31e-02 5.83e+03 6.35e+00 ... (remaining 8850 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 11516 2.11 - 4.22: 387 4.22 - 6.33: 61 6.33 - 8.43: 18 8.43 - 10.54: 7 Bond angle restraints: 11989 Sorted by residual: angle pdb=" N SER A 13 " pdb=" CA SER A 13 " pdb=" C SER A 13 " ideal model delta sigma weight residual 107.28 117.82 -10.54 1.75e+00 3.27e-01 3.63e+01 angle pdb=" C SER A 339 " pdb=" CA SER A 339 " pdb=" CB SER A 339 " ideal model delta sigma weight residual 109.83 115.12 -5.29 9.90e-01 1.02e+00 2.86e+01 angle pdb=" N GLY B 202 " pdb=" CA GLY B 202 " pdb=" C GLY B 202 " ideal model delta sigma weight residual 111.04 102.18 8.86 1.77e+00 3.19e-01 2.51e+01 angle pdb=" C TYR C 223 " pdb=" CA TYR C 223 " pdb=" CB TYR C 223 " ideal model delta sigma weight residual 109.56 117.59 -8.03 1.64e+00 3.72e-01 2.40e+01 angle pdb=" C SER A 13 " pdb=" CA SER A 13 " pdb=" CB SER A 13 " ideal model delta sigma weight residual 111.51 105.11 6.40 1.38e+00 5.25e-01 2.15e+01 ... (remaining 11984 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.49: 4866 15.49 - 30.98: 290 30.98 - 46.48: 66 46.48 - 61.97: 21 61.97 - 77.46: 2 Dihedral angle restraints: 5245 sinusoidal: 2049 harmonic: 3196 Sorted by residual: dihedral pdb=" CB CYS R 657 " pdb=" SG CYS R 657 " pdb=" SG CYS R 733 " pdb=" CB CYS R 733 " ideal model delta sinusoidal sigma weight residual -86.00 -126.67 40.67 1 1.00e+01 1.00e-02 2.32e+01 dihedral pdb=" CA GLY B 202 " pdb=" C GLY B 202 " pdb=" N ALA B 203 " pdb=" CA ALA B 203 " ideal model delta harmonic sigma weight residual -180.00 -159.30 -20.70 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA SER A 13 " pdb=" C SER A 13 " pdb=" N ALA A 14 " pdb=" CA ALA A 14 " ideal model delta harmonic sigma weight residual 180.00 160.02 19.98 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 5242 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1072 0.064 - 0.129: 273 0.129 - 0.193: 28 0.193 - 0.257: 6 0.257 - 0.321: 3 Chirality restraints: 1382 Sorted by residual: chirality pdb=" CA PRO B 236 " pdb=" N PRO B 236 " pdb=" C PRO B 236 " pdb=" CB PRO B 236 " both_signs ideal model delta sigma weight residual False 2.72 2.40 0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CA LEU B 308 " pdb=" N LEU B 308 " pdb=" C LEU B 308 " pdb=" CB LEU B 308 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CG LEU B 55 " pdb=" CB LEU B 55 " pdb=" CD1 LEU B 55 " pdb=" CD2 LEU B 55 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 1379 not shown) Planarity restraints: 1502 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU R 817 " 0.014 2.00e-02 2.50e+03 2.79e-02 7.78e+00 pdb=" C LEU R 817 " -0.048 2.00e-02 2.50e+03 pdb=" O LEU R 817 " 0.018 2.00e-02 2.50e+03 pdb=" N ALA R 818 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 196 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.79e+00 pdb=" C SER C 196 " 0.045 2.00e-02 2.50e+03 pdb=" O SER C 196 " -0.017 2.00e-02 2.50e+03 pdb=" N GLY C 197 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 62 " 0.019 2.00e-02 2.50e+03 1.87e-02 5.25e+00 pdb=" CG HIS B 62 " -0.040 2.00e-02 2.50e+03 pdb=" ND1 HIS B 62 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 HIS B 62 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 HIS B 62 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS B 62 " 0.008 2.00e-02 2.50e+03 ... (remaining 1499 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1700 2.76 - 3.30: 8447 3.30 - 3.83: 14526 3.83 - 4.37: 17482 4.37 - 4.90: 30504 Nonbonded interactions: 72659 Sorted by model distance: nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.230 3.040 nonbonded pdb=" O LEU A 291 " pdb=" OG1 THR A 347 " model vdw 2.257 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.266 3.040 nonbonded pdb=" O ARG A 314 " pdb=" OH TYR A 326 " model vdw 2.270 3.040 nonbonded pdb=" O GLN B 75 " pdb=" OG SER B 98 " model vdw 2.287 3.040 ... (remaining 72654 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.030 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:8.