Starting phenix.real_space_refine on Wed Feb 4 04:25:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lxr_63489/02_2026/9lxr_63489_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lxr_63489/02_2026/9lxr_63489.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lxr_63489/02_2026/9lxr_63489_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lxr_63489/02_2026/9lxr_63489_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lxr_63489/02_2026/9lxr_63489.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lxr_63489/02_2026/9lxr_63489.map" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.038 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 41 5.16 5 C 5509 2.51 5 N 1434 2.21 5 O 1584 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8572 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 2729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2729 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 25, 'TRANS': 320} Chain breaks: 2 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1547 Classifications: {'peptide': 205} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 195} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1560 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 11, 'TRANS': 195} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "L" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 278 Classifications: {'peptide': 33} Link IDs: {'TRANS': 32} Chain: "R" Number of atoms: 2458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2458 Classifications: {'peptide': 301} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 295} Chain breaks: 5 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 15 Time building chain proxies: 1.93, per 1000 atoms: 0.23 Number of scatterers: 8572 At special positions: 0 Unit cell: (86.87, 103.66, 180.31, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 41 16.00 P 4 15.00 O 1584 8.00 N 1434 7.00 C 5509 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 279 " - pdb=" SG CYS C 59 " distance=2.03 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 195 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.71 Conformation dependent library (CDL) restraints added in 313.3 milliseconds 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2064 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 16 sheets defined 31.0% alpha, 33.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'B' and resid 13 through 17 removed outlier: 3.733A pdb=" N GLY B 16 " --> pdb=" O SER B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 49 Processing helix chain 'B' and resid 68 through 72 Processing helix chain 'B' and resid 98 through 109 Processing helix chain 'B' and resid 278 through 282 removed outlier: 4.000A pdb=" N ARG B 282 " --> pdb=" O CYS B 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 94 Processing helix chain 'C' and resid 195 through 199 removed outlier: 3.779A pdb=" N LEU C 199 " --> pdb=" O SER C 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 84 removed outlier: 3.890A pdb=" N PHE E 84 " --> pdb=" O PRO E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 128 Processing helix chain 'E' and resid 184 through 190 Processing helix chain 'L' and resid 2 through 33 Processing helix chain 'R' and resid 33 through 44 removed outlier: 3.790A pdb=" N ALA R 44 " --> pdb=" O LEU R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 173 through 178 removed outlier: 3.506A pdb=" N GLU R 177 " --> pdb=" O PHE R 173 " (cutoff:3.500A) Processing helix chain 'R' and resid 179 through 212 Processing helix chain 'R' and resid 213 through 216 Processing helix chain 'R' and resid 217 through 246 Processing helix chain 'R' and resid 276 through 312 removed outlier: 3.892A pdb=" N CYS R 281 " --> pdb=" O GLY R 277 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA R 284 " --> pdb=" O GLY R 280 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY R 303 " --> pdb=" O ILE R 299 " (cutoff:3.500A) Processing helix chain 'R' and resid 317 through 347 removed outlier: 4.346A pdb=" N LEU R 331 " --> pdb=" O PHE R 327 " (cutoff:3.500A) Proline residue: R 332 - end of helix Processing helix chain 'R' and resid 359 through 389 removed outlier: 4.050A pdb=" N ILE R 363 " --> pdb=" O LYS R 359 " (cutoff:3.500A) Proline residue: R 366 - end of helix Processing helix chain 'R' and resid 402 through 418 removed outlier: 3.801A pdb=" N LEU R 406 " --> pdb=" O GLN R 402 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS R 408 " --> pdb=" O ARG R 404 " (cutoff:3.500A) Proline residue: R 415 - end of helix Processing helix chain 'R' and resid 419 through 423 Processing helix chain 'R' and resid 434 through 460 removed outlier: 3.625A pdb=" N TYR R 443 " --> pdb=" O VAL R 439 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LEU R 446 " --> pdb=" O HIS R 442 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLY R 452 " --> pdb=" O ASN R 448 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N PHE R 453 " --> pdb=" O SER R 449 " (cutoff:3.500A) Processing helix chain 'R' and resid 464 through 473 removed outlier: 3.647A pdb=" N ALA R 468 " --> pdb=" O GLY R 464 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 112 through 117 removed outlier: 