Starting phenix.real_space_refine on Wed Aug 5 01:55:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n29_48827/08_2026/9n29_48827.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n29_48827/08_2026/9n29_48827.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9n29_48827/08_2026/9n29_48827.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n29_48827/08_2026/9n29_48827.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9n29_48827/08_2026/9n29_48827.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n29_48827/08_2026/9n29_48827.map" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.036 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 55 5.16 5 C 4999 2.51 5 N 1347 2.21 5 O 1460 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7861 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2586 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "G" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 434 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "A" Number of atoms: 1795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1795 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "R" Number of atoms: 2054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2054 Classifications: {'peptide': 266} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 10, 'TRANS': 255} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 3, 'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "R" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'2PM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.00, per 1000 atoms: 0.25 Number of scatterers: 7861 At special positions: 0 Unit cell: (72.98, 95.94, 127.92, 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 55 16.00 O 1460 8.00 N 1347 7.00 C 4999 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.02 Simple disulfide: pdb=" SG CYS R 105 " - pdb=" SG CYS R 185 " distance=2.03 Simple disulfide: pdb=" SG CYS R 426 " - pdb=" SG CYS R 429 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.61 Conformation dependent library (CDL) restraints added in 476.8 milliseconds 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1914 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 10 sheets defined 44.1% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'B' and resid 2 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.530A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 24 removed outlier: 3.517A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.610A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'A' and resid 2 through 27 removed outlier: 3.720A pdb=" N ARG A 27 " --> pdb=" O GLU A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 44 removed outlier: 3.905A pdb=" N GLY A 40 " --> pdb=" O ASP A 37 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N LYS A 41 " --> pdb=" O ASN A 38 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N SER A 42 " --> pdb=" O SER A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 98 removed outlier: 4.516A pdb=" N ASP A 97 " --> pdb=" O CYS A 94 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL A 98 " --> pdb=" O PHE A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 Processing helix chain 'A' and resid 140 through 151 Processing helix chain 'A' and resid 154 through 159 removed outlier: 3.812A pdb=" N TYR A 158 " --> pdb=" O LYS A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 165 removed outlier: 4.181A pdb=" N ARG A 164 " --> pdb=" O PRO A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 199 removed outlier: 4.070A pdb=" N SER A 199 " --> pdb=" O ILE A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 238 Processing helix chain 'R' and resid 33 through 60 removed outlier: 3.696A pdb=" N THR R 37 " --> pdb=" O VAL R 33 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N VAL R 38 " --> pdb=" O PHE R 34 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 64 Processing helix chain 'R' and resid 66 through 84 removed outlier: 4.126A pdb=" N PHE R 70 " --> pdb=" O VAL R 66 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU R 71 " --> pdb=" O ASN R 67 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 96 Processing helix chain 'R' and resid 101 through 136 removed outlier: 3.504A pdb=" N CYS R 105 " --> pdb=" O GLY R 101 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 144 Processing helix chain 'R' and resid 145 through 170 removed outlier: 3.998A pdb=" N PHE R 161 " --> pdb=" O TRP R 157 " (cutoff:3.500A) Proline residue: R 166 - end of helix Processing helix chain 'R' and resid 170 through 175 Processing helix chain 'R' and resid 187 through 191 removed outlier: 4.127A pdb=" N SER R 191 " --> pdb=" O GLN R 188 " (cutoff:3.500A) Processing helix chain 'R' and resid 192 through 204 removed outlier: 3.504A pdb=" N THR R 196 " --> pdb=" O ASN R 192 " (cutoff:3.500A) Processing helix chain 'R' and resid 204 through 222 Processing helix chain 'R' and resid 393 through 420 removed outlier: 3.551A pdb=" N THR R 399 " --> pdb=" O GLU R 395 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR R 412 " --> pdb=" O ALA R 408 " (cutoff:3.500A) Proline residue: R 415 - end of helix Processing helix chain 'R' and resid 431 through 453 removed outlier: 3.873A pdb=" N ASN R 445 " --> pdb=" O LEU R 441 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N SER R 446 " --> pdb=" O CYS R 442 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N THR R 447 " --> pdb=" O TYR R 443 " (cutoff:3.500A) Proline residue: R 450 - end of helix Processing helix chain 'R' and resid 457 through 464 Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.420A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.889A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.703A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.526A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.271A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.524A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.860A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.825A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 65 through 71 removed outlier: 6.321A pdb=" N VAL A 29 " --> pdb=" O HIS A 77 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N PHE A 79 " --> pdb=" O VAL A 29 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU A 31 " --> pdb=" O PHE A 79 " (cutoff:3.500A) removed outlier: 9.414A pdb=" N ALA A 100 " --> pdb=" O GLU A 28 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS A 30 " --> pdb=" O ALA A 100 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N ILE A 102 " --> pdb=" O LYS A 30 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LEU A 32 " --> pdb=" O ILE A 102 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N VAL A 104 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU A 34 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N ASP A 106 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ILE A 101 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N PHE A 137 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N PHE A 103 " --> pdb=" O PHE A 137 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ASN A 139 " --> pdb=" O PHE A 103 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N VAL A 105 " --> pdb=" O ASN A 139 " (cutoff:3.500A) 417 hydrogen bonds defined for protein. 1167 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: 1.30 Time building geometry restraints manager: 0.84 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: 2505 1.34 - 1.46: 1854 1.46 - 1.58: 3587 1.58 - 1.70: 0 1.70 - 1.82: 77 Bond restraints: 8023 Sorted by residual: bond pdb=" C THR R 414 " pdb=" N PRO R 415 " ideal model delta sigma weight residual 1.335 1.363 -0.027 1.36e-02 5.41e+03 4.07e+00 bond pdb=" C TYR R 140 " pdb=" N PRO R 141 " ideal model delta sigma weight residual 1.335 1.358 -0.023 1.28e-02 6.10e+03 3.24e+00 bond pdb=" CB VAL N 48 " pdb=" CG2 VAL N 48 " ideal model delta sigma weight residual 1.521 1.464 0.057 3.30e-02 9.18e+02 2.99e+00 bond pdb=" C LEU R 206 " pdb=" N PRO R 207 " ideal model delta sigma weight residual 1.336 1.353 -0.017 1.08e-02 8.57e+03 2.62e+00 bond pdb=" CB ARG N 118 " pdb=" CG ARG N 118 " ideal model delta sigma weight residual 1.520 1.475 0.045 3.00e-02 1.11e+03 2.29e+00 ... (remaining 8018 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 10307 1.63 - 3.26: 493 3.26 - 4.90: 81 4.90 - 6.53: 17 6.53 - 8.16: 7 Bond angle restraints: 10905 Sorted by residual: angle pdb=" C VAL R 422 " pdb=" N ASN R 423 " pdb=" CA ASN R 423 " ideal model delta sigma weight residual 120.54 125.75 -5.21 1.35e+00 5.49e-01 1.49e+01 angle pdb=" CA PRO R 207 " pdb=" N PRO R 207 " pdb=" CD PRO R 207 " ideal model delta sigma weight residual 112.00 107.04 4.96 1.40e+00 5.10e-01 1.25e+01 angle pdb=" N LEU R 421 " pdb=" CA LEU R 421 " pdb=" C LEU R 421 " ideal model delta sigma weight residual 112.94 108.34 4.60 1.41e+00 5.03e-01 1.07e+01 angle pdb=" CA PHE R 189 " pdb=" CB PHE R 189 " pdb=" CG PHE R 189 " ideal model delta sigma weight residual 113.80 116.94 -3.14 1.00e+00 1.00e+00 9.83e+00 angle pdb=" C ASP B 333 " pdb=" N SER B 334 " pdb=" CA SER B 334 " ideal model delta sigma weight residual 123.93 128.73 -4.80 1.54e+00 4.22e-01 9.71e+00 ... (remaining 10900 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 4469 17.14 - 34.27: 208 34.27 - 51.41: 45 51.41 - 68.55: 18 68.55 - 85.68: 2 Dihedral angle restraints: 4742 sinusoidal: 1784 harmonic: 2958 Sorted by residual: dihedral pdb=" CA THR B 249 " pdb=" C THR B 249 " pdb=" N CYS B 250 " pdb=" CA CYS B 250 " ideal model delta harmonic sigma weight residual 180.00 160.12 19.88 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA TYR N 60 " pdb=" C TYR N 60 " pdb=" N THR N 61 " pdb=" CA THR N 61 " ideal model delta harmonic sigma weight residual 180.00 160.57 19.43 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 160.81 19.19 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 4739 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1117 0.084 - 0.169: 131 0.169 - 0.253: 6 0.253 - 0.338: 1 0.338 - 0.422: 1 Chirality restraints: 1256 Sorted by residual: chirality pdb=" CB VAL R 420 " pdb=" CA VAL R 420 " pdb=" CG1 VAL R 420 " pdb=" CG2 VAL R 420 " both_signs ideal model delta sigma weight residual False -2.63 -2.21 -0.42 2.00e-01 2.50e+01 4.45e+00 chirality pdb=" CG LEU R 190 " pdb=" CB LEU R 190 " pdb=" CD1 LEU R 190 " pdb=" CD2 LEU R 190 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CA ASP N 109 " pdb=" N ASP N 109 " pdb=" C ASP N 109 " pdb=" CB ASP N 109 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 1253 not shown) Planarity restraints: 1387 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE R 197 " 0.020 2.00e-02 2.50e+03 4.09e-02 1.67e+01 pdb=" C PHE R 197 " -0.071 2.00e-02 2.50e+03 pdb=" O PHE R 197 " 0.026 2.00e-02 2.50e+03 pdb=" N GLY R 198 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 189 " -0.025 2.00e-02 2.50e+03 2.35e-02 9.68e+00 pdb=" CG PHE R 189 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE R 189 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE R 189 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE R 189 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE R 189 " -0.012 2.00e-02 2.50e+03 pdb=" CZ PHE R 189 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER R 160 " 0.014 2.00e-02 2.50e+03 2.81e-02 7.88e+00 