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 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 : 0.010 0.076 8857 Z= 0.456 Angle : 0.954 10.542 11993 Z= 0.541 Chirality : 0.057 0.321 1382 Planarity : 0.005 0.046 1502 Dihedral : 11.502 77.459 3169 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.69 (0.25), residues: 1086 helix: 0.60 (0.28), residues: 361 sheet: -0.86 (0.27), residues: 302 loop : -0.93 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 219 TYR 0.032 0.004 TYR B 105 PHE 0.034 0.004 PHE B 151 TRP 0.026 0.003 TRP B 99 HIS 0.018 0.002 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00998 ( 8855) covalent geometry : angle 0.95389 (11989) SS BOND : bond 0.01440 ( 2) SS BOND : angle 1.33226 ( 4) hydrogen bonds : bond 0.14813 ( 443) hydrogen bonds : angle 7.12348 ( 1239) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: A 43 ILE cc_start: 0.7002 (mt) cc_final: 0.6552 (tt) REVERT: A 235 PHE cc_start: 0.8013 (m-80) cc_final: 0.7514 (m-80) REVERT: A 285 VAL cc_start: 0.7074 (t) cc_final: 0.6797 (m) REVERT: C 180 MET cc_start: 0.6158 (ttm) cc_final: 0.5955 (tpp) REVERT: R 833 PHE cc_start: 0.7256 (m-10) cc_final: 0.7027 (m-80) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.4445 time to fit residues: 101.6094 Evaluate side-chains 192 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 8.9990 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 0.0770 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN E 44 HIS R 820 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.179517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.151306 restraints weight = 12551.244| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 2.39 r_work: 0.3837 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8857 Z= 0.178 Angle : 0.653 9.062 11993 Z= 0.337 Chirality : 0.045 0.186 1382 Planarity : 0.004 0.043 1502 Dihedral : 5.206 23.061 1185 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.20 % Allowed : 11.11 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.18 (0.26), residues: 1086 helix: 1.43 (0.28), residues: 356 sheet: -0.78 (0.28), residues: 296 loop : -0.84 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 685 TYR 0.016 0.002 TYR C 178 PHE 0.019 0.002 PHE A 357 TRP 0.022 0.002 TRP B 211 HIS 0.006 0.001 HIS A 345 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 8855) covalent geometry : angle 0.65307 (11989) SS BOND : bond 0.00845 ( 2) SS BOND : angle 1.00423 ( 4) hydrogen bonds : bond 0.04813 ( 443) hydrogen bonds : angle 5.35696 ( 1239) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 194 time to evaluate : 0.339 Fit side-chains REVERT: A 233 LYS cc_start: 0.7686 (mmtt) cc_final: 0.7377 (mmtt) REVERT: A 235 PHE cc_start: 0.7966 (m-80) cc_final: 0.7380 (m-80) REVERT: A 343 PHE cc_start: 0.7146 (m-10) cc_final: 0.6911 (m-80) REVERT: B 130 GLU cc_start: 0.7883 (mp0) cc_final: 0.7590 (mp0) REVERT: B 230 ASN cc_start: 0.8052 (m-40) cc_final: 0.7832 (m110) REVERT: B 325 MET cc_start: 0.7572 (mmt) cc_final: 0.7186 (mtt) REVERT: C 90 ASP cc_start: 0.7250 (m-30) cc_final: 0.6950 (m-30) REVERT: C 180 MET cc_start: 0.6278 (ttm) cc_final: 0.6055 (tpp) REVERT: R 582 PHE cc_start: 0.7637 (m-80) cc_final: 0.7292 (m-80) REVERT: R 827 ASN cc_start: 0.7104 (m-40) cc_final: 0.6577 (m-40) REVERT: R 833 PHE cc_start: 0.7241 (m-10) cc_final: 0.6973 (m-80) outliers start: 21 outliers final: 8 residues processed: 201 average time/residue: 0.4374 time to fit residues: 94.8407 Evaluate side-chains 185 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 177 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 212 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 83 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 14 optimal weight: 0.0970 chunk 92 optimal weight: 0.3980 chunk 6 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN B 176 GLN R 820 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.177599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.149390 restraints weight = 12420.676| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 2.36 r_work: 0.3822 