Starting phenix.real_space_refine on Sat Jul 26 15:26:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wz7_32905/07_2025/7wz7_32905_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wz7_32905/07_2025/7wz7_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_32905/07_2025/7wz7_32905.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wz7_32905/07_2025/7wz7_32905.map" model { file = "/net/cci-nas-00/data/ceres_data/7wz7_32905/07_2025/7wz7_32905_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wz7_32905/07_2025/7wz7_32905_neut.cif" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 5.26, per 1000 atoms: 0.61 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: 2.39 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.34 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: 2.77 Time building geometry restraints manager: 2.80 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.380 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.060 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.020 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (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 TRP 0.026 0.003 TRP B 99 HIS 0.018 0.002 HIS B 62 PHE 0.034 0.004 PHE B 151 TYR 0.032 0.004 TYR B 105 ARG 0.009 0.001 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.14813 ( 443) hydrogen bonds : angle 7.12348 ( 1239) SS BOND : bond 0.01440 ( 2) SS BOND : angle 1.33226 ( 4) covalent geometry : bond 0.00998 ( 8855) covalent geometry : angle 0.95389 (11989) *********************** 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 : 0.949 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: 0.9569 time to fit residues: 219.1785 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 : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.0980 chunk 82 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 85 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 63 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.4297 r_free = 0.4297 target = 0.179871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.151673 restraints weight = 12407.551| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 2.39 r_work: 0.3841 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.1590 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= 0.169 Angle : 0.649 9.190 11993 Z= 0.334 Chirality : 0.045 0.190 1382 Planarity : 0.004 0.043 1502 Dihedral : 5.198 23.263 1185 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.20 % Allowed : 10.90 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.26), residues: 1086 helix: 1.44 (0.28), residues: 356 sheet: -0.70 (0.28), residues: 291 loop : -0.85 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 211 HIS 0.006 0.001 HIS A 345 PHE 0.021 0.002 PHE A 357 TYR 0.016 0.002 TYR C 178 ARG 0.007 0.000 ARG R 685 Details of bonding type rmsd hydrogen bonds : bond 0.04697 ( 443) hydrogen bonds : angle 5.35116 ( 1239) SS BOND : bond 0.00881 ( 2) SS BOND : angle 0.92564 ( 4) covalent geometry : bond 0.00381 ( 8855) covalent geometry : angle 0.64897 (11989) *********************** 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 : 0.907 Fit side-chains REVERT: A 233 LYS cc_start: 0.7675 (mmtt) cc_final: 0.7369 (mmtt) REVERT: A 235 PHE cc_start: 0.7957 (m-80) cc_final: 0.7372 (m-80) REVERT: A 343 PHE cc_start: 0.7132 (m-10) cc_final: 0.6901 (m-80) REVERT: B 130 GLU cc_start: 0.7859 (mp0) cc_final: 0.7564 (mp0) REVERT: B 230 ASN cc_start: 0.8039 (m-40) cc_final: 0.7817 (m110) REVERT: B 325 MET cc_start: 0.7589 (mmt) cc_final: 0.7197 (mtt) REVERT: C 90 ASP cc_start: 0.7237 (m-30) cc_final: 0.6919 (m-30) REVERT: C 180 MET cc_start: 0.6255 (ttm) cc_final: 0.6026 (tpp) REVERT: R 582 PHE cc_start: 0.7611 (m-80) cc_final: 0.7275 (m-80) REVERT: R 827 ASN cc_start: 0.7128 (m-40) cc_final: 0.6610 (m-40) REVERT: R 833 PHE cc_start: 0.7259 (m-10) cc_final: 0.7000 (m-80) outliers start: 21 outliers final: 8 residues processed: 201 average time/residue: 0.9948 time to fit residues: 216.0896 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 : 0.871 ------------------------------------------------------------------------------- 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 104 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 92 optimal weight: 0.2980 chunk 49 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN B 88 ASN B 176 GLN E 18 GLN R 820 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.177939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.149756 restraints weight = 12587.190| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 2.38 r_work: 0.3826 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8857 Z= 0.213 Angle : 0.646 8.334 11993 Z= 0.332 Chirality : 0.045 0.168 1382 Planarity : 0.004 0.042 1502 Dihedral : 5.114 25.753 1185 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.14 % Allowed : 13.