pdb=" C SER R 160 " -0.049 2.00e-02 2.50e+03 pdb=" O SER R 160 " 0.019 2.00e-02 2.50e+03 pdb=" N PHE R 161 " 0.016 2.00e-02 2.50e+03 ... (remaining 1384 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1957 2.80 - 3.32: 7604 3.32 - 3.85: 14307 3.85 - 4.37: 16942 4.37 - 4.90: 28685 Nonbonded interactions: 69495 Sorted by model distance: nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.271 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.276 3.040 nonbonded pdb=" OD1 ASP N 50 " pdb=" OG SER N 59 " model vdw 2.293 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.300 3.040 nonbonded pdb=" OG1 THR R 46 " pdb=" OG1 THR R 447 " model vdw 2.301 3.040 ... (remaining 69490 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.040 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 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 0.064 8026 Z= 0.237 Angle : 0.824 8.161 10911 Z= 0.465 Chirality : 0.055 0.422 1256 Planarity : 0.006 0.064 1387 Dihedral : 11.553 85.681 2819 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.36 % Allowed : 4.19 % Favored : 95.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.27), residues: 1004 helix: 0.95 (0.26), residues: 370 sheet: -0.95 (0.34), residues: 208 loop : -0.05 (0.33), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG R 144 TYR 0.022 0.002 TYR N 95 PHE 0.054 0.003 PHE R 189 TRP 0.022 0.002 TRP A 91 HIS 0.007 0.002 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.24 ( 8023) covalent geometry : angle 0.82325 / 0.46 (10905) SS BOND : bond 0.00712 / 0.36 ( 3) SS BOND : angle 1.85755 / 0.94 ( 6) hydrogen bonds : bond 0.16862 / 11.66 ( 417) hydrogen bonds : angle 7.25324 / 5.18 ( 1167) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 181 time to evaluate : 0.294 Fit side-chains REVERT: B 6 GLN cc_start: 0.8731 (pp30) cc_final: 0.8521 (pp30) REVERT: B 7 LEU cc_start: 0.7162 (mt) cc_final: 0.6901 (mt) REVERT: B 9 GLN cc_start: 0.7296 (mm110) cc_final: 0.7023 (mm-40) REVERT: B 25 CYS cc_start: 0.6720 (m) cc_final: 0.6486 (m) REVERT: B 270 ILE cc_start: 0.8429 (pt) cc_final: 0.8161 (pp) REVERT: N 87 LYS cc_start: 0.8516 (mtmt) cc_final: 0.8024 (mtmm) REVERT: N 90 ASP cc_start: 0.8384 (m-30) cc_final: 0.8150 (m-30) REVERT: A 13 MET cc_start: 0.7894 (tmm) cc_final: 0.7622 (tmm) REVERT: R 32 MET cc_start: 0.4284 (mmt) cc_final: 0.3778 (mpp) REVERT: R 64 GLN cc_start: 0.8782 (mt0) cc_final: 0.8510 (mp10) REVERT: R 67 ASN cc_start: 0.8154 (m-40) cc_final: 0.7905 (m110) REVERT: R 72 PHE cc_start: 0.7457 (t80) cc_final: 0.7112 (t80) REVERT: R 106 ASP cc_start: 0.7362 (m-30) cc_final: 0.7023 (m-30) REVERT: R 140 TYR cc_start: 0.8527 (t80) cc_final: 0.8325 (t80) REVERT: R 143 ARG cc_start: 0.7767 (mtm180) cc_final: 0.7564 (mtm-85) REVERT: R 212 THR cc_start: 0.8308 (m) cc_final: 0.8051 (p) REVERT: R 407 LEU cc_start: 0.8309 (mp) cc_final: 0.8007 (mt) REVERT: R 411 LEU cc_start: 0.9023 (mt) cc_final: 0.8775 (pp) REVERT: R 453 TYR cc_start: 0.8290 (m-80) cc_final: 0.8069 (m-80) outliers start: 3 outliers final: 1 residues processed: 184 average time/residue: 0.5809 time to fit residues: 112.9740 Evaluate side-chains 117 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 116 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 108 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.0010 chunk 45 optimal weight: 2.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 266 HIS N 1 GLN N 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.124950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.100672 restraints weight = 14150.175| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.27 r_work: 0.3490 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8026 Z= 0.164 Angle : 0.570 5.617 10911 Z= 0.306 Chirality : 0.043 0.155 1256 Planarity : 0.004 0.040 1387 Dihedral : 5.248 55.429 1108 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.51 % Allowed : 13.04 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.74 (0.28), residues: 1004 helix: 1.70 (0.26), residues: 372 sheet: -1.01 (0.36), residues: 199 loop : 0.33 (0.33), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG N 19 TYR 0.018 0.001 TYR B 145 PHE 0.023 0.001 PHE R 189 TRP 0.018 0.002 TRP B 211 HIS 0.003 0.001 HIS G 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 ( 8023) covalent geometry : angle 0.56996 / 0.31 (10905) SS BOND : bond 0.00139 / 0.07 ( 3) SS BOND : angle 0.92851 / 0.52 ( 6) hydrogen bonds : bond 0.04199 / 2.87 ( 417) hydrogen bonds : angle 5.22962 / 3.63 ( 1167) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 25 CYS cc_start: 0.6630 (m) cc_final: 0.6415 (m) REVERT: B 234 PHE cc_start: 0.8814 (OUTLIER) cc_final: 0.7890 (m-80) REVERT: B 243 THR cc_start: 0.8912 (OUTLIER) cc_final: 0.8672 (p) REVERT: B 270 ILE cc_start: 0.8505 (pt) cc_final: 0.8209 (pp) REVERT: N 6 GLU cc_start: 0.8069 (mp0) cc_final: 0.7823 (mp0) REVERT: N 82 GLN cc_start: 0.7881 (tp40) cc_final: 0.7621 (tp-100) REVERT: N 87 LYS cc_start: 0.8460 (mtmt) cc_final: 0.7743 (mtmm) REVERT: N 89 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7204 (pm20) REVERT: A 13 MET cc_start: 0.8164 (tmm) cc_final: 0.7824 (tmm) REVERT: R 32 MET cc_start: 0.4029 (mmt) cc_final: 0.3610 (mpp) REVERT: R 72 PHE cc_start: 0.7404 (t80) cc_final: 0.6946 (t80) REVERT: R 98 TRP cc_start: 0.8414 (t-100) cc_final: 0.8116 (t-100) REVERT: R 140 TYR cc_start: 0.8712 (t80) cc_final: 0.8426 (t80) REVERT: R 143 ARG cc_start: 0.7748 (mtm180) cc_final: 0.7513 (ptp-110) REVERT: R 172 GLN cc_start: 0.7352 (pm20) cc_final: 0.7132 (mt0) REVERT: R 188 GLN cc_start: 0.8517 (tp40) cc_final: 0.8270 (tp40) REVERT: R 212 THR cc_start: 0.8462 (m) cc_final: 0.8159 (p) REVERT: R 