3.814A pdb=" N TYR B 113 " --> pdb=" O VAL B 41 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU B 22 " --> pdb=" O PHE B 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 33 through 34 removed outlier: 3.810A pdb=" N TYR B 144 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N LYS B 170 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 9.882A pdb=" N VAL B 142 " --> pdb=" O LYS B 170 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL B 53 " --> pdb=" O GLN B 85 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N GLN B 85 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL B 55 " --> pdb=" O ASN B 83 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ASN B 83 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU B 57 " --> pdb=" O CYS B 81 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N CYS B 81 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N CYS B 59 " --> pdb=" O LEU B 79 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 33 through 34 removed outlier: 3.810A pdb=" N TYR B 144 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N LYS B 170 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 9.882A pdb=" N VAL B 142 " --> pdb=" O LYS B 170 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N CYS B 140 " --> pdb=" O LEU B 129 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 183 through 187 removed outlier: 3.617A pdb=" N LYS B 270 " --> pdb=" O VAL B 218 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 207 through 208 removed outlier: 3.913A pdb=" N TYR B 321 " --> pdb=" O PHE B 349 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N LEU B 351 " --> pdb=" O VAL B 319 " (cutoff:3.500A) removed outlier: 9.121A pdb=" N VAL B 319 " --> pdb=" O LEU B 351 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N GLN B 237 " --> pdb=" O PRO B 252 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ALA B 239 " --> pdb=" O LYS B 250 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N LYS B 250 " --> pdb=" O ALA B 239 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ILE B 241 " --> pdb=" O GLN B 248 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N GLN B 248 " --> pdb=" O ILE B 241 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 6 through 10 removed outlier: 3.553A pdb=" N VAL C 8 " --> pdb=" O ALA C 26 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 13 through 15 removed outlier: 3.531A pdb=" N GLY C 13 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR C 120 " --> pdb=" O GLY C 13 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N SER C 35 " --> pdb=" O SER C 55 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N SER C 55 " --> pdb=" O SER C 35 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE C 37 " --> pdb=" O SER C 53 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N SER C 53 " --> pdb=" O ILE C 37 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N TRP C 39 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 13 through 15 removed outlier: 3.531A pdb=" N GLY C 13 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR C 120 " --> pdb=" O GLY C 13 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N TYR C 112 " --> pdb=" O ARG C 101 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 130 through 134 removed outlier: 3.716A pdb=" N GLY C 149 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N TYR C 186 " --> pdb=" O ASP C 154 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 130 through 134 removed outlier: 3.716A pdb=" N GLY C 149 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N TYR C 186 " --> pdb=" O ASP C 154 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 161 through 164 Processing sheet with id=AB3, first strand: chain 'E' and resid 5 through 7 removed outlier: 5.932A pdb=" N VAL E 20 " --> pdb=" O ILE E 76 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 11 through 14 removed outlier: 6.626A pdb=" N VAL E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N TYR E 50 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 11 through 14 removed outlier: 3.792A pdb=" N THR E 98 " --> pdb=" O GLN E 91 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 117 through 119 removed outlier: 3.705A pdb=" N VAL E 134 " --> pdb=" O PHE E 119 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N LEU E 176 " --> pdb=" O LEU E 137 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ASN E 139 " --> pdb=" O TYR E 174 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N TYR E 174 " --> pdb=" O ASN E 139 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER E 175 " --> pdb=" O THR E 165 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 147 through 151 removed outlier: 3.554A pdb=" N LYS E 208 " --> pdb=" O CYS E 195 " (cutoff:3.500A) 466 hydrogen bonds defined for protein. 