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.26), residues: 1086 helix: 1.61 (0.28), residues: 356 sheet: -0.83 (0.28), residues: 290 loop : -0.81 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 211 HIS 0.007 0.001 HIS A 345 PHE 0.028 0.002 PHE A 357 TYR 0.018 0.002 TYR C 178 ARG 0.010 0.001 ARG R 685 Details of bonding type rmsd hydrogen bonds : bond 0.04528 ( 443) hydrogen bonds : angle 5.19246 ( 1239) SS BOND : bond 0.01022 ( 2) SS BOND : angle 1.29532 ( 4) covalent geometry : bond 0.00485 ( 8855) covalent geometry : angle 0.64547 (11989) *********************** 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 215 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 185 time to evaluate : 1.012 Fit side-chains REVERT: A 233 LYS cc_start: 0.7707 (mmtt) cc_final: 0.7410 (mmtt) REVERT: A 235 PHE cc_start: 0.7894 (m-10) cc_final: 0.7318 (m-80) REVERT: A 285 VAL cc_start: 0.7265 (t) cc_final: 0.7042 (m) REVERT: A 294 MET cc_start: 0.6816 (ptt) cc_final: 0.6589 (ptt) REVERT: A 343 PHE cc_start: 0.7175 (m-10) cc_final: 0.6936 (m-80) REVERT: B 38 ASP cc_start: 0.8172 (m-30) cc_final: 0.7916 (m-30) REVERT: B 129 ARG cc_start: 0.8439 (mmm-85) cc_final: 0.7931 (mmm-85) REVERT: B 130 GLU cc_start: 0.7916 (mp0) cc_final: 0.7618 (mp0) REVERT: B 325 MET cc_start: 0.7564 (mmt) cc_final: 0.7211 (mtt) REVERT: C 65 LYS cc_start: 0.7982 (tppt) cc_final: 0.7768 (tttm) REVERT: C 90 ASP cc_start: 0.7324 (m-30) cc_final: 0.7073 (m-30) REVERT: R 582 PHE cc_start: 0.7666 (m-80) cc_final: 0.7347 (m-80) REVERT: R 693 MET cc_start: 0.6528 (ptt) cc_final: 0.6283 (ptt) outliers start: 30 outliers final: 17 residues processed: 196 average time/residue: 0.9999 time to fit residues: 211.3427 Evaluate side-chains 201 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 184 time to evaluate : 0.866 ------------------------------------------------------------------------------- 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 61 MET Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 218 CYS 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 763 LEU Chi-restraints excluded: chain R residue 822 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 5 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 26 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 105 optimal weight: 0.0020 chunk 101 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 33 optimal weight: 0.3980 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN B 230 ASN 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 = 0.179633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.151608 restraints weight = 12394.946| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 2.34 r_work: 0.3850 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8857 Z= 0.158 Angle : 0.603 8.908 11993 Z= 0.309 Chirality : 0.043 0.160 1382 Planarity : 0.004 0.053 1502 Dihedral : 4.907 25.661 1185 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.73 % Allowed : 14.88 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.26), residues: 1086 helix: 1.72 (0.27), residues: 360 sheet: -0.90 (0.28), residues: 295 loop : -0.61 (0.32), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 211 HIS 0.008 0.001 HIS A 345 PHE 0.028 0.002 PHE A 357 TYR 0.015 0.002 TYR C 178 ARG 0.007 0.000 ARG R 685 Details of bonding type rmsd hydrogen bonds : bond 0.04045 ( 443) hydrogen bonds : angle 4.99201 ( 1239) SS BOND : bond 0.00976 ( 2) SS BOND : angle 1.15967 ( 4) covalent geometry : bond 0.00365 ( 8855) covalent geometry : angle 0.60322 (11989) *********************** 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 210 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 184 time to evaluate : 0.865 Fit side-chains REVERT: A 233 LYS cc_start: 0.7723 (mmtt) cc_final: 0.7355 (mmtt) REVERT: A 235 PHE cc_start: 0.7882 (m-10) cc_final: 0.7416 (m-80) REVERT: A 266 