453 TYR cc_start: 0.8301 (m-80) cc_final: 0.8088 (m-80) outliers start: 21 outliers final: 5 residues processed: 147 average time/residue: 0.5268 time to fit residues: 82.2048 Evaluate side-chains 129 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 121 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain R residue 144 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 63 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 90 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 1 GLN N 120 GLN A 70 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.121791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.096287 restraints weight = 13807.800| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.35 r_work: 0.3343 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8026 Z= 0.180 Angle : 0.560 6.761 10911 Z= 0.295 Chirality : 0.043 0.142 1256 Planarity : 0.004 0.039 1387 Dihedral : 5.297 59.157 1108 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.47 % Allowed : 14.47 % Favored : 82.06 % 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: 0.86 (0.28), residues: 1004 helix: 1.97 (0.26), residues: 373 sheet: -1.10 (0.36), residues: 199 loop : 0.32 (0.33), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 144 TYR 0.014 0.001 TYR N 95 PHE 0.017 0.001 PHE R 189 TRP 0.018 0.002 TRP B 82 HIS 0.003 0.001 HIS B 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.18 ( 8023) covalent geometry : angle 0.55995 / 0.30 (10905) SS BOND : bond 0.00234 / 0.12 ( 3) SS BOND : angle 0.85135 / 0.48 ( 6) hydrogen bonds : bond 0.04077 / 2.79 ( 417) hydrogen bonds : angle 4.98786 / 3.47 ( 1167) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 CYS cc_start: 0.6557 (m) cc_final: 0.6332 (m) REVERT: B 35 ASN cc_start: 0.8205 (m-40) cc_final: 0.7580 (m-40) REVERT: B 146 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8461 (mt) REVERT: B 217 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.7883 (pmt) REVERT: B 234 PHE cc_start: 0.8750 (OUTLIER) cc_final: 0.7885 (m-80) REVERT: B 243 THR cc_start: 0.8891 (OUTLIER) cc_final: 0.8633 (p) REVERT: B 270 ILE cc_start: 0.8530 (pt) cc_final: 0.8199 (pp) REVERT: N 82 GLN cc_start: 0.7936 (tp40) cc_final: 0.7471 (tp-100) REVERT: N 87 LYS cc_start: 0.8450 (mtmt) cc_final: 0.7874 (mtmm) REVERT: A 13 MET cc_start: 0.8272 (tmm) cc_final: 0.7874 (tmm) REVERT: R 32 MET cc_start: 0.4038 (mmt) cc_final: 0.3556 (mpp) REVERT: R 64 GLN cc_start: 0.8739 (mt0) cc_final: 0.8483 (mm-40) REVERT: R 72 PHE cc_start: 0.7502 (t80) cc_final: 0.6916 (t80) REVERT: R 98 TRP cc_start: 0.8423 (t-100) cc_final: 0.8096 (t-100) REVERT: R 112 ASP cc_start: 0.8217 (OUTLIER) cc_final: 0.7967 (t70) REVERT: R 140 TYR cc_start: 0.8700 (t80) cc_final: 0.8379 (t80) REVERT: R 143 ARG cc_start: 0.7762 (mtm180) cc_final: 0.7460 (ptp90) REVERT: R 212 THR cc_start: 0.8372 (m) cc_final: 0.8066 (p) REVERT: R 453 TYR cc_start: 0.8264 (m-80) cc_final: 0.7974 (m-80) outliers start: 29 outliers final: 11 residues processed: 144 average time/residue: 0.4974 time to fit residues: 76.5139 Evaluate side-chains 126 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 194 ARG Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain R residue 39 THR Chi-restraints excluded: chain R residue 112 ASP Chi-restraints excluded: chain R residue 144 ARG Chi-restraints excluded: chain R residue 184 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 59 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 36 optimal weight: 0.0870 chunk 19 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 266 HIS N 1 GLN N 120 GLN R 67 ASN R 172 GLN R 188 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.121091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.095101 restraints weight = 14039.352| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.39 r_work: 0.3325 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8026 Z= 0.198 Angle : 0.564 7.693 10911 Z= 0.298 Chirality : 0.043 0.143 1256 Planarity : 0.004 0.035 1387 Dihedral : 5.331 56.345 1108 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.71 % Allowed : 15.55 % Favored : 80.74 % 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: 0.94 (0.28), residues: 1004 helix: 2.05 (0.26), residues: 374 sheet: -1.21 (0.36), residues: 197 loop : 0.42 (0.33), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 144 TYR 0.016 0.001 TYR N 95 PHE 0.017 0.001 PHE R 416 TRP 0.018 0.002 TRP B 82 HIS 0.003 0.001 HIS G 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.20 ( 8023) covalent geometry : angle 0.56375 / 0.30 (10905) SS BOND : bond 0.00314 / 0.15 ( 3) SS BOND : angle 1.04456 / 0.60 ( 6) hydrogen bonds : bond 0.04112 / 2.82 ( 417) hydrogen bonds : angle 4.90102 / 3.41 ( 1167) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 122 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 35 ASN cc_start: 0.8287 (m-40) cc_final: 0.7629 (m-40) REVERT: B 146 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8471 (mt) REVERT: B 217 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.7928 (pmt) REVERT: B 234 PHE cc_start: 0.8794 (OUTLIER) cc_final: 0.8112 (m-80) REVERT: B 243 THR cc_start: 0.8894 (OUTLIER) cc_final: 0.8637 (p) REVERT: B 246 ASP cc_start: 0.8798 (m-30) cc_final: 0.8453 (m-30) REVERT: B 270 ILE cc_start: 0.8570 (pt) cc_final: 0.8224 (pp) REVERT: G 36 ASP cc_start: 0.7690 (m-30) cc_final: 0.7383 (p0) REVERT: N 43 LYS cc_start: 0.8331 (mttt) cc_final: 0.8086 (mttt) REVERT: N 82 GLN cc_start: 0.7944 (tp40) cc_final: 0.7420 (tp-100) REVERT: N 87 LYS cc_start: 0.8381 (mtmt) cc_final: 0.7796 (mtmm) REVERT: A 13 MET cc_start: 0.8286 (tmm) cc_final: 0.7901 (tmm) REVERT: R 32 MET cc_start: 0.4336 (mmt) cc_final: 0.3817 (mpp) REVERT: R 64 GLN cc_start: 0.8788 (mt0) cc_final: 0.8537 (mm-40) REVERT: R 72 PHE cc_start: 0.7485 (t80) cc_final: 0.6958 (t80) REVERT: R 98 TRP cc_start: 0.8413 (t-100) cc_final: 0.8011 (t-100) REVERT: R 112 ASP cc_start: 0.8050 (OUTLIER) cc_final: 0.7764 (t70) REVERT: R 140 TYR cc_start: 0.8723 (t80) cc_final: 0.8409 (t80) REVERT: R 143 ARG cc_start: 0.7801 (mtm180) cc_final: 0.7535 (ptp90) REVERT: R 172 GLN cc_start: 0.7703 (OUTLIER) cc_final: 0.7200 (pm20) REVERT: R 212 THR cc_start: 0.8400 (m) cc_final: 0.8076 (p) REVERT: R 453 TYR cc_start: 0.8336 (m-80) cc_final: 0.7924 (m-80) outliers start: 31 outliers final: 10 residues processed: 144 average time/residue: 0.5162 time to fit residues: 79.3492 Evaluate side-chains 126 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain R residue 39 THR Chi-restraints excluded: chain R residue 112 ASP Chi-restraints excluded: chain R residue 172 GLN Chi-restraints excluded: chain R residue 184 GLN Chi-restraints excluded: chain R residue 439 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 89 optimal weight: 0.5980 chunk 92 optimal weight: 0.9980 chunk 55 optimal weight: 0.4980 chunk 15 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 266 HIS N 120 GLN A 234 ASN R 172 GLN R 188 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.121756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.096036 restraints weight = 13838.567| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.36 r_work: 0.3342 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8026 Z= 0.170 Angle : 0.552 7.773 10911 Z= 0.291 Chirality : 0.043 0.139 1256 Planarity : 0.004 0.034 1387 Dihedral : 5.219 54.082 1108 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.11 % Allowed : 17.46 % Favored : 79.43 % 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: 0.97 (0.28), residues: 1004 helix: 2.12 (0.27), residues: 375 sheet: -1.22 (0.36), residues: 189 loop : 0.36 (0.33), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 85 TYR 0.015 0.001 TYR N 95 PHE 0.018 0.001 PHE R 416 TRP 0.016 0.002 TRP B 82 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.17 ( 8023) covalent geometry : angle 0.55207 / 0.29 (10905) SS BOND : bond 0.00182 / 0.09 ( 3) SS BOND : angle 0.95860 / 0.54 ( 6) hydrogen bonds : bond 0.03925 / 2.69 ( 417) hydrogen bonds : angle 4.79677 / 3.33 ( 1167) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 120 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 35 ASN cc_start: 0.8355 (m-40) cc_final: 0.7707 (m-40) REVERT: B 146 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8446 (mt) REVERT: B 217 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.7929 (pmt) REVERT: B 234 PHE cc_start: 0.8776 (OUTLIER) cc_final: 0.8106 (m-80) REVERT: B 243 THR cc_start: 0.8883 (OUTLIER) cc_final: 0.8630 (p) REVERT: B 246 ASP cc_start: 0.8791 (m-30) cc_final: 0.8409 (m-30) REVERT: B 262 MET cc_start: 0.8092 (OUTLIER) cc_final: 0.7817 (ttm) REVERT: B 270 ILE cc_start: 0.8526 (pt) cc_final: 0.8186 (pp) REVERT: G 36 ASP cc_start: 0.7677 (m-30) cc_final: 0.7392 (p0) REVERT: N 82 GLN cc_start: 0.7916 (tp40) cc_final: 0.7384 (tp-100) REVERT: N 87 LYS cc_start: 0.8389 (mtmt) cc_final: 0.7802 (mtmm) REVERT: A 13 MET cc_start: 0.8291 (tmm) cc_final: 0.7905 (tmm) REVERT: R 32 MET cc_start: 0.4568 (mmt) cc_final: 0.3979 (mpp) REVERT: R 64 GLN cc_start: 0.8797 (mt0) cc_final: 0.8570 (mm-40) REVERT: R 72 PHE cc_start: 0.7448 (t80) cc_final: 0.6944 (t80) REVERT: R 98 TRP cc_start: 0.8390 (t-100) cc_final: 0.8078 (t-100) REVERT: R 112 ASP cc_start: 0.8060 (OUTLIER) cc_final: 0.7675 (t70) REVERT: R 140 TYR cc_start: 0.8709 (t80) cc_final: 0.8409 (t80) REVERT: R 143 ARG cc_start: 0.7785 (mtm180) cc_final: 0.7552 (ptp-170) REVERT: R 172 GLN cc_start: 0.7662 (OUTLIER) cc_final: 0.7012 (mp10) REVERT: R 212 THR cc_start: 0.8378 (m) cc_final: 0.8067 (p) REVERT: R 453 TYR cc_start: 0.8330 (m-80) cc_final: 0.7971 (m-80) outliers start: 26 outliers final: 8 residues processed: 138 average time/residue: 0.5001 time to fit residues: 73.2568 Evaluate side-chains 129 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain R residue 39 THR Chi-restraints excluded: chain R residue 112 ASP Chi-restraints excluded: chain R residue 172 GLN Chi-restraints excluded: chain R residue 184 GLN Chi-restraints excluded: chain R residue 420 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 36 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 266 HIS N 120 GLN R 188 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.121353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.095538 restraints weight = 13794.956| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.36 r_work: 0.3333 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8026 Z= 0.188 Angle : 0.574 8.732 10911 Z= 0.299 Chirality : 0.044 0.311 1256 Planarity : 0.004 0.035 1387 Dihedral : 5.240 53.798 1108 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.35 % Allowed : 17.70 % Favored : 78.95 % 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: 0.92 (0.28), residues: 1004 helix: 2.07 (0.27), residues: 375 sheet: -1.25 (0.36), residues: 189 loop : 0.33 (0.33), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 105 TYR 0.017 0.001 TYR N 95 PHE 0.018 0.001 PHE R 72 TRP 0.017 0.002 TRP B 82 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.19 ( 8023) covalent geometry : angle 0.57349 / 0.30 (10905) SS BOND : bond 0.00315 / 0.15 ( 3) SS BOND : angle 1.06054 / 0.60 ( 6) hydrogen bonds : bond 0.03981 / 2.74 ( 417) hydrogen bonds : angle 4.81991 / 3.35 ( 1167) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 35 ASN cc_start: 0.8409 (m-40) cc_final: 