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8857 Z= 0.223 Angle : 0.648 8.248 11993 Z= 0.333 Chirality : 0.046 0.166 1382 Planarity : 0.004 0.042 1502 Dihedral : 5.147 25.874 1185 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.83 % Allowed : 13.63 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.15 (0.26), residues: 1086 helix: 1.56 (0.28), residues: 357 sheet: -0.86 (0.28), residues: 290 loop : -0.86 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 685 TYR 0.018 0.002 TYR C 178 PHE 0.030 0.002 PHE A 357 TRP 0.022 0.002 TRP B 211 HIS 0.006 0.001 HIS A 345 Details of bonding type rmsd covalent geometry : bond 0.00514 ( 8855) covalent geometry : angle 0.64746 (11989) SS BOND : bond 0.01017 ( 2) SS BOND : angle 1.29145 ( 4) hydrogen bonds : bond 0.04575 ( 443) hydrogen bonds : angle 5.21397 ( 1239) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 182 time to evaluate : 0.314 Fit side-chains REVERT: A 233 LYS cc_start: 0.7708 (mmtt) cc_final: 0.7420 (mmtt) REVERT: A 235 PHE cc_start: 0.7852 (m-10) cc_final: 0.7274 (m-80) REVERT: A 294 MET cc_start: 0.6809 (ptt) cc_final: 0.6580 (ptt) REVERT: A 343 PHE cc_start: 0.7193 (m-10) cc_final: 0.6955 (m-80) REVERT: B 38 ASP cc_start: 0.8168 (m-30) cc_final: 0.7910 (m-30) REVERT: B 129 ARG cc_start: 0.8440 (mmm-85) cc_final: 0.7928 (mmm-85) REVERT: B 130 GLU cc_start: 0.7890 (mp0) cc_final: 0.7598 (mp0) REVERT: B 325 MET cc_start: 0.7552 (mmt) cc_final: 0.7210 (mtt) REVERT: C 65 LYS cc_start: 0.7986 (tppt) cc_final: 0.7775 (tttm) REVERT: C 90 ASP cc_start: 0.7321 (m-30) cc_final: 0.7066 (m-30) REVERT: E 50 LEU cc_start: 0.7886 (mt) cc_final: 0.7562 (mt) REVERT: R 582 PHE cc_start: 0.7653 (m-80) cc_final: 0.7339 (m-80) REVERT: R 693 MET cc_start: 0.6543 (ptt) cc_final: 0.6304 (ptt) outliers start: 27 outliers final: 16 residues processed: 192 average time/residue: 0.4703 time to fit residues: 97.2334 Evaluate side-chains 196 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 180 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain R residue 745 LEU Chi-restraints excluded: chain R residue 763 LEU Chi-restraints excluded: chain R residue 821 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 30 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 6 optimal weight: 0.0970 chunk 78 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 24 optimal weight: 0.2980 chunk 40 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 176 GLN B 230 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.179375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.151402 restraints weight = 12576.577| |-----------------------------------------------------------------------------| r_work (start): 0.3966 rms_B_bonded: 2.37 r_work: 0.3846 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8857 Z= 0.161 Angle : 0.604 8.153 11993 Z= 0.309 Chirality : 0.043 0.161 1382 Planarity : 0.004 0.041 1502 Dihedral : 4.924 25.653 1185 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.14 % Allowed : 14.26 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.00 (0.26), residues: 1086 helix: 1.74 (0.27), residues: 357 sheet: -0.94 (0.28), residues: 294 loop : -0.70 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG R 685 TYR 0.015 0.002 TYR C 178 PHE 0.025 0.002 PHE A 357 TRP 0.023 0.002 TRP B 211 HIS 0.008 0.001 HIS A 345 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 8855) covalent geometry : angle 0.60373 (11989) SS BOND : bond 0.01011 ( 2) SS BOND : angle 1.20295 ( 4) hydrogen bonds : bond 0.04036 ( 443) hydrogen bonds : angle 5.02002 ( 1239) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 185 time to evaluate : 0.303 Fit side-chains REVERT: A 233 LYS cc_start: 0.7718 (mmtt) cc_final: 0.7342 (mmtt) REVERT: A 235 PHE cc_start: 0.7866 (m-10) cc_final: 0.7372 (m-80) REVERT: A 266 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7393 (pp) REVERT: A 270 MET cc_start: 0.6867 (ttt) cc_final: 0.6394 (tpp) REVERT: A 294 MET cc_start: 0.6882 (ptt) cc_final: 0.6579 (ptt) REVERT: A 343 PHE cc_start: 0.7105 (m-10) cc_final: 0.6902 (m-80) REVERT: B 