1248 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: 1.44 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2013 1.33 - 1.45: 1848 1.45 - 1.57: 4843 1.57 - 1.69: 14 1.69 - 1.81: 56 Bond restraints: 8774 Sorted by residual: bond pdb=" OG1 TPO R 503 " pdb=" P TPO R 503 " ideal model delta sigma weight residual 1.717 1.608 0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" OG1 TPO R 506 " pdb=" P TPO R 506 " ideal model delta sigma weight residual 1.717 1.609 0.108 2.00e-02 2.50e+03 2.89e+01 bond pdb=" CA GLN B 130 " pdb=" C GLN B 130 " ideal model delta sigma weight residual 1.528 1.479 0.048 1.08e-02 8.57e+03 1.99e+01 bond pdb=" O2P TPO R 506 " pdb=" P TPO R 506 " ideal model delta sigma weight residual 1.528 1.610 -0.082 2.00e-02 2.50e+03 1.70e+01 bond pdb=" O3P TPO R 506 " pdb=" P TPO R 506 " ideal model delta sigma weight residual 1.528 1.610 -0.082 2.00e-02 2.50e+03 1.69e+01 ... (remaining 8769 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.04: 11885 5.04 - 10.08: 37 10.08 - 15.13: 2 15.13 - 20.17: 1 20.17 - 25.21: 1 Bond angle restraints: 11926 Sorted by residual: angle pdb=" N GLU B 313 " pdb=" CA GLU B 313 " pdb=" C GLU B 313 " ideal model delta sigma weight residual 109.15 83.94 25.21 1.44e+00 4.82e-01 3.07e+02 angle pdb=" N ILE B 314 " pdb=" CA ILE B 314 " pdb=" C ILE B 314 " ideal model delta sigma weight residual 108.48 92.34 16.14 1.44e+00 4.82e-01 1.26e+02 angle pdb=" CA ASP B 29 " pdb=" CB ASP B 29 " pdb=" CG ASP B 29 " ideal model delta sigma weight residual 112.60 117.84 -5.24 1.00e+00 1.00e+00 2.74e+01 angle pdb=" C GLU B 313 " pdb=" CA GLU B 313 " pdb=" CB GLU B 313 " ideal model delta sigma weight residual 110.67 118.52 -7.85 1.52e+00 4.33e-01 2.67e+01 angle pdb=" N GLN B 130 " pdb=" CA GLN B 130 " pdb=" C GLN B 130 " ideal model delta sigma weight residual 109.83 115.42 -5.59 1.27e+00 6.20e-01 1.93e+01 ... (remaining 11921 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.88: 4960 16.88 - 33.75: 183 33.75 - 50.63: 43 50.63 - 67.50: 6 67.50 - 84.38: 3 Dihedral angle restraints: 5195 sinusoidal: 1996 harmonic: 3199 Sorted by residual: dihedral pdb=" N GLU B 313 " pdb=" C GLU B 313 " pdb=" CA GLU B 313 " pdb=" CB GLU B 313 " ideal model delta harmonic sigma weight residual 122.80 105.73 17.07 0 2.50e+00 1.60e-01 4.66e+01 dihedral pdb=" CA ALA B 139 " pdb=" C ALA B 139 " pdb=" N CYS B 140 " pdb=" CA CYS B 140 " ideal model delta harmonic sigma weight residual 180.00 149.97 30.03 0 5.00e+00 4.00e-02 3.61e+01 dihedral pdb=" CA GLU B 66 " pdb=" C GLU B 66 " pdb=" N ASP B 67 " pdb=" CA ASP B 67 " ideal model delta harmonic sigma weight residual 180.00 150.02 29.98 0 5.00e+00 4.00e-02 3.60e+01 ... (remaining 5192 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1228 0.095 - 0.189: 123 0.189 - 0.284: 7 0.284 - 0.378: 1 0.378 - 0.473: 3 Chirality restraints: 1362 Sorted by residual: chirality pdb=" CA ASN B 122 " pdb=" N ASN B 122 " pdb=" C ASN B 122 " pdb=" CB ASN B 122 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.59e+00 chirality pdb=" CA ILE B 314 " pdb=" N ILE B 314 " pdb=" C ILE B 314 " pdb=" CB ILE B 314 " both_signs ideal model delta sigma weight residual False 2.43 2.87 -0.43 2.00e-01 2.50e+01 4.66e+00 chirality pdb=" CA GLU B 313 " pdb=" N GLU B 313 " pdb=" C GLU B 313 " pdb=" CB GLU B 313 " both_signs ideal model delta sigma weight residual False 2.51 2.92 -0.41 2.00e-01 2.50e+01 4.26e+00 ... (remaining 1359 not shown) Planarity restraints: 1489 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 63 " -0.089 2.00e-02 2.50e+03 4.50e-02 4.06e+01 pdb=" CG TYR B 63 " 0.056 2.00e-02 2.50e+03 pdb=" CD1 TYR B 63 " 0.043 2.00e-02 2.50e+03 pdb=" CD2 TYR B 63 " 0.038 2.00e-02 2.50e+03 pdb=" CE1 TYR B 63 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 63 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 63 " -0.007 2.00e-02 2.50e+03 pdb=" OH TYR B 63 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 321 " -0.065 2.00e-02 2.50e+03 3.49e-02 2.44e+01 pdb=" CG TYR B 321 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR B 321 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 TYR B 321 " 0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR B 321 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR B 321 " 0.020 2.00e-02 2.50e+03 pdb=" CZ TYR B 321 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 321 " -0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 305 " -0.050 2.00e-02 2.50e+03 2.66e-02 1.42e+01 pdb=" CG TYR R 305 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR R 305 " 0.039 2.00e-02 2.50e+03 pdb=" CD2 TYR R 305 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR R 305 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR R 305 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYR R 305 " -0.012 2.00e-02 2.50e+03 pdb=" OH TYR R 305 " -0.020 2.00e-02 2.50e+03 ... (remaining 1486 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 168 2.68 - 3.24: 8354 3.24 - 3.79: 12903 3.79 - 4.35: 17842 4.35 - 4.90: 30016 Nonbonded interactions: 69283 Sorted by model distance: nonbonded pdb=" N ASP B 69 " pdb=" OD1 ASP B 69 " model vdw 2.129 3.120 nonbonded pdb=" NZ LYS B 107 " pdb=" O ASN R 507 " model vdw 2.174 3.120 nonbonded pdb=" NH1 ARG L 20 " pdb=" O MET R 32 " model vdw 2.201 3.120 nonbonded pdb=" O PRO C 133 " pdb=" OG SER E 122 " model vdw 2.217 3.040 nonbonded pdb=" OD2 ASP B 290 " pdb=" ND2 ASN B 299 " model vdw 2.298 3.120 ... (remaining 69278 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: 6.470 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.650 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:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 