0.7747 (m-40) REVERT: B 146 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8459 (mt) REVERT: B 217 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.7941 (pmt) REVERT: B 234 PHE cc_start: 0.8813 (OUTLIER) cc_final: 0.8124 (m-80) REVERT: B 243 THR cc_start: 0.8895 (OUTLIER) cc_final: 0.8643 (p) REVERT: B 246 ASP cc_start: 0.8790 (m-30) cc_final: 0.8429 (m-30) REVERT: B 270 ILE cc_start: 0.8528 (pt) cc_final: 0.8179 (pp) REVERT: G 36 ASP cc_start: 0.7721 (m-30) cc_final: 0.7346 (p0) REVERT: N 5 GLN cc_start: 0.8705 (mm-40) cc_final: 0.7900 (tp40) REVERT: N 82 GLN cc_start: 0.7952 (tp40) cc_final: 0.7386 (tp-100) REVERT: N 87 LYS cc_start: 0.8365 (mtmt) cc_final: 0.7788 (mtmm) REVERT: A 13 MET cc_start: 0.8300 (tmm) cc_final: 0.7911 (tmm) REVERT: R 32 MET cc_start: 0.4590 (mmt) cc_final: 0.3902 (mpp) REVERT: R 64 GLN cc_start: 0.8808 (mt0) cc_final: 0.8487 (mm-40) REVERT: R 72 PHE cc_start: 0.7452 (t80) cc_final: 0.6887 (t80) REVERT: R 98 TRP cc_start: 0.8389 (t-100) cc_final: 0.8041 (t-100) REVERT: R 143 ARG cc_start: 0.7751 (mtm180) cc_final: 0.7521 (ptp-170) REVERT: R 172 GLN cc_start: 0.7491 (mt0) cc_final: 0.6928 (mp10) REVERT: R 212 THR cc_start: 0.8404 (m) cc_final: 0.8090 (p) REVERT: R 453 TYR cc_start: 0.8336 (m-80) cc_final: 0.7941 (m-80) outliers start: 28 outliers final: 10 residues processed: 139 average time/residue: 0.4834 time to fit residues: 71.5553 Evaluate side-chains 127 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain R residue 39 THR Chi-restraints excluded: chain R residue 187 ILE Chi-restraints excluded: chain R residue 420 VAL Chi-restraints excluded: chain R residue 456 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 17 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 91 optimal weight: 0.0030 chunk 87 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 93 optimal weight: 0.8980 chunk 69 optimal weight: 0.0020 chunk 45 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 overall best weight: 0.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 266 HIS N 120 GLN R 172 GLN R 188 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.123986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.098757 restraints weight = 13790.834| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.34 r_work: 0.3386 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8026 Z= 0.128 Angle : 0.544 8.783 10911 Z= 0.283 Chirality : 0.043 0.294 1256 Planarity : 0.003 0.034 1387 Dihedral : 5.081 52.813 1108 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.99 % Allowed : 17.94 % Favored : 79.07 % 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: 1.08 (0.28), residues: 1004 helix: 2.30 (0.27), residues: 376 sheet: -1.18 (0.35), residues: 203 loop : 0.40 (0.34), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 105 TYR 0.020 0.001 TYR R 140 PHE 0.019 0.001 PHE R 72 TRP 0.015 0.002 TRP B 169 HIS 0.003 0.001 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 ( 8023) covalent geometry : angle 0.54399 / 0.28 (10905) SS BOND : bond 0.00135 / 0.07 ( 3) SS BOND : angle 1.06025 / 0.61 ( 6) hydrogen bonds : bond 0.03650 / 2.52 ( 417) hydrogen bonds : angle 4.60192 / 3.20 ( 1167) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: B 35 ASN cc_start: 0.8385 (m-40) cc_final: 0.7770 (m-40) REVERT: B 155 ASN cc_start: 0.8225 (t0) cc_final: 0.8000 (t0) REVERT: B 217 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.7986 (pmt) REVERT: B 234 PHE cc_start: 0.8726 (OUTLIER) cc_final: 0.8001 (m-80) REVERT: B 243 THR cc_start: 0.8870 (OUTLIER) cc_final: 0.8631 (p) REVERT: B 246 ASP cc_start: 0.8687 (m-30) cc_final: 0.8340 (m-30) REVERT: B 270 ILE cc_start: 0.8461 (pt) cc_final: 0.8137 (pp) REVERT: N 5 GLN cc_start: 0.8587 (mm-40) cc_final: 0.7879 (tp40) REVERT: N 82 GLN cc_start: 0.7933 (tp40) cc_final: 0.7429 (tp-100) REVERT: N 87 LYS cc_start: 0.8391 (mtmt) cc_final: 0.7809 (mtmm) REVERT: A 13 MET cc_start: 0.8265 (tmm) cc_final: 0.7885 (tmm) REVERT: R 32 MET cc_start: 0.4654 (mmt) cc_final: 0.3943 (mpp) REVERT: R 64 GLN cc_start: 0.8773 (mt0) cc_final: 0.8559 (mm-40) REVERT: R 72 PHE cc_start: 0.7434 (t80) cc_final: 0.6905 (t80) REVERT: R 78 ASP cc_start: 0.8141 (m-30) cc_final: 0.7853 (m-30) REVERT: R 98 TRP cc_start: 0.8343 (t-100) cc_final: 0.7960 (t-100) REVERT: R 143 ARG cc_start: 0.7753 (mtm180) cc_final: 0.7479 (ptp90) REVERT: R 148 MET cc_start: 0.6576 (OUTLIER) cc_final: 0.6366 (tmt) REVERT: R 172 GLN cc_start: 0.7563 (OUTLIER) cc_final: 0.6916 (mp10) REVERT: R 212 THR cc_start: 0.8394 (m) cc_final: 0.8091 (p) REVERT: R 411 LEU cc_start: 0.8904 (mm) cc_final: 0.8607 (pp) REVERT: R 453 TYR cc_start: 0.8277 (m-80) cc_final: 0.7868 (m-80) outliers start: 25 outliers final: 6 residues processed: 144 average time/residue: 0.4541 time to fit residues: 69.8414 Evaluate side-chains 124 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 113 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain R residue 39 THR Chi-restraints excluded: chain R residue 148 MET Chi-restraints excluded: chain R residue 172 GLN Chi-restraints excluded: chain R residue 187 ILE Chi-restraints excluded: chain R residue 420 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 38 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 chunk 94 optimal weight: 0.0470 chunk 11 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 6 optimal weight: 0.4980 chunk 21 optimal weight: 0.0030 chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 0.8980 chunk 97 optimal weight: 6.9990 overall best weight: 0.4088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 266 HIS N 120 GLN A 96 ASN R 172 GLN R 188 