38 ASP cc_start: 0.8093 (m-30) cc_final: 0.7846 (m-30) REVERT: B 129 ARG cc_start: 0.8415 (mmm-85) cc_final: 0.7941 (mmm-85) REVERT: B 130 GLU cc_start: 0.7809 (mp0) cc_final: 0.7526 (mp0) REVERT: B 230 ASN cc_start: 0.8063 (m-40) cc_final: 0.7776 (m110) REVERT: B 262 MET cc_start: 0.6631 (ttm) cc_final: 0.6407 (ttm) REVERT: B 325 MET cc_start: 0.7536 (mmt) cc_final: 0.7210 (mtt) REVERT: C 90 ASP cc_start: 0.7146 (m-30) cc_final: 0.6869 (m-30) REVERT: E 50 LEU cc_start: 0.7861 (mt) cc_final: 0.7543 (mt) REVERT: R 582 PHE cc_start: 0.7730 (m-80) cc_final: 0.7363 (m-80) REVERT: R 693 MET cc_start: 0.6609 (ptt) cc_final: 0.6288 (ptt) REVERT: R 833 PHE cc_start: 0.7101 (m-80) cc_final: 0.6549 (m-80) outliers start: 30 outliers final: 16 residues processed: 195 average time/residue: 0.4853 time to fit residues: 101.7148 Evaluate side-chains 197 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 180 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain R residue 763 LEU Chi-restraints excluded: chain R residue 793 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.4980 chunk 24 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 71 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN R 820 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.178729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.150588 restraints weight = 12505.562| |-----------------------------------------------------------------------------| r_work (start): 0.3961 rms_B_bonded: 2.35 r_work: 0.3836 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8857 Z= 0.188 Angle : 0.612 9.520 11993 Z= 0.313 Chirality : 0.044 0.156 1382 Planarity : 0.004 0.064 1502 Dihedral : 4.879 25.555 1185 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.04 % Allowed : 15.20 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.08 (0.26), residues: 1086 helix: 1.77 (0.27), residues: 360 sheet: -0.89 (0.28), residues: 288 loop : -0.64 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG R 685 TYR 0.016 0.002 TYR C 178 PHE 0.015 0.002 PHE B 241 TRP 0.020 0.002 TRP B 211 HIS 0.008 0.001 HIS A 345 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 8855) covalent geometry : angle 0.61191 (11989) SS BOND : bond 0.00879 ( 2) SS BOND : angle 1.11246 ( 4) hydrogen bonds : bond 0.04094 ( 443) hydrogen bonds : angle 4.96497 ( 1239) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 184 time to evaluate : 0.321 Fit side-chains REVERT: A 233 LYS cc_start: 0.7737 (mmtt) cc_final: 0.7359 (mmtt) REVERT: A 235 PHE cc_start: 0.7916 (m-10) cc_final: 0.7314 (m-80) REVERT: A 266 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7434 (pp) REVERT: A 270 MET cc_start: 0.6985 (ttt) cc_final: 0.6432 (tpp) REVERT: A 294 MET cc_start: 0.6923 (ptt) cc_final: 0.6572 (ptt) REVERT: B 38 ASP cc_start: 0.8131 (m-30) cc_final: 0.7880 (m-30) REVERT: B 130 GLU cc_start: 0.7843 (mp0) cc_final: 0.7562 (mp0) REVERT: B 325 MET cc_start: 0.7533 (mmt) cc_final: 0.7228 (mtt) REVERT: C 90 ASP cc_start: 0.7229 (m-30) cc_final: 0.6989 (m-30) REVERT: C 174 GLN cc_start: 0.7975 (tt0) cc_final: 0.7730 (pt0) REVERT: C 221 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7497 (tm) REVERT: E 50 LEU cc_start: 0.7932 (mt) cc_final: 0.7590 (mt) REVERT: R 582 PHE cc_start: 0.7777 (m-80) cc_final: 0.7336 (m-80) REVERT: R 693 MET cc_start: 0.6553 (ptt) cc_final: 0.6295 (ptt) REVERT: R 799 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8203 (tp) REVERT: R 833 PHE cc_start: 0.7112 (m-80) cc_final: 0.6530 (m-80) outliers start: 29 outliers final: 18 residues processed: 197 average time/residue: 0.4860 time to fit residues: 103.0664 Evaluate side-chains 202 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 181 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain R residue 698 MET Chi-restraints excluded: chain R residue 763 LEU Chi-restraints excluded: chain R residue 799 LEU Chi-restraints excluded: chain R residue 811 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 5 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 106 optimal weight: 0.3980 