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 : 0.005 0.109 8776 Z= 0.310 Angle : 0.895 25.212 11930 Z= 0.554 Chirality : 0.056 0.473 1362 Planarity : 0.006 0.077 1489 Dihedral : 9.797 84.377 3125 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.43 % Allowed : 3.32 % Favored : 96.26 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.27), residues: 1057 helix: 2.68 (0.31), residues: 270 sheet: 0.86 (0.30), residues: 338 loop : -0.31 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 307 TYR 0.089 0.003 TYR B 63 PHE 0.044 0.002 PHE R 314 TRP 0.005 0.001 TRP R 352 HIS 0.011 0.001 HIS B 210 Details of bonding type rmsd covalent geometry : bond 0.00530 ( 8774) covalent geometry : angle 0.89533 (11926) SS BOND : bond 0.00200 ( 2) SS BOND : angle 0.42973 ( 4) hydrogen bonds : bond 0.18024 ( 432) hydrogen bonds : angle 7.61841 ( 1248) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 225 time to evaluate : 0.239 Fit side-chains revert: symmetry clash REVERT: B 44 ASP cc_start: 0.6992 (t0) cc_final: 0.6656 (p0) REVERT: B 69 ASP cc_start: 0.6483 (OUTLIER) cc_final: 0.6238 (p0) REVERT: B 176 GLU cc_start: 0.8491 (mm-30) cc_final: 0.7927 (mp0) REVERT: C 62 TYR cc_start: 0.7886 (m-80) cc_final: 0.7649 (m-80) REVERT: C 68 LYS cc_start: 0.7594 (ttmm) cc_final: 0.7389 (mttm) REVERT: C 76 ASP cc_start: 0.7556 (t0) cc_final: 0.7248 (t0) REVERT: C 86 MET cc_start: 0.7305 (mtp) cc_final: 0.7026 (mtp) REVERT: C 162 VAL cc_start: 0.7902 (t) cc_final: 0.7700 (p) REVERT: E 93 LYS cc_start: 0.7345 (tttt) cc_final: 0.6986 (tttp) REVERT: R 282 ARG cc_start: 0.4476 (ppt170) cc_final: 0.3370 (ppt170) REVERT: R 319 LYS cc_start: 0.6802 (tptp) cc_final: 0.6223 (pttt) REVERT: R 403 TYR cc_start: 0.4693 (m-10) cc_final: 0.4336 (m-10) outliers start: 4 outliers final: 1 residues processed: 229 average time/residue: 0.1161 time to fit residues: 33.9037 Evaluate side-chains 157 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 155 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain R residue 191 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 38 optimal weight: 0.0870 overall best weight: 1.5764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 ASN B 245 ASN R 166 ASN R 364 GLN ** R 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 440 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.126313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.100968 restraints weight = 18937.868| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.39 r_work: 0.3473 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 8776 Z= 0.282 Angle : 0.765 10.311 11930 Z= 0.394 Chirality : 0.049 0.225 1362 Planarity : 0.005 0.050 1489 Dihedral : 5.343 34.932 1196 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.78 % Allowed : 9.30 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.52 (0.25), residues: 1057 helix: 1.62 (0.29), residues: 278 sheet: 0.63 (0.28), residues: 348 loop : -0.70 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 62 TYR 0.026 0.002 TYR B 63 PHE 0.027 0.003 PHE R 184 TRP 0.013 0.002 TRP C 106 HIS 0.010 0.002 HIS B 198 Details of bonding type rmsd covalent geometry : bond 0.00671 ( 8774) covalent geometry : angle 0.76436 (11926) SS BOND : bond 0.00818 ( 2) SS BOND : angle 1.21258 ( 4) hydrogen bonds : bond 0.04697 ( 432) hydrogen bonds : angle 5.72537 ( 1248) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 160 time to evaluate : 0.344 Fit side-chains REVERT: B 44 ASP cc_start: 0.7391 (t0) cc_final: 0.6469 (p0) REVERT: B 69 ASP cc_start: 0.6804 (OUTLIER) cc_final: 0.6532 (p0) REVERT: B 153 ASN cc_start: 0.8184 (p0) cc_final: 0.7954 (p0) REVERT: B 176 GLU cc_start: 0.8732 (mm-30) cc_final: 0.8158 (mp0) REVERT: C 127 LYS cc_start: 0.8109 (ttmt) cc_final: 0.7900 (tttm) REVERT: C 162 VAL cc_start: 0.7800 (t) cc_final: 0.7575 (p) REVERT: C 186 TYR cc_start: 0.8372 (m-80) cc_final: 0.8156 (m-80) REVERT: E 117 PHE cc_start: 0.6979 (m-80) cc_final: 0.6714 (m-80) REVERT: R 202 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7494 (mm) REVERT: R 319 LYS cc_start: 0.7246 (tptp) cc_final: 0.6596 (pttt) REVERT: R 404 ARG cc_start: 0.6805 (ptm160) cc_final: 0.6120 (mmt180) outliers start: 26 outliers final: 17 residues processed: 179 average time/residue: 0.1168 time to fit residues: 27.4729 Evaluate side-chains 162 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 153 LYS Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain L residue 23 PHE Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 229 SER Chi-restraints excluded: chain R residue 407 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 83 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 31 optimal weight: 0.2980 chunk 11 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 53 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 58 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 217 ASN R 420 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.126976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.101823 restraints weight = 18788.952| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.39 r_work: 0.3491 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8776 Z= 0.159 Angle : 0.615 