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.124653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.099347 restraints weight = 13867.493| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.35 r_work: 0.3395 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8026 Z= 0.130 Angle : 0.549 8.487 10911 Z= 0.284 Chirality : 0.043 0.287 1256 Planarity : 0.003 0.035 1387 Dihedral : 5.036 52.400 1108 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.75 % Allowed : 19.14 % Favored : 78.11 % 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: 1.10 (0.28), residues: 1004 helix: 2.31 (0.27), residues: 375 sheet: -1.09 (0.35), residues: 200 loop : 0.35 (0.33), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 105 TYR 0.019 0.001 TYR R 140 PHE 0.017 0.001 PHE R 72 TRP 0.014 0.002 TRP B 82 HIS 0.003 0.001 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 8023) covalent geometry : angle 0.54834 / 0.28 (10905) SS BOND : bond 0.00128 / 0.06 ( 3) SS BOND : angle 0.98400 / 0.57 ( 6) hydrogen bonds : bond 0.03629 / 2.51 ( 417) hydrogen bonds : angle 4.54654 / 3.16 ( 1167) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: B 35 ASN cc_start: 0.8435 (m-40) cc_final: 0.7811 (m-40) REVERT: B 155 ASN cc_start: 0.8229 (t0) cc_final: 0.7968 (t0) REVERT: B 217 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.7950 (pmt) REVERT: B 234 PHE cc_start: 0.8727 (OUTLIER) cc_final: 0.8087 (m-80) REVERT: B 243 THR cc_start: 0.8860 (OUTLIER) cc_final: 0.8621 (p) REVERT: B 246 ASP cc_start: 0.8662 (m-30) cc_final: 0.8308 (m-30) REVERT: B 270 ILE cc_start: 0.8423 (pt) cc_final: 0.8108 (pp) REVERT: N 5 GLN cc_start: 0.8544 (mm-40) cc_final: 0.7837 (tp40) REVERT: N 82 GLN cc_start: 0.7911 (tp40) cc_final: 0.7357 (tp-100) REVERT: N 87 LYS cc_start: 0.8398 (mtmt) cc_final: 0.7808 (mtmm) REVERT: A 13 MET cc_start: 0.8306 (tmm) cc_final: 0.7969 (tmm) REVERT: R 32 MET cc_start: 0.4682 (mmt) cc_final: 0.3958 (mpp) REVERT: R 64 GLN cc_start: 0.8783 (mt0) cc_final: 0.8564 (mm-40) REVERT: R 72 PHE cc_start: 0.7427 (t80) cc_final: 0.6936 (t80) REVERT: R 78 ASP cc_start: 0.8157 (m-30) cc_final: 0.7908 (m-30) REVERT: R 98 TRP cc_start: 0.8305 (t-100) cc_final: 0.7975 (t-100) REVERT: R 143 ARG cc_start: 0.7698 (mtm180) cc_final: 0.7470 (ptp-170) REVERT: R 172 GLN cc_start: 0.7597 (OUTLIER) cc_final: 0.6951 (mp10) REVERT: R 212 THR cc_start: 0.8400 (m) cc_final: 0.8100 (p) REVERT: R 411 LEU cc_start: 0.8873 (mm) cc_final: 0.8608 (pp) REVERT: R 440 TRP cc_start: 0.7171 (m100) cc_final: 0.5801 (m-10) REVERT: R 441 LEU cc_start: 0.7528 (OUTLIER) cc_final: 0.7314 (mt) REVERT: R 453 TYR cc_start: 0.8262 (m-80) cc_final: 0.7917 (m-80) outliers start: 23 outliers final: 6 residues processed: 142 average time/residue: 0.5001 time to fit residues: 75.5115 Evaluate side-chains 128 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain A residue 111 ASN Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain R residue 39 THR Chi-restraints excluded: chain R residue 172 GLN Chi-restraints excluded: chain R residue 420 VAL Chi-restraints excluded: chain R residue 441 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 5 optimal weight: 2.9990 chunk 89 optimal weight: 0.0970 chunk 17 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 16 optimal weight: 0.0870 chunk 84 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 266 HIS N 120 GLN A 96 ASN R 50 ASN R 172 GLN R 188 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.123753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.098284 restraints weight = 13809.063| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.36 r_work: 0.3376 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8026 Z= 0.151 Angle : 0.565 7.674 10911 Z= 0.293 Chirality : 0.043 0.282 1256 Planarity : 0.004 0.034 1387 Dihedral : 5.115 52.690 1108 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.27 % Allowed : 19.26 % Favored : 78.47 % 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: 1.11 (0.28), residues: 1004 helix: 2.34 (0.27), residues: 376 sheet: -1.15 (0.34), residues: 204 loop : 0.39 (0.34), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 105 TYR 0.021 0.002 TYR R 140 PHE 0.016 0.001 PHE R 72 TRP 0.021 0.002 TRP B 82 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 ( 8023) covalent geometry : angle 0.56502 / 0.29 (10905) SS BOND : bond 0.00166 / 0.08 ( 3) SS BOND : angle 1.02823 / 0.60 ( 6) hydrogen bonds : bond 0.03695 / 2.56 ( 417) hydrogen bonds : angle 4.57035 / 3.17 ( 1167) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: B 35 ASN cc_start: 0.8474 (m-40) cc_final: 0.7848 (m-40) REVERT: B 155 ASN cc_start: 0.8264 (t0) cc_final: 0.7990 (t0) REVERT: B 217 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.7955 (pmt) REVERT: B 234 PHE cc_start: 0.8753 (OUTLIER) cc_final: 0.8080 (m-80) REVERT: B 243 THR cc_start: 0.8865 (OUTLIER) cc_final: 0.8622 (p) REVERT: B 246 ASP cc_start: 0.8690 (m-30) cc_final: 0.8325 (m-30) REVERT: B 270 ILE cc_start: 0.8470 (pt) cc_final: 0.8146 (pp) REVERT: N 5 GLN cc_start: 0.8511 (mm-40) cc_final: 0.7845 (tp40) REVERT: N 82 GLN cc_start: 0.7930 (tp40) cc_final: 0.7376 (tp-100) REVERT: N 87 LYS cc_start: 0.8398 (mtmt) cc_final: 0.7813 (mtmm) REVERT: A 13 MET cc_start: 0.8307 (tmm) cc_final: 0.7910 (tmm) REVERT: R 32 MET cc_start: 0.4693 (mmt) cc_final: 0.3746 (mpp) REVERT: R 64 GLN cc_start: 0.8707 (mt0) cc_final: 0.8492 (mm-40) REVERT: R 69 TYR cc_start: 0.7923 (m-10) cc_final: 0.7697 (m-10) REVERT: R 72 PHE cc_start: 0.7473 (t80) cc_final: 0.6922 (t80) REVERT: R 78 ASP cc_start: 0.8118 (m-30) cc_final: 0.7844 (m-30) REVERT: R 98 TRP cc_start: 0.8305 (t-100) cc_final: 0.7973 (t-100) REVERT: R 172 GLN cc_start: 0.7620 (OUTLIER) cc_final: 