chunk 61 optimal weight: 0.2980 chunk 51 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN R 820 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.179692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.151458 restraints weight = 12453.170| |-----------------------------------------------------------------------------| r_work (start): 0.3966 rms_B_bonded: 2.34 r_work: 0.3846 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8857 Z= 0.165 Angle : 0.601 9.258 11993 Z= 0.308 Chirality : 0.044 0.149 1382 Planarity : 0.004 0.059 1502 Dihedral : 4.786 24.109 1185 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.77 % Allowed : 15.72 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.20 (0.26), residues: 1086 helix: 1.89 (0.27), residues: 360 sheet: -0.67 (0.29), residues: 275 loop : -0.71 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 685 TYR 0.015 0.002 TYR C 178 PHE 0.016 0.002 PHE B 241 TRP 0.020 0.002 TRP B 211 HIS 0.006 0.001 HIS A 345 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 8855) covalent geometry : angle 0.60081 (11989) SS BOND : bond 0.00889 ( 2) SS BOND : angle 1.12773 ( 4) hydrogen bonds : bond 0.03909 ( 443) hydrogen bonds : angle 4.88855 ( 1239) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 175 time to evaluate : 0.334 Fit side-chains REVERT: A 233 LYS cc_start: 0.7710 (mmtt) cc_final: 0.7364 (mmtt) REVERT: A 235 PHE cc_start: 0.7975 (m-10) cc_final: 0.7507 (m-80) REVERT: A 266 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.7189 (pp) REVERT: A 270 MET cc_start: 0.7013 (ttt) cc_final: 0.6627 (tpp) REVERT: A 294 MET cc_start: 0.7004 (ptt) cc_final: 0.6610 (ptt) REVERT: A 343 PHE cc_start: 0.7140 (m-80) cc_final: 0.6860 (m-10) REVERT: B 38 ASP cc_start: 0.8055 (m-30) cc_final: 0.7812 (m-30) REVERT: B 130 GLU cc_start: 0.7757 (mp0) cc_final: 0.7491 (mp0) REVERT: B 325 MET cc_start: 0.7505 (mmt) cc_final: 0.7243 (mtt) REVERT: C 90 ASP cc_start: 0.7250 (m-30) cc_final: 0.6969 (m-30) REVERT: C 174 GLN cc_start: 0.7968 (tt0) cc_final: 0.7727 (pt0) REVERT: C 180 MET cc_start: 0.6147 (OUTLIER) cc_final: 0.5478 (ttp) REVERT: R 582 PHE cc_start: 0.7729 (m-80) cc_final: 0.7274 (m-80) REVERT: R 693 MET cc_start: 0.6588 (ptt) cc_final: 0.6317 (ptt) REVERT: R 799 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8212 (tp) REVERT: R 833 PHE cc_start: 0.7144 (m-80) cc_final: 0.6559 (m-80) outliers start: 36 outliers final: 21 residues processed: 196 average time/residue: 0.4541 time to fit residues: 96.0670 Evaluate side-chains 199 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 175 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain R residue 745 LEU Chi-restraints excluded: chain R residue 763 LEU Chi-restraints excluded: chain R residue 793 LEU Chi-restraints excluded: chain R residue 799 LEU Chi-restraints excluded: chain R residue 811 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 5 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 76 optimal weight: 0.4980 chunk 53 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 83 optimal weight: 0.0770 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN B 266 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.179365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.151002 restraints weight = 12470.285| |-----------------------------------------------------------------------------| r_work (start): 0.3961 rms_B_bonded: 2.35 r_work: 0.3835 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8857 Z= 0.183 Angle : 0.615 10.167 11993 Z= 0.316 Chirality : 0.044 0.148 1382 Planarity : 0.004 0.045 1502 Dihedral : 4.815 25.294 1185 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.67 % Allowed : 16.98 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.19 (0.26), residues: 1086 helix: 1.92 (0.27), residues: 360 sheet: -0.66 (0.30), residues: 275 loop : -0.78 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 685 TYR 0.015 0.002 TYR C 178 PHE 0.017 0.002 PHE B 241 TRP 0.023 0.002 TRP B 211 HIS 0.006 0.001 HIS R 820 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 