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7355 (pp) REVERT: A 270 MET cc_start: 0.6909 (ttt) cc_final: 0.6486 (tpp) REVERT: A 285 VAL cc_start: 0.7194 (t) cc_final: 0.6974 (m) REVERT: A 294 MET cc_start: 0.6895 (ptt) cc_final: 0.6579 (ptt) REVERT: A 343 PHE cc_start: 0.7089 (m-10) cc_final: 0.6884 (m-80) REVERT: B 38 ASP cc_start: 0.8077 (m-30) cc_final: 0.7827 (m-30) REVERT: B 129 ARG cc_start: 0.8392 (mmm-85) cc_final: 0.7913 (mmm-85) REVERT: B 130 GLU cc_start: 0.7789 (mp0) cc_final: 0.7509 (mp0) REVERT: B 230 ASN cc_start: 0.8062 (m-40) cc_final: 0.7775 (m110) REVERT: B 262 MET cc_start: 0.6637 (ttm) cc_final: 0.6406 (ttm) REVERT: B 325 MET cc_start: 0.7551 (mmt) cc_final: 0.7249 (mtt) REVERT: C 90 ASP cc_start: 0.7140 (m-30) cc_final: 0.6846 (m-30) REVERT: R 582 PHE cc_start: 0.7738 (m-80) cc_final: 0.7377 (m-80) REVERT: R 693 MET cc_start: 0.6595 (ptt) cc_final: 0.6286 (ptt) REVERT: R 833 PHE cc_start: 0.7124 (m-80) cc_final: 0.6544 (m-80) outliers start: 26 outliers final: 17 residues processed: 192 average time/residue: 1.0371 time to fit residues: 214.2885 Evaluate side-chains 198 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 180 time to evaluate : 0.973 ------------------------------------------------------------------------------- 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 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 218 CYS Chi-restraints excluded: chain B residue 275 SER 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 811 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 81 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 108 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 chunk 98 optimal weight: 0.2980 chunk 42 optimal weight: 0.6980 chunk 11 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: 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 = 0.4287 r_free = 0.4287 target = 0.179079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.151175 restraints weight = 12393.741| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 2.33 r_work: 0.3841 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8857 Z= 0.177 Angle : 0.613 9.565 11993 Z= 0.313 Chirality : 0.044 0.154 1382 Planarity : 0.004 0.047 1502 Dihedral : 4.877 25.516 1185 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.94 % Allowed : 15.72 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.26), residues: 1086 helix: 1.80 (0.27), residues: 360 sheet: -0.86 (0.28), residues: 289 loop : -0.61 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 211 HIS 0.007 0.001 HIS A 345 PHE 0.015 0.002 PHE A 357 TYR 0.016 0.002 TYR C 178 ARG 0.007 0.000 ARG R 685 Details of bonding type rmsd hydrogen bonds : bond 0.04048 ( 443) hydrogen bonds : angle 4.93423 ( 1239) SS BOND : bond 0.00960 ( 2) SS BOND : angle 1.11326 ( 4) covalent geometry : bond 0.00410 ( 8855) covalent geometry : angle 0.61240 (11989) *********************** 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 216 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 188 time to evaluate : 0.855 Fit side-chains REVERT: A 233 LYS cc_start: 0.7732 (mmtt) cc_final: 0.7358 (mmtt) REVERT: A 235 PHE cc_start: 0.7918 (m-10) cc_final: 0.7342 (m-80) REVERT: A 266 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7353 (pp) REVERT: A 270 MET cc_start: 0.7049 (ttt) cc_final: 0.6606 (tpp) REVERT: A 285 VAL cc_start: 0.7262 (t) cc_final: 0.7050 (m) REVERT: A 294 MET cc_start: 0.6937 (ptt) cc_final: 0.6582 (ptt) REVERT: B 38 ASP cc_start: 0.8131 (m-30) cc_final: 0.7887 (m-30) REVERT: B 130 GLU cc_start: 0.7819 (mp0) cc_final: 0.7526 (mp0) REVERT: B 325 MET cc_start: 0.7549 (mmt) cc_final: 0.7174 (mtt) REVERT: C 90 ASP cc_start: 0.7264 (m-30) cc_final: 0.6993 (m-30) REVERT: C 174 GLN cc_start: 0.7967 (tt0) cc_final: 0.7707 (pt0) REVERT: C 180 MET cc_start: 0.6153 (OUTLIER) cc_final: 0.5561 (ttp) REVERT: C 221 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7538 (tm) REVERT: R 582 PHE cc_start: 0.7752 (m-80) cc_final: 0.7344 (m-80) REVERT: R 693 MET cc_start: 0.6546 (ptt) cc_final: 0.6235 (ptt) REVERT: R 799 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8200 (tp) REVERT: R 833 PHE cc_start: 0.7105 (m-80) cc_final: 0.6533 (m-80) outliers start: 28 outliers final: 16 residues processed: 198 average time/residue: 1.0238 time to fit residues: 218.1551 Evaluate side-chains 202 