6.825 11930 Z= 0.324 Chirality : 0.044 0.204 1362 Planarity : 0.004 0.048 1489 Dihedral : 5.041 34.818 1196 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.78 % Allowed : 11.23 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.60 (0.26), residues: 1057 helix: 1.78 (0.31), residues: 280 sheet: 0.61 (0.28), residues: 347 loop : -0.67 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 99 TYR 0.026 0.002 TYR R 191 PHE 0.023 0.002 PHE R 184 TRP 0.009 0.001 TRP R 437 HIS 0.012 0.001 HIS B 198 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 8774) covalent geometry : angle 0.61517 (11926) SS BOND : bond 0.00571 ( 2) SS BOND : angle 0.88182 ( 4) hydrogen bonds : bond 0.04056 ( 432) hydrogen bonds : angle 5.36059 ( 1248) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 0.355 Fit side-chains REVERT: B 104 LEU cc_start: 0.7240 (OUTLIER) cc_final: 0.6835 (mp) REVERT: B 105 ILE cc_start: 0.7080 (OUTLIER) cc_final: 0.6776 (pt) REVERT: B 153 ASN cc_start: 0.8164 (p0) cc_final: 0.7673 (p0) REVERT: B 176 GLU cc_start: 0.8779 (mm-30) cc_final: 0.8264 (mp0) REVERT: B 229 LYS cc_start: 0.7810 (mptt) cc_final: 0.7372 (mptt) REVERT: C 162 VAL cc_start: 0.7740 (t) cc_final: 0.7498 (p) REVERT: E 117 PHE cc_start: 0.6898 (m-80) cc_final: 0.6547 (m-80) REVERT: R 319 LYS cc_start: 0.7156 (tptp) cc_final: 0.6465 (pttt) REVERT: R 441 MET cc_start: 0.7470 (tpp) cc_final: 0.7235 (mmt) outliers start: 26 outliers final: 19 residues processed: 161 average time/residue: 0.1162 time to fit residues: 24.6592 Evaluate side-chains 158 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain L residue 23 PHE Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 229 SER Chi-restraints excluded: chain R residue 299 ILE Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 465 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 84 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 24 optimal weight: 0.0050 chunk 63 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 48 optimal weight: 0.2980 chunk 58 optimal weight: 0.9990 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.126714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.101550 restraints weight = 18937.302| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.41 r_work: 0.3523 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8776 Z= 0.151 Angle : 0.603 9.530 11930 Z= 0.315 Chirality : 0.043 0.217 1362 Planarity : 0.004 0.048 1489 Dihedral : 4.836 32.184 1192 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.99 % Allowed : 12.62 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.55 (0.26), residues: 1057 helix: 1.67 (0.31), residues: 280 sheet: 0.60 (0.29), residues: 342 loop : -0.66 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 99 TYR 0.026 0.002 TYR R 191 PHE 0.024 0.002 PHE R 184 TRP 0.009 0.001 TRP R 437 HIS 0.007 0.001 HIS B 198 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 8774) covalent geometry : angle 0.60246 (11926) SS BOND : bond 0.00524 ( 2) SS BOND : angle 0.71556 ( 4) hydrogen bonds : bond 0.03817 ( 432) hydrogen bonds : angle 5.16925 ( 1248) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 148 time to evaluate : 0.305 Fit side-chains REVERT: B 31 ILE cc_start: 0.8277 (mm) cc_final: 0.8020 (mm) REVERT: B 105 ILE cc_start: 0.7064 (OUTLIER) cc_final: 0.6777 (pt) REVERT: B 153 ASN cc_start: 0.8172 (p0) cc_final: 0.7833 (p0) REVERT: B 176 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8215 (mp0) REVERT: E 117 PHE cc_start: 0.6931 (m-80) cc_final: 0.6566 (m-80) REVERT: R 319 LYS cc_start: 0.7170 (tptp) cc_final: 0.6436 (pttt) REVERT: R 441 MET cc_start: 0.7467 (tpp) cc_final: 0.7252 (mmt) REVERT: R 458 ILE cc_start: 0.8236 (mt) cc_final: 0.7886 (mt) outliers start: 28 outliers final: 19 residues processed: 165 average time/residue: 0.1044 time to fit residues: 22.8794 Evaluate side-chains 157 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain L residue 23 PHE Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 299 ILE Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 465 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 57 optimal weight: 0.9990 chunk 33 optimal weight: 0.0970 chunk 72 optimal weight: 7.9990 chunk 45 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 38 optimal weight: 0.0980 chunk 87 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 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 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 216 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.127236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.102430 restraints weight = 18935.217| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.36 r_work: 0.3544 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8776 Z= 0.135 Angle : 0.580 6.750 11930 Z= 0.304 Chirality : 0.043 0.210 1362 Planarity : 0.004 0.048 1489 Dihedral : 4.716 29.589 1192 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.10 % Allowed : 13.26 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.58 (0.26), residues: 1057 helix: 1.74 (0.30), residues: 282 sheet: 0.59 (0.29), residues: 342 loop : -0.65 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 99 TYR 0.025 0.001 TYR R 191 PHE 0.026 0.002 PHE R 