8855) covalent geometry : angle 0.61514 (11989) SS BOND : bond 0.00981 ( 2) SS BOND : angle 1.16507 ( 4) hydrogen bonds : bond 0.03923 ( 443) hydrogen bonds : angle 4.86898 ( 1239) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 179 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: A 37 VAL cc_start: 0.7277 (OUTLIER) cc_final: 0.7049 (p) REVERT: A 233 LYS cc_start: 0.7721 (mmtt) cc_final: 0.7366 (mmtt) REVERT: A 235 PHE cc_start: 0.7947 (m-10) cc_final: 0.7359 (m-80) REVERT: A 270 MET cc_start: 0.7022 (ttt) cc_final: 0.6595 (tpp) REVERT: A 343 PHE cc_start: 0.7180 (m-80) cc_final: 0.6918 (m-10) REVERT: B 38 ASP cc_start: 0.8088 (m-30) cc_final: 0.7849 (m-30) REVERT: B 130 GLU cc_start: 0.7791 (mp0) cc_final: 0.7528 (mp0) REVERT: B 325 MET cc_start: 0.7496 (mmt) cc_final: 0.7242 (mtt) REVERT: C 45 LEU cc_start: 0.6420 (OUTLIER) cc_final: 0.6175 (pt) REVERT: C 90 ASP cc_start: 0.7345 (m-30) cc_final: 0.7085 (m-30) REVERT: C 174 GLN cc_start: 0.7975 (tt0) cc_final: 0.7746 (pt0) REVERT: C 180 MET cc_start: 0.6187 (OUTLIER) cc_final: 0.5559 (ttp) REVERT: C 221 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7537 (tp) REVERT: R 582 PHE cc_start: 0.7794 (m-80) cc_final: 0.7306 (m-80) REVERT: R 693 MET cc_start: 0.6616 (ptt) cc_final: 0.6327 (ptt) REVERT: R 799 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8223 (tp) REVERT: R 833 PHE cc_start: 0.7148 (m-80) cc_final: 0.6586 (m-80) outliers start: 35 outliers final: 21 residues processed: 197 average time/residue: 0.4543 time to fit residues: 96.4618 Evaluate side-chains 208 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 182 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain R residue 671 LEU Chi-restraints excluded: chain R residue 745 LEU Chi-restraints excluded: chain R residue 763 LEU Chi-restraints excluded: chain R residue 799 LEU Chi-restraints excluded: chain R residue 811 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 71 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 77 optimal weight: 0.4980 chunk 20 optimal weight: 0.1980 chunk 21 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 108 optimal weight: 20.0000 chunk 78 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN B 176 GLN B 230 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.179698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.151442 restraints weight = 12334.257| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 2.33 r_work: 0.3837 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 8857 Z= 0.177 Angle : 0.617 11.321 11993 Z= 0.315 Chirality : 0.044 0.147 1382 Planarity : 0.004 0.040 1502 Dihedral : 4.815 26.910 1185 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.88 % Allowed : 16.98 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.24 (0.26), residues: 1086 helix: 1.95 (0.27), residues: 361 sheet: -0.61 (0.30), residues: 275 loop : -0.77 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 685 TYR 0.015 0.002 TYR C 178 PHE 0.025 0.002 PHE C 200 TRP 0.023 0.002 TRP B 211 HIS 0.004 0.001 HIS A 345 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 8855) covalent geometry : angle 0.61655 (11989) SS BOND : bond 0.00842 ( 2) SS BOND : angle 1.08152 ( 4) hydrogen bonds : bond 0.03867 ( 443) hydrogen bonds : angle 4.86470 ( 1239) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 176 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 233 LYS cc_start: 0.7724 (mmtt) cc_final: 0.7372 (mmtt) REVERT: A 235 PHE cc_start: 0.7942 (m-10) cc_final: 0.7481 (m-80) REVERT: A 270 MET cc_start: 0.7053 (ttt) cc_final: 0.6606 (tpp) REVERT: A 343 PHE cc_start: 0.7233 (m-80) cc_final: 0.6963 (m-10) REVERT: B 38 ASP cc_start: 0.8082 (m-30) cc_final: 0.7842 (m-30) REVERT: B 129 ARG cc_start: 0.8407 (mmm-85) cc_final: 0.7977 (mmm-85) REVERT: B 130 GLU cc_start: 0.7750 (mp0) cc_final: 0.7502 (mp0) REVERT: B 325 MET cc_start: 0.7490 (mmt) cc_final: 0.7269 (mtt) REVERT: C 45 LEU cc_start: 0.6370 (OUTLIER) cc_final: 0.6152 (pt) REVERT: C 90 ASP cc_start: 0.7349 (m-30) cc_final: 0.7081 (m-30) REVERT: C 174 GLN