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 182 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 266 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 180 MET 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 77 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 52 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 106 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 R 820 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.178820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.150466 restraints weight = 12376.598| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 2.35 r_work: 0.3834 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8857 Z= 0.198 Angle : 0.619 9.289 11993 Z= 0.317 Chirality : 0.044 0.151 1382 Planarity : 0.004 0.050 1502 Dihedral : 4.862 24.758 1185 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 4.09 % Allowed : 16.14 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.26), residues: 1086 helix: 1.81 (0.27), residues: 360 sheet: -0.71 (0.29), residues: 276 loop : -0.75 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 211 HIS 0.007 0.001 HIS A 345 PHE 0.017 0.002 PHE B 241 TYR 0.017 0.002 TYR B 85 ARG 0.009 0.001 ARG R 685 Details of bonding type rmsd hydrogen bonds : bond 0.04045 ( 443) hydrogen bonds : angle 4.94118 ( 1239) SS BOND : bond 0.00835 ( 2) SS BOND : angle 1.11470 ( 4) covalent geometry : bond 0.00461 ( 8855) covalent geometry : angle 0.61860 (11989) *********************** 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 218 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 179 time to evaluate : 0.961 Fit side-chains REVERT: A 233 LYS cc_start: 0.7729 (mmtt) cc_final: 0.7364 (mmtt) REVERT: A 235 PHE cc_start: 0.7935 (m-10) cc_final: 0.7335 (m-80) REVERT: A 266 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7420 (pp) REVERT: A 270 MET cc_start: 0.7114 (ttt) cc_final: 0.6636 (tpp) REVERT: A 285 VAL cc_start: 0.7259 (t) cc_final: 0.7051 (m) REVERT: A 294 MET cc_start: 0.6997 (ptt) cc_final: 0.6613 (ptt) REVERT: A 343 PHE cc_start: 0.7184 (m-80) cc_final: 0.6890 (m-10) REVERT: B 38 ASP cc_start: 0.8102 (m-30) cc_final: 0.7858 (m-30) REVERT: B 130 GLU cc_start: 0.7806 (mp0) cc_final: 0.7522 (mp0) REVERT: B 325 MET cc_start: 0.7549 (mmt) cc_final: 0.7199 (mtt) REVERT: C 90 ASP cc_start: 0.7324 (m-30) cc_final: 0.7099 (m-30) REVERT: C 174 GLN cc_start: 0.7968 (OUTLIER) cc_final: 0.7712 (pt0) REVERT: C 180 MET cc_start: 0.6193 (OUTLIER) cc_final: 0.5632 (ttp) REVERT: R 582 PHE cc_start: 0.7763 (m-80) cc_final: 0.7315 (m-80) REVERT: R 693 MET cc_start: 0.6584 (ptt) cc_final: 0.6228 (ptt) REVERT: R 799 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8212 (tp) REVERT: R 833 PHE cc_start: 0.7216 (m-80) cc_final: 0.6634 (m-80) outliers start: 39 outliers final: 18 residues processed: 200 average time/residue: 0.9692 time to fit residues: 209.6630 Evaluate side-chains 203 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 181 time to evaluate : 0.894 ------------------------------------------------------------------------------- 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 266 LEU 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 218 CYS 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 174 GLN 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 698 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 73 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 14 optimal weight: 7.9990 chunk 67 optimal weight: 0.0970 chunk 12 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 106 optimal weight: 0.7980 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 = 0.4291 r_free = 0.4291 target = 0.179544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.151338 restraints weight = 12402.255| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 2.34 r_work: 0.3843 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.2604 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= 0.173 Angle : 0.617 9.846 11993 Z= 0.314 Chirality : 0.044 0.156 1382 Planarity : 0.004 0.042 1502 Dihedral : 4.820 25.169 1185 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 4.30 % Allowed : 16.04 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.26), residues: 1086 helix: 1.91 (0.27), residues: 360 sheet: -0.66 (0.29), residues: 276 loop : -0.77 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 211 HIS 