184 TRP 0.007 0.001 TRP R 437 HIS 0.007 0.001 HIS B 198 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 8774) covalent geometry : angle 0.57951 (11926) SS BOND : bond 0.00428 ( 2) SS BOND : angle 0.57773 ( 4) hydrogen bonds : bond 0.03638 ( 432) hydrogen bonds : angle 5.02161 ( 1248) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 146 time to evaluate : 0.333 Fit side-chains REVERT: B 104 LEU cc_start: 0.7215 (OUTLIER) cc_final: 0.6872 (mp) REVERT: B 105 ILE cc_start: 0.7049 (OUTLIER) cc_final: 0.6778 (pt) REVERT: B 153 ASN cc_start: 0.8153 (p0) cc_final: 0.7850 (p0) REVERT: B 176 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8264 (mp0) REVERT: B 368 ASN cc_start: 0.7320 (t0) cc_final: 0.6043 (m-40) REVERT: C 76 ASP cc_start: 0.8088 (t0) cc_final: 0.7828 (t70) REVERT: E 117 PHE cc_start: 0.6896 (m-80) cc_final: 0.6559 (m-80) REVERT: R 182 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7783 (tm-30) REVERT: R 319 LYS cc_start: 0.7151 (tptp) cc_final: 0.6416 (pttt) REVERT: R 441 MET cc_start: 0.7420 (tpp) cc_final: 0.7220 (mmt) REVERT: R 458 ILE cc_start: 0.8276 (mt) cc_final: 0.7960 (mt) REVERT: R 470 ILE cc_start: 0.8018 (tt) cc_final: 0.7724 (pt) outliers start: 29 outliers final: 20 residues processed: 165 average time/residue: 0.1041 time to fit residues: 23.0116 Evaluate side-chains 159 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 229 SER Chi-restraints excluded: chain R residue 299 ILE Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 443 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 69 optimal weight: 9.9990 chunk 82 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN L 9 HIS R 440 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.124911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.099640 restraints weight = 18891.698| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.39 r_work: 0.3448 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 8776 Z= 0.248 Angle : 0.662 8.932 11930 Z= 0.344 Chirality : 0.046 0.224 1362 Planarity : 0.005 0.048 1489 Dihedral : 4.954 26.720 1192 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.74 % Allowed : 14.12 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.25), residues: 1057 helix: 1.53 (0.30), residues: 276 sheet: 0.38 (0.28), residues: 343 loop : -0.83 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 21 TYR 0.025 0.002 TYR R 191 PHE 0.028 0.002 PHE B 115 TRP 0.011 0.002 TRP C 106 HIS 0.007 0.001 HIS B 198 Details of bonding type rmsd covalent geometry : bond 0.00593 ( 8774) covalent geometry : angle 0.66206 (11926) SS BOND : bond 0.00541 ( 2) SS BOND : angle 0.91962 ( 4) hydrogen bonds : bond 0.04051 ( 432) hydrogen bonds : angle 5.18004 ( 1248) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 149 time to evaluate : 0.334 Fit side-chains REVERT: B 104 LEU cc_start: 0.7208 (OUTLIER) cc_final: 0.6800 (mp) REVERT: B 105 ILE cc_start: 0.7112 (OUTLIER) cc_final: 0.6795 (pt) REVERT: B 153 ASN cc_start: 0.8207 (p0) cc_final: 0.7936 (p0) REVERT: B 176 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8265 (mp0) REVERT: B 368 ASN cc_start: 0.7423 (t0) cc_final: 0.6077 (m-40) REVERT: R 241 ASP cc_start: 0.7689 (t0) cc_final: 0.7482 (t70) REVERT: R 319 LYS cc_start: 0.7260 (tptp) cc_final: 0.6502 (pttt) REVERT: R 458 ILE cc_start: 0.8416 (mt) cc_final: 0.8115 (mt) REVERT: R 502 HIS cc_start: 0.7329 (OUTLIER) cc_final: 0.6999 (t-90) outliers start: 35 outliers final: 25 residues processed: 171 average time/residue: 0.1135 time to fit residues: 25.5242 Evaluate side-chains 171 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 143 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 208 ILE Chi-restraints excluded: chain R residue 209 LEU Chi-restraints excluded: chain R residue 229 SER Chi-restraints excluded: chain R residue 389 LEU Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 443 TYR Chi-restraints excluded: chain R residue 502 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 64 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 95 optimal weight: 4.9990 chunk 69 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 14 optimal weight: 5.9990 chunk 58 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 93 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.126303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.101166 restraints weight = 19025.987| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.41 r_work: 0.3518 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8776 Z= 0.150 Angle : 0.608 8.926 11930 Z= 0.316 Chirality : 0.043 0.175 1362 Planarity : 0.004 0.047 1489 Dihedral : 4.787 25.411 1192 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.21 % Allowed : 15.61 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.40 (0.26), residues: 1057 helix: 1.73 (0.31), residues: 274 sheet: 0.51 (0.29), residues: 343 loop : -0.84 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 21 TYR 0.023 0.001 TYR R 191 PHE 0.024 0.002 PHE R 184 TRP 0.010 0.001 TRP R 437 HIS 0.005 0.001 HIS B 198 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 8774) covalent geometry : angle 0.60751 (11926) SS BOND : bond 0.00437 ( 2) SS BOND : angle 0.61630 ( 4) hydrogen bonds : bond 0.03671 ( 432) hydrogen bonds : angle 5.04226 ( 1248) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 149 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: B 104 LEU cc_start: 0.7211 (OUTLIER) cc_final: 0.6816 (mp) REVERT: B 153 ASN cc_start: 0.8189 (p0) cc_final: 0.7957 (p0) REVERT: B 176 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8292 (mp0) REVERT: B 229 LYS cc_start: 0.7775 (mptt) cc_final: 0.7367 (mptt) REVERT: E 25 ARG cc_start: 0.7679 (ttm-80) cc_final: 0.7449 (tpp80) REVERT: E 117 PHE cc_start: 0.6906 (m-80) cc_final: 0.6622 (m-80) REVERT: R 182 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7748 (tm-30) REVERT: R 319 LYS cc_start: 0.7222 (tptp) cc_final: 0.6442 (pttt) REVERT: R 458 ILE cc_start: 0.8391 (mt) cc_final: 0.8108 (mt) REVERT: R 471 LYS cc_start: 0.6320 (mttm) cc_final: 0.6032 (mttp) REVERT: R 502 HIS cc_start: 0.7281 (OUTLIER) cc_final: 0.6977 (t-90) outliers start: 30 outliers final: 23 residues processed: 168 average time/residue: 0.1181 time to fit residues: 26.3710 Evaluate side-chains 165 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 198 HIS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 229 SER Chi-restraints excluded: chain R residue 389 LEU Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 443 TYR Chi-restraints excluded: chain R residue 502 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 78 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 76 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 73 optimal weight: 0.0870 chunk 66 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 overall best weight: 0.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.125351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.100153 restraints weight = 18802.996| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.39 r_work: 0.3459 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8776 Z= 0.190 Angle : 0.645 9.154 11930 Z= 0.333 Chirality : 0.045 0.218 1362 Planarity : 0.005 0.047 1489 Dihedral : 4.858 24.184 1192 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.42 % Allowed : 15.29 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1057 helix: 1.65 (0.30), residues: 275 sheet: 0.38 (0.29), residues: 337 loop : -0.90 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 99 TYR 0.024 0.002 TYR R 191 PHE 0.024 0.002 PHE R 184 TRP 0.009 0.001 TRP C 106 HIS 0.006 0.001 HIS B 198 Details of bonding type rmsd covalent geometry : bond 0.00451 ( 8774) covalent geometry : angle 0.64447 (11926) SS BOND : bond 0.00470 ( 2) SS BOND : angle 0.78350 ( 4) hydrogen bonds : bond 0.03807 ( 432) hydrogen bonds : angle 5.05690 ( 1248) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 142 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: B 104 LEU cc_start: 0.7210 (OUTLIER) cc_final: 0.6809 (mp) REVERT: B 153 ASN cc_start: 0.8228 (p0) cc_final: 0.8006 (p0) REVERT: B 176 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8307 (mp0) REVERT: B 229 LYS cc_start: 0.7766 (mptt) cc_final: 0.7329 (mptt) REVERT: E 25 ARG cc_start: 0.7720 (ttm-80) cc_final: 0.7461 (tpp80) REVERT: E 117 PHE cc_start: 0.6910 (m-80) cc_final: 0.6545 (m-80) REVERT: R 319 LYS cc_start: 0.7221 (tptp) cc_final: 0.6465 (pttt) REVERT: R 446 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7941 (tp) REVERT: R 458 ILE cc_start: 0.8434 (mt) cc_final: 0.8155 (mt) REVERT: R 471 LYS cc_start: 0.6328 (mttm) cc_final: 0.6036 (mttp) REVERT: R 502 HIS cc_start: 0.7305 (OUTLIER) cc_final: 0.6963 (t-90) outliers start: 32 outliers final: 24 residues processed: 163 average time/residue: 0.1124 time to fit residues: 24.4775 Evaluate side-chains 168 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 141 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain L residue 21 ARG Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 229 SER Chi-restraints excluded: chain R residue 389 LEU Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 446 LEU Chi-restraints excluded: chain R residue 502 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 29 optimal weight: 0.1980 chunk 38 optimal weight: 0.0000 chunk 5 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 52 optimal weight: 0.3980 chunk 76 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 94 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.126924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.102216 restraints weight = 18967.577| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.35 r_work: 0.3502 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8776 Z= 0.132 Angle : 0.612 9.536 11930 Z= 0.315 Chirality : 0.043 0.170 1362 Planarity : 0.004 0.047 1489 Dihedral : 4.704 24.458 1192 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.78 % Allowed : 15.83 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.37 (0.26), residues: 1057 helix: 1.89 (0.31), residues: 273 sheet: 0.39 (0.29), residues: 337 loop : -0.89 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 99 TYR 0.025 0.001 TYR R 191 PHE 0.024 0.002 PHE R 184 TRP 0.013 0.001 TRP R 437 HIS 0.005 0.001 HIS B 198 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 8774) covalent geometry : angle 0.61216 (11926) SS BOND : bond 0.00411 ( 2) SS BOND : angle 0.59629 ( 