cc_start: 0.7979 (tt0) cc_final: 0.7760 (pt0) REVERT: C 180 MET cc_start: 0.6182 (OUTLIER) cc_final: 0.5482 (ttp) REVERT: C 221 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7528 (tp) REVERT: R 582 PHE cc_start: 0.7793 (m-80) cc_final: 0.7363 (m-80) REVERT: R 693 MET cc_start: 0.6637 (ptt) cc_final: 0.6339 (ptt) REVERT: R 799 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8234 (tp) REVERT: R 833 PHE cc_start: 0.7144 (m-80) cc_final: 0.6583 (m-80) outliers start: 37 outliers final: 20 residues processed: 195 average time/residue: 0.4266 time to fit residues: 90.3187 Evaluate side-chains 199 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 175 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain R residue 763 LEU Chi-restraints excluded: chain R residue 799 LEU Chi-restraints excluded: chain R residue 811 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 60 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 9 optimal weight: 0.0020 chunk 29 optimal weight: 0.4980 chunk 19 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN R 827 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.179969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.151575 restraints weight = 12379.374| |-----------------------------------------------------------------------------| r_work (start): 0.3966 rms_B_bonded: 2.35 r_work: 0.3847 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 8857 Z= 0.172 Angle : 0.629 11.746 11993 Z= 0.320 Chirality : 0.044 0.149 1382 Planarity : 0.004 0.038 1502 Dihedral : 4.843 24.144 1185 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.25 % Allowed : 17.82 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.27 (0.26), residues: 1086 helix: 1.98 (0.27), residues: 361 sheet: -0.53 (0.30), residues: 279 loop : -0.80 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 685 TYR 0.016 0.002 TYR C 178 PHE 0.027 0.002 PHE C 200 TRP 0.023 0.002 TRP B 211 HIS 0.004 0.001 HIS A 345 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 8855) covalent geometry : angle 0.62851 (11989) SS BOND : bond 0.00956 ( 2) SS BOND : angle 1.25061 ( 4) hydrogen bonds : bond 0.03845 ( 443) hydrogen bonds : angle 4.88028 ( 1239) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 176 time to evaluate : 0.283 Fit side-chains revert: symmetry clash REVERT: A 233 LYS cc_start: 0.7723 (mmtt) cc_final: 0.7363 (mmtt) REVERT: A 235 PHE cc_start: 0.7927 (m-10) cc_final: 0.7397 (m-80) REVERT: A 270 MET cc_start: 0.7038 (ttt) cc_final: 0.6573 (tpp) REVERT: A 343 PHE cc_start: 0.7290 (m-80) cc_final: 0.7044 (m-10) REVERT: B 38 ASP cc_start: 0.8102 (m-30) cc_final: 0.7862 (m-30) REVERT: B 129 ARG cc_start: 0.8406 (mmm-85) cc_final: 0.7981 (mmm-85) REVERT: B 130 GLU cc_start: 0.7752 (mp0) cc_final: 0.7494 (mp0) REVERT: B 230 ASN cc_start: 0.8036 (m-40) cc_final: 0.7708 (m-40) REVERT: B 325 MET cc_start: 0.7511 (mmt) cc_final: 0.7298 (mtt) REVERT: C 45 LEU cc_start: 0.6182 (OUTLIER) cc_final: 0.5956 (pt) REVERT: C 90 ASP cc_start: 0.7283 (m-30) cc_final: 0.6999 (m-30) REVERT: C 174 GLN cc_start: 0.7977 (tt0) cc_final: 0.7743 (pt0) REVERT: R 582 PHE cc_start: 0.7781 (m-80) cc_final: 0.7348 (m-80) REVERT: R 693 MET cc_start: 0.6699 (ptt) cc_final: 0.6400 (ptt) REVERT: R 799 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8236 (tp) REVERT: R 833 PHE cc_start: 0.7156 (m-80) cc_final: 0.6587 (m-80) outliers start: 31 outliers final: 21 residues processed: 193 average time/residue: 0.4682 time to fit residues: 97.5573 Evaluate side-chains 197 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 174 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain R residue 671 LEU Chi-restraints excluded: chain R residue 763 LEU Chi-restraints excluded: chain R residue 799 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 56 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 81 optimal weight: 0.9980 chunk 46 optimal weight: 0.0470 chunk 7 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 chunk 80 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 108 optimal weight: 9.9990 