0.005 0.001 HIS A 345 PHE 0.016 0.002 PHE B 241 TYR 0.015 0.002 TYR C 178 ARG 0.006 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.03923 ( 443) hydrogen bonds : angle 4.87075 ( 1239) SS BOND : bond 0.00865 ( 2) SS BOND : angle 1.16074 ( 4) covalent geometry : bond 0.00406 ( 8855) covalent geometry : angle 0.61632 (11989) *********************** 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 223 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 182 time to evaluate : 0.926 Fit side-chains revert: symmetry clash REVERT: A 233 LYS cc_start: 0.7713 (mmtt) cc_final: 0.7363 (mmtt) REVERT: A 235 PHE cc_start: 0.7912 (m-10) cc_final: 0.7324 (m-80) REVERT: A 266 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7199 (pp) REVERT: A 270 MET cc_start: 0.7110 (ttt) cc_final: 0.6615 (tpp) REVERT: A 343 PHE cc_start: 0.7184 (m-80) cc_final: 0.6956 (m-10) REVERT: B 38 ASP cc_start: 0.8075 (m-30) cc_final: 0.7831 (m-30) REVERT: B 130 GLU cc_start: 0.7742 (mp0) cc_final: 0.7474 (mp0) REVERT: B 325 MET cc_start: 0.7628 (mmt) cc_final: 0.7399 (mtt) REVERT: C 45 LEU cc_start: 0.6433 (OUTLIER) cc_final: 0.6182 (pt) REVERT: C 90 ASP cc_start: 0.7200 (m-30) cc_final: 0.6936 (m-30) REVERT: C 174 GLN cc_start: 0.7949 (tt0) cc_final: 0.7715 (pt0) REVERT: C 180 MET cc_start: 0.6189 (OUTLIER) cc_final: 0.5615 (ttp) REVERT: C 221 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7554 (tm) REVERT: R 582 PHE cc_start: 0.7761 (m-80) cc_final: 0.7293 (m-80) REVERT: R 693 MET cc_start: 0.6516 (ptt) cc_final: 0.6236 (ptt) REVERT: R 799 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8221 (tp) outliers start: 41 outliers final: 18 residues processed: 202 average time/residue: 0.9788 time to fit residues: 214.2350 Evaluate side-chains 205 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 182 time to evaluate : 0.894 ------------------------------------------------------------------------------- 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 266 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 218 CYS 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 183 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 23 optimal weight: 1.9990 chunk 35 optimal weight: 0.0970 chunk 66 optimal weight: 0.3980 chunk 18 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 86 optimal weight: 0.4980 chunk 73 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN B 230 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.180641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.152205 restraints weight = 12571.467| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 2.39 r_work: 0.3851 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8857 Z= 0.152 Angle : 0.605 11.196 11993 Z= 0.309 Chirality : 0.043 0.155 1382 Planarity : 0.004 0.038 1502 Dihedral : 4.760 26.474 1185 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.46 % Allowed : 17.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.26), residues: 1086 helix: 2.08 (0.27), residues: 357 sheet: -0.70 (0.29), residues: 286 loop : -0.71 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 211 HIS 0.004 0.001 HIS R 665 PHE 0.016 0.002 PHE B 241 TYR 0.015 0.002 TYR C 178 ARG 0.010 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.03768 ( 443) hydrogen bonds : angle 4.78930 ( 1239) SS BOND : bond 0.00874 ( 2) SS BOND : angle 1.06557 ( 4) covalent geometry : bond 0.00356 ( 8855) covalent geometry : angle 0.60519 (11989) *********************** 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 209 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 176 time to evaluate : 0.859 Fit side-chains revert: symmetry clash REVERT: A 233 LYS cc_start: 0.7705 (mmtt) cc_final: 0.7348 (mmtt) REVERT: A 235 PHE cc_start: 0.7909 (m-10) cc_final: 0.7328 (m-80) REVERT: A 270 MET cc_start: 0.7071 (ttt) cc_final: 0.6586 (tpp) REVERT: A 343 PHE cc_start: 0.7239 (m-80) cc_final: 0.7013 (m-10) REVERT: B 38 ASP cc_start: 0.8095 (m-30) cc_final: 0.7850 (m-30) REVERT: B 129 ARG cc_start: 0.8360 (mmm-85) cc_final: 0.7940 (mmm-85) REVERT: B 130 GLU cc_start: 0.7728 (mp0) cc_final: 0.7473 (mp0) REVERT: B 325 MET cc_start: 0.7554 (mmt) cc_final: 0.7294 (mtt) REVERT: C 45 LEU cc_start: 0.6431 (OUTLIER) cc_final: 0.6210 (pt) REVERT: C 90 ASP cc_start: 0.7240 (m-30) cc_final: 0.6947 (m-30) REVERT: C 174 GLN cc_start: 0.7929 (tt0) cc_final: 0.7718 (pt0) REVERT: C 180 MET cc_start: 0.6177 (OUTLIER) cc_final: 0.5591 (ttp) REVERT: R 582 PHE cc_start: 0.7778 (m-80) cc_final: 0.7347 (m-80) REVERT: R 693 MET cc_start: 0.6529 (ptt) cc_final: 0.6311 (ptt) REVERT: R 799 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8242 (tp) outliers start: 33 outliers final: 19 residues processed: 192 average time/residue: 0.9958 time to fit residues: 206.4186 Evaluate side-chains 196 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 174 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 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 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 218 CYS 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 96 CYS 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 C residue 234 GLU Chi-restraints excluded: chain R residue 763 LEU Chi-restraints excluded: chain R residue 799 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 101 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 52 optimal weight: 0.0370 chunk 56 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 overall best weight: 0.6258 ------------------------------------------------------------------------------- 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 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 = 0.179413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.151316 restraints weight = 12418.636| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 2.34 r_work: 0.3839 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 8857 Z= 0.177 Angle : 0.635 11.618 11993 Z= 0.324 Chirality : 0.044 0.158 1382 Planarity : 0.004 0.042 1502 Dihedral : 4.847 24.795 1185 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.25 % Allowed : 18.13 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.26), residues: 1086 helix: 2.09 (0.27), residues: 358 sheet: -0.70 (0.29), residues: 278 loop : -0.74 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 211 HIS 0.004 0.001 HIS A 345 PHE 0.028 0.002 PHE C 200 TYR 0.016 0.002 TYR C 163 ARG 0.009 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.03907 ( 443) hydrogen bonds : angle 4.82657 ( 1239) SS BOND : bond 0.00930 ( 2) SS BOND : angle 1.17500 ( 4) covalent geometry : bond 0.00417 ( 8855) covalent geometry : angle 0.63438 (11989) *********************** 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 210 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 179 time to evaluate : 0.869 Fit side-chains revert: symmetry clash REVERT: A 233 LYS cc_start: 0.7726 (mmtt) cc_final: 0.7361 (mmtt) REVERT: A 235 PHE cc_start: 0.7888 (m-10) cc_final: 0.7229 (m-80) REVERT: A 270 MET cc_start: 0.7126 (ttt) cc_final: 0.6628 (tpp) REVERT: A 343 PHE cc_start: 0.7297 (m-80) cc_final: 0.7064 (m-10) REVERT: B 38 ASP cc_start: 0.8087 (m-30) cc_final: 0.7843 (m-30) REVERT: B 129 ARG cc_start: 0.8376 (mmm-85) cc_final: 0.7953 (mmm-85) REVERT: B 130 GLU cc_start: 0.7745 (mp0) cc_final: 0.7491 (mp0) REVERT: B 195 ASP cc_start: 0.7488 (p0) cc_final: 0.7132 (p0) REVERT: B 197 ARG cc_start: 0.7499 (mtm180) cc_final: 0.7211 (mtm180) REVERT: B 230 ASN cc_start: 0.8052 (m-40) cc_final: 0.7726 (m-40) REVERT: B 325 MET cc_start: 0.7497 (mmt) cc_final: 0.7219 (mtt) REVERT: C 45 LEU cc_start: 0.6208 (OUTLIER) cc_final: 0.5979 (pt) REVERT: C 90 ASP cc_start: 0.7323 (m-30) cc_final: 0.7075 (m-30) REVERT: C 174 GLN cc_start: 0.7948 (tt0) cc_final: 0.7708 (pt0) REVERT: C 180 MET cc_start: 0.6199 (OUTLIER) cc_final: 0.5567 (ttp) REVERT: R 582 PHE cc_start: 0.7800 (m-80) cc_final: 0.7361 (m-80) REVERT: R 693 MET cc_start: 0.6574 (ptt) cc_final: 0.6342 (ptt) REVERT: R 799 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8246 (tp) outliers start: 31 outliers final: 21 residues processed: 196 average time/residue: 0.9634 time to fit residues: 203.9753 Evaluate side-chains 200 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 176 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 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 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 187 VAL Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 262 MET 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 96 CYS 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 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 85 optimal weight: 5.9990 chunk 21 optimal weight: 0.4980 chunk 3 optimal weight: 0.2980 