4) hydrogen bonds : bond 0.03544 ( 432) hydrogen bonds : angle 4.90876 ( 1248) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 0.327 Fit side-chains REVERT: B 104 LEU cc_start: 0.7219 (OUTLIER) cc_final: 0.6830 (mp) REVERT: B 176 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8327 (mp0) REVERT: B 192 MET cc_start: 0.6475 (pmm) cc_final: 0.6265 (pmm) REVERT: B 229 LYS cc_start: 0.7760 (mptt) cc_final: 0.7326 (mptt) REVERT: E 117 PHE cc_start: 0.6865 (m-80) cc_final: 0.6575 (m-80) REVERT: R 185 ASP cc_start: 0.7014 (m-30) cc_final: 0.6807 (m-30) REVERT: R 319 LYS cc_start: 0.7168 (tptp) cc_final: 0.6426 (pttt) REVERT: R 441 MET cc_start: 0.6840 (mmm) cc_final: 0.6488 (tpp) REVERT: R 446 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7914 (tp) REVERT: R 458 ILE cc_start: 0.8392 (mt) cc_final: 0.8109 (mt) REVERT: R 471 LYS cc_start: 0.6388 (mttm) cc_final: 0.6108 (mttp) outliers start: 26 outliers final: 21 residues processed: 160 average time/residue: 0.1155 time to fit residues: 24.6023 Evaluate side-chains 162 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 229 SER Chi-restraints excluded: chain R residue 389 LEU Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 446 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 30 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 8 optimal weight: 0.0570 chunk 60 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 82 optimal weight: 0.3980 chunk 29 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.126566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.101566 restraints weight = 18838.325| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.41 r_work: 0.3487 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.4316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8776 Z= 0.146 Angle : 0.620 9.774 11930 Z= 0.318 Chirality : 0.044 0.201 1362 Planarity : 0.004 0.047 1489 Dihedral : 4.685 24.146 1192 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.10 % Allowed : 15.83 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.36 (0.26), residues: 1057 helix: 1.84 (0.31), residues: 275 sheet: 0.39 (0.29), residues: 337 loop : -0.89 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 99 TYR 0.024 0.001 TYR R 191 PHE 0.024 0.002 PHE R 184 TRP 0.015 0.001 TRP R 437 HIS 0.005 0.001 HIS B 198 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 8774) covalent geometry : angle 0.61992 (11926) SS BOND : bond 0.00379 ( 2) SS BOND : angle 0.68120 ( 4) hydrogen bonds : bond 0.03585 ( 432) hydrogen bonds : angle 4.87181 ( 1248) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 141 time to evaluate : 0.404 Fit side-chains REVERT: B 87 PHE cc_start: 0.8163 (t80) cc_final: 0.7860 (t80) REVERT: B 104 LEU cc_start: 0.7200 (OUTLIER) cc_final: 0.6776 (mp) REVERT: B 176 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8338 (mp0) REVERT: B 192 MET cc_start: 0.6475 (pmm) cc_final: 0.6262 (pmm) REVERT: B 229 LYS cc_start: 0.7775 (mptt) cc_final: 0.7301 (mptt) REVERT: E 19 ARG cc_start: 0.8024 (ttp-170) cc_final: 0.7792 (ttt-90) REVERT: E 117 PHE cc_start: 0.6835 (m-80) cc_final: 0.6567 (m-80) REVERT: R 319 LYS cc_start: 0.7204 (tptp) cc_final: 0.6414 (pttt) REVERT: R 441 MET cc_start: 0.6956 (mmm) cc_final: 0.6587 (tpp) REVERT: R 446 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7950 (tp) REVERT: R 458 ILE cc_start: 0.8412 (mt) cc_final: 0.8131 (mt) REVERT: R 471 LYS cc_start: 0.6410 (mttm) cc_final: 0.6124 (mttp) outliers start: 29 outliers final: 23 residues processed: 160 average time/residue: 0.1161 time to fit residues: 24.5335 Evaluate side-chains 163 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 229 SER Chi-restraints excluded: chain R residue 389 LEU Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 446 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 42 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 36 optimal weight: 0.0470 chunk 14 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.124883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.099693 restraints weight = 18794.956| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.34 r_work: 0.3459 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.4449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8776 Z= 0.208 Angle : 0.668 9.785 11930 Z= 0.344 Chirality : 0.046 0.249 1362 Planarity : 0.005 0.046 1489 Dihedral : 4.870 23.020 1192 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.10 % Allowed : 16.15 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.17 (0.26), residues: 1057 helix: 1.68 (0.30), residues: 275 sheet: 0.30 (0.29), residues: 337 loop : -1.02 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 21 TYR 0.024 0.002 TYR R 191 PHE 0.030 0.002 PHE R 424 TRP 0.014 0.001 TRP R 437 HIS 0.005 0.001 HIS B 210 Details of bonding type rmsd covalent geometry : bond 0.00496 ( 8774) covalent geometry : angle 0.66830 (11926) SS BOND : bond 0.00492 ( 2) SS BOND : angle 0.85585 ( 4) hydrogen bonds : bond 0.03899 ( 432) hydrogen bonds : angle 5.03167 ( 1248) =============================================================================== Job complete usr+sys time: 3033.81 seconds wall clock time: 52 minutes 40.25 seconds (3160.25 seconds total)