chunk 71 optimal weight: 0.6980 chunk 70 optimal weight: 0.0980 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.181078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.152854 restraints weight = 12501.014| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 2.36 r_work: 0.3864 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8857 Z= 0.143 Angle : 0.619 12.331 11993 Z= 0.314 Chirality : 0.043 0.156 1382 Planarity : 0.004 0.039 1502 Dihedral : 4.746 23.752 1185 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.73 % Allowed : 18.03 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.35 (0.26), residues: 1086 helix: 2.12 (0.27), residues: 362 sheet: -0.60 (0.29), residues: 290 loop : -0.73 (0.32), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 685 TYR 0.015 0.002 TYR C 178 PHE 0.024 0.002 PHE C 200 TRP 0.022 0.002 TRP B 211 HIS 0.003 0.001 HIS A 345 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 8855) covalent geometry : angle 0.61898 (11989) SS BOND : bond 0.00891 ( 2) SS BOND : angle 1.10027 ( 4) hydrogen bonds : bond 0.03679 ( 443) hydrogen bonds : angle 4.81382 ( 1239) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 182 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: A 233 LYS cc_start: 0.7733 (mmtt) cc_final: 0.7351 (mmtt) REVERT: A 235 PHE cc_start: 0.7941 (m-10) cc_final: 0.7409 (m-80) REVERT: A 304 VAL cc_start: 0.5217 (p) cc_final: 0.5014 (t) REVERT: A 343 PHE cc_start: 0.7285 (m-80) cc_final: 0.7061 (m-10) REVERT: B 38 ASP cc_start: 0.8030 (m-30) cc_final: 0.7795 (m-30) REVERT: B 129 ARG cc_start: 0.8394 (mmm-85) cc_final: 0.7993 (mmm-85) REVERT: B 130 GLU cc_start: 0.7702 (mp0) cc_final: 0.7477 (mp0) REVERT: B 289 TYR cc_start: 0.8180 (m-80) cc_final: 0.7576 (m-80) REVERT: B 325 MET cc_start: 0.7558 (mmt) cc_final: 0.7292 (mtt) REVERT: C 45 LEU cc_start: 0.6212 (OUTLIER) cc_final: 0.6006 (pt) REVERT: C 90 ASP cc_start: 0.7177 (m-30) cc_final: 0.6960 (m-30) REVERT: C 174 GLN cc_start: 0.7939 (tt0) cc_final: 0.7723 (pt0) REVERT: R 582 PHE cc_start: 0.7754 (m-80) cc_final: 0.7302 (m-80) REVERT: R 693 MET cc_start: 0.6706 (ptt) cc_final: 0.6413 (ptt) REVERT: R 799 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8237 (tp) REVERT: R 833 PHE cc_start: 0.7129 (m-80) cc_final: 0.6541 (m-80) outliers start: 26 outliers final: 18 residues processed: 197 average time/residue: 0.4378 time to fit residues: 93.1623 Evaluate side-chains 197 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 177 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain R residue 763 LEU Chi-restraints excluded: chain R residue 799 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 29 optimal weight: 0.2980 chunk 69 optimal weight: 0.3980 chunk 70 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 6 optimal weight: 0.0970 chunk 76 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.180633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.153026 restraints weight = 12456.731| |-----------------------------------------------------------------------------| r_work (start): 0.3984 rms_B_bonded: 2.32 r_work: 0.3859 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 8857 Z= 0.148 Angle : 0.622 12.075 11993 Z= 0.317 Chirality : 0.044 0.166 1382 Planarity : 0.004 0.038 1502 Dihedral : 4.716 25.053 1185 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.20 % Allowed : 18.97 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.45 (0.26), residues: 1086 helix: 2.21 (0.27), residues: 362 sheet: -0.59 (0.29), residues: 292 loop : -0.65 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 46 TYR 0.015 0.002 TYR C 178 PHE 0.024 0.002 PHE C 200 TRP 0.023 0.002 TRP B 211 HIS 0.003 0.001 HIS A 345 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 8855) covalent geometry : angle 0.62178 (11989) SS BOND : bond 0.00801 ( 2) SS BOND : angle 0.90261 ( 4) hydrogen bonds : bond 0.03718 ( 443) hydrogen bonds : angle 4.81185 ( 1239) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3127.12 seconds wall clock time: 53 minutes 58.60 seconds (3238.60 seconds total)