chunk 77 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 chunk 14 optimal weight: 0.0070 chunk 70 optimal weight: 0.0970 chunk 86 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 overall best weight: 0.3596 ------------------------------------------------------------------------------- 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 = 0.4312 r_free = 0.4312 target = 0.181324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.153332 restraints weight = 12419.213| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 2.36 r_work: 0.3865 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8857 Z= 0.137 Angle : 0.616 11.374 11993 Z= 0.313 Chirality : 0.043 0.169 1382 Planarity : 0.004 0.040 1502 Dihedral : 4.733 23.530 1185 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.73 % Allowed : 18.66 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.26), residues: 1086 helix: 2.21 (0.27), residues: 359 sheet: -0.63 (0.29), residues: 283 loop : -0.70 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 211 HIS 0.003 0.001 HIS R 665 PHE 0.028 0.002 PHE C 200 TYR 0.014 0.002 TYR B 124 ARG 0.009 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.03719 ( 443) hydrogen bonds : angle 4.77031 ( 1239) SS BOND : bond 0.00826 ( 2) SS BOND : angle 0.96160 ( 4) covalent geometry : bond 0.00322 ( 8855) covalent geometry : angle 0.61595 (11989) ********************** 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 211 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 185 time to evaluate : 0.866 Fit side-chains revert: symmetry clash REVERT: A 233 LYS cc_start: 0.7718 (mmtt) cc_final: 0.7359 (mmtt) REVERT: A 235 PHE cc_start: 0.7891 (m-10) cc_final: 0.7315 (m-80) REVERT: A 270 MET cc_start: 0.7108 (ttt) cc_final: 0.6597 (tpp) REVERT: A 343 PHE cc_start: 0.7272 (m-80) cc_final: 0.7044 (m-10) REVERT: B 38 ASP cc_start: 0.8012 (m-30) cc_final: 0.7772 (m-30) REVERT: B 129 ARG cc_start: 0.8345 (mmm-85) cc_final: 0.7955 (mmm-85) REVERT: B 130 GLU cc_start: 0.7641 (mp0) cc_final: 0.7407 (mp0) REVERT: B 289 TYR cc_start: 0.8192 (m-80) cc_final: 0.7584 (m-80) REVERT: C 90 ASP cc_start: 0.7166 (m-30) cc_final: 0.6951 (m-30) REVERT: C 174 GLN cc_start: 0.7898 (tt0) cc_final: 0.7686 (pt0) REVERT: C 180 MET cc_start: 0.6097 (OUTLIER) cc_final: 0.5430 (ttp) REVERT: C 221 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7390 (tp) REVERT: R 582 PHE cc_start: 0.7743 (m-80) cc_final: 0.7318 (m-80) REVERT: R 693 MET cc_start: 0.6485 (ptt) cc_final: 0.6265 (ptt) REVERT: R 799 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8255 (tp) outliers start: 26 outliers final: 17 residues processed: 198 average time/residue: 0.9461 time to fit residues: 202.6141 Evaluate side-chains 200 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 180 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 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 B residue 43 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 262 MET 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 C residue 221 LEU Chi-restraints excluded: chain C residue 234 GLU 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 78 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 = 0.4287 r_free = 0.4287 target = 0.179003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.150884 restraints weight = 12483.371| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 2.37 r_work: 0.3834 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 8857 Z= 0.210 Angle : 0.669 11.051 11993 Z= 0.339 Chirality : 0.046 0.188 1382 Planarity : 0.004 0.043 1502 Dihedral : 4.896 25.685 1185 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.41 % Allowed : 19.92 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.26), residues: 1086 helix: 2.09 (0.27), residues: 360 sheet: -0.65 (0.29), residues: 290 loop : -0.70 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 211 HIS 0.005 0.001 HIS A 345 PHE 0.033 0.002 PHE C 200 TYR 0.021 0.002 TYR C 216 ARG 0.009 0.001 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.04064 ( 443) hydrogen bonds : angle 4.86125 ( 1239) SS BOND : bond 0.00756 ( 2) SS BOND : angle 0.97065 ( 4) covalent geometry : bond 0.00500 ( 8855) covalent geometry : angle 0.66901 (11989) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6723.47 seconds wall clock time: 115 minutes 17.54 seconds (6917.54 seconds total)