0.6998 (mp10) REVERT: R 212 THR cc_start: 0.8411 (m) cc_final: 0.8113 (p) REVERT: R 440 TRP cc_start: 0.7348 (m100) cc_final: 0.5785 (m-10) REVERT: R 441 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.7393 (mt) REVERT: R 453 TYR cc_start: 0.8287 (m-80) cc_final: 0.7906 (m-80) outliers start: 19 outliers final: 7 residues processed: 135 average time/residue: 0.4669 time to fit residues: 67.1029 Evaluate side-chains 126 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain A residue 111 ASN Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain R residue 39 THR Chi-restraints excluded: chain R residue 172 GLN Chi-restraints excluded: chain R residue 420 VAL Chi-restraints excluded: chain R residue 441 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 95 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 chunk 20 optimal weight: 0.0270 chunk 16 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 266 HIS A 96 ASN R 172 GLN R 188 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.124115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.098699 restraints weight = 13690.504| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.34 r_work: 0.3388 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8026 Z= 0.146 Angle : 0.575 7.768 10911 Z= 0.297 Chirality : 0.043 0.284 1256 Planarity : 0.003 0.034 1387 Dihedral : 5.092 52.441 1108 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.51 % Allowed : 19.62 % Favored : 77.87 % 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: 1.11 (0.28), residues: 1004 helix: 2.37 (0.27), residues: 376 sheet: -1.14 (0.34), residues: 202 loop : 0.35 (0.33), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 105 TYR 0.020 0.001 TYR R 140 PHE 0.016 0.001 PHE R 416 TRP 0.019 0.002 TRP B 82 HIS 0.002 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 ( 8023) covalent geometry : angle 0.57468 / 0.30 (10905) SS BOND : bond 0.00175 / 0.09 ( 3) SS BOND : angle 0.96498 / 0.56 ( 6) hydrogen bonds : bond 0.03682 / 2.56 ( 417) hydrogen bonds : angle 4.55643 / 3.16 ( 1167) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 0.283 Fit side-chains revert: symmetry clash REVERT: B 35 ASN cc_start: 0.8445 (m-40) cc_final: 0.7808 (m-40) REVERT: B 155 ASN cc_start: 0.8273 (t0) cc_final: 0.8003 (t0) REVERT: B 217 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.7938 (pmt) REVERT: B 234 PHE cc_start: 0.8726 (OUTLIER) cc_final: 0.8043 (m-80) REVERT: B 243 THR cc_start: 0.8864 (OUTLIER) cc_final: 0.8614 (p) REVERT: B 246 ASP cc_start: 0.8670 (m-30) cc_final: 0.8300 (m-30) REVERT: B 270 ILE cc_start: 0.8444 (pt) cc_final: 0.8112 (pp) REVERT: N 5 GLN cc_start: 0.8524 (mm-40) cc_final: 0.7794 (tp40) REVERT: N 82 GLN cc_start: 0.7905 (tp40) cc_final: 0.7327 (tp-100) REVERT: N 87 LYS cc_start: 0.8380 (mtmt) cc_final: 0.7785 (mtmm) REVERT: A 13 MET cc_start: 0.8289 (tmm) cc_final: 0.7944 (tmm) REVERT: R 32 MET cc_start: 0.4700 (mmt) cc_final: 0.3733 (mpp) REVERT: R 64 GLN cc_start: 0.8736 (mt0) cc_final: 0.8501 (mm-40) REVERT: R 78 ASP cc_start: 0.8152 (m-30) cc_final: 0.7864 (m-30) REVERT: R 86 MET cc_start: 0.7698 (tpp) cc_final: 0.7488 (mmt) REVERT: R 98 TRP cc_start: 0.8303 (t-100) cc_final: 0.7954 (t-100) REVERT: R 172 GLN cc_start: 0.7577 (OUTLIER) cc_final: 0.6942 (mp10) REVERT: R 212 THR cc_start: 0.8405 (m) cc_final: 0.8107 (p) REVERT: R 411 LEU cc_start: 0.8887 (mm) cc_final: 0.8601 (pp) REVERT: R 440 TRP cc_start: 0.7333 (m100) cc_final: 0.5767 (m-10) REVERT: R 441 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7379 (mt) REVERT: R 453 TYR cc_start: 0.8261 (m-80) cc_final: 0.7889 (m-80) outliers start: 21 outliers final: 7 residues processed: 134 average time/residue: 0.4943 time to fit residues: 70.4585 Evaluate side-chains 127 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain R residue 39 THR Chi-restraints excluded: chain R residue 172 GLN Chi-restraints excluded: chain R residue 420 VAL Chi-restraints excluded: chain R residue 441 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 34 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 43 optimal weight: 0.0010 chunk 44 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 57 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 63 optimal weight: 0.1980 chunk 97 optimal weight: 0.7980 chunk 82 optimal weight: 0.2980 overall best weight: 0.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 266 HIS N 120 GLN A 96 ASN R 172 GLN R 188 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.125493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.100292 restraints weight = 13725.507| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.36 r_work: 0.3414 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8026 Z= 0.127 Angle : 0.571 10.467 10911 Z= 0.293 Chirality : 0.043 0.287 1256 Planarity : 0.004 0.034 1387 Dihedral : 5.023 52.114 1108 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.03 % Allowed : 20.57 % Favored : 77.39 % 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: 1.11 (0.28), residues: 1004 helix: 2.38 (0.27), residues: 379 sheet: -1.11 (0.35), residues: 198 loop : 0.27 (0.33), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 105 TYR 0.018 0.001 TYR R 140 PHE 0.027 0.001 PHE R 72 TRP 0.017 0.002 TRP B 82 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 ( 8023) covalent geometry : angle 0.57113 / 0.29 (10905) SS BOND : bond 0.00138 / 0.07 ( 3) SS BOND : angle 0.90410 / 0.53 ( 6) hydrogen bonds : bond 0.03564 / 2.47 ( 417) hydrogen bonds : angle 4.49606 / 3.12 ( 1167) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3143.33 seconds wall clock time: 54 minutes 19.10 seconds (3259.10 seconds total)