Starting phenix.real_space_refine on Sat Dec 28 08:58:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hs3_34984/12_2024/8hs3_34984.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hs3_34984/12_2024/8hs3_34984.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hs3_34984/12_2024/8hs3_34984.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hs3_34984/12_2024/8hs3_34984.map" model { file = "/net/cci-nas-00/data/ceres_data/8hs3_34984/12_2024/8hs3_34984.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hs3_34984/12_2024/8hs3_34984.cif" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.030 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 59 5.16 5 C 5223 2.51 5 N 1453 2.21 5 O 1523 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8258 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1709 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 29 Chain: "B" Number of atoms: 2590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2590 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 438 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "R" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 1761 Classifications: {'peptide': 279} Incomplete info: {'backbone_only': 4, 'n_c_alpha_c_only': 44, 'truncation_to_alanine': 46} Link IDs: {'PTRANS': 14, 'TRANS': 264} Chain breaks: 1 Unresolved chain link angles: 50 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 420 Unresolved non-hydrogen angles: 561 Unresolved non-hydrogen dihedrals: 283 Unresolved non-hydrogen chiralities: 80 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 3, 'TYR:plan': 3, 'TRP:plan': 2, 'ASP:plan': 1, 'PHE:plan': 7, 'GLU:plan': 2, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 180 Chain: "S" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1760 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Time building chain proxies: 5.24, per 1000 atoms: 0.63 Number of scatterers: 8258 At special positions: 0 Unit cell: (95.68, 115.648, 129.792, 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 59 16.00 O 1523 8.00 N 1453 7.00 C 5223 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " 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: 2.08 Conformation dependent library (CDL) restraints added in 1.4 seconds 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2006 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 15 sheets defined 35.9% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.922A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.771A pdb=" N MET A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.390A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 232 removed outlier: 3.531A pdb=" N ASP A 229 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR A 230 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU A 232 " --> pdb=" O ASP A 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 226 through 232' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.585A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.819A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.999A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 9 through 22 Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.543A pdb=" N HIS C 44 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 37 through 42 Processing helix chain 'R' and resid 56 through 80 WARNING: missing atoms! removed outlier: 3.579A pdb=" N LEU R 68 " --> pdb=" O PHE R 64 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL R 69 " --> pdb=" O LEU R 65 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU R 70 " --> pdb=" O ALA R 66 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN R 71 " --> pdb=" O GLY R 67 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 113 Proline residue: R 107 - end of helix removed outlier: 4.222A pdb=" N PHE R 110 " --> pdb=" O LEU R 106 " (cutoff:3.500A) Processing helix chain 'R' and resid 128 through 133 removed outlier: 3.892A pdb=" N LEU R 132 " --> pdb=" O LEU R 128 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 153 removed outlier: 3.614A pdb=" N VAL R 153 " --> pdb=" O TYR R 149 " (cutoff:3.500A) Processing helix chain 'R' and resid 163 through 185 removed outlier: 3.530A pdb=" N SER R 184 " --> pdb=" O ALA R 180 " (cutoff:3.500A) Processing helix chain 'R' and resid 198 through 206 Processing helix chain 'R' and resid 206 through 224 Processing helix chain 'R' and resid 229 through 231 No H-bonds generated for 'chain 'R' and resid 229 through 231' Processing helix chain 'R' and resid 232 through 254 removed outlier: 3.572A pdb=" N ARG R 236 " --> pdb=" O GLY R 232 " (cutoff:3.500A) Processing helix chain 'R' and resid 254 through 267 removed outlier: 4.100A pdb=" N HIS R 258 " --> pdb=" O PHE R 254 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA R 265 " --> pdb=" O GLN R 261 " (cutoff:3.500A) Processing helix chain 'R' and resid 271 through 288 removed outlier: 3.726A pdb=" N TYR R 279 " --> pdb=" O SER R 275 " (cutoff:3.500A) Processing helix chain 'R' and resid 288 through 299 Proline residue: R 294 - end of helix Processing helix chain 'R' and resid 301 through 308 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.709A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 208 through 212 removed outlier: 3.857A pdb=" N VAL S 212 " --> pdb=" O ALA S 209 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.963A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N CYS A 224 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 267 through 268 Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.987A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.695A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 104 through 105 removed outlier: 3.558A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.727A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.920A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 4.684A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 275 through 277 removed outlier: 3.729A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.670A pdb=" N VAL S 5 " --> pdb=" O SER S 23 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.649A pdb=" N GLY S 10 " --> pdb=" O THR S 116 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR S 118 " --> pdb=" O GLY S 10 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR S 115 " --> pdb=" O TYR S 94 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 58 through 60 removed outlier: 5.352A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 128 through 129 Processing sheet with id=AB5, first strand: chain 'S' and resid 134 through 136 removed outlier: 3.815A pdb=" N GLU S 234 " --> pdb=" O VAL S 135 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 182 through 183 removed outlier: 5.742A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) 387 hydrogen bonds defined for protein. 1092 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.68 Time building geometry restraints manager: 2.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2716 1.34 - 1.46: 1986 1.46 - 1.58: 3626 1.58 - 1.70: 4 1.70 - 1.81: 83 Bond restraints: 8415 Sorted by residual: bond pdb=" CB PRO R 226 " pdb=" CG PRO R 226 " ideal model delta sigma weight residual 1.492 1.663 -0.171 5.00e-02 4.00e+02 1.17e+01 bond pdb=" CB PRO R 268 " pdb=" CG PRO R 268 " ideal model delta sigma weight residual 1.492 1.645 -0.153 5.00e-02 4.00e+02 9.38e+00 bond pdb=" CB PRO R 271 " pdb=" CG PRO R 271 " ideal model delta sigma weight residual 1.492 1.638 -0.146 5.00e-02 4.00e+02 8.57e+00 bond pdb=" CB PRO S 75 " pdb=" CG PRO S 75 " ideal model delta sigma weight residual 1.492 1.636 -0.144 5.00e-02 4.00e+02 8.31e+00 bond pdb=" CG PRO R 268 " pdb=" CD PRO R 268 " ideal model delta sigma weight residual 1.503 1.430 0.073 3.40e-02 8.65e+02 4.62e+00 ... (remaining 8410 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.31: 11288 3.31 - 6.61: 67 6.61 - 9.92: 7 9.92 - 13.22: 4 13.22 - 16.53: 3 Bond angle restraints: 11369 Sorted by residual: angle pdb=" CA PRO R 268 " pdb=" N PRO R 268 " pdb=" CD PRO R 268 " ideal model delta sigma weight residual 112.00 95.47 16.53 1.40e+00 5.10e-01 1.39e+02 angle pdb=" CA PRO R 271 " pdb=" N PRO R 271 " pdb=" CD PRO R 271 " ideal model delta sigma weight residual 112.00 97.72 14.28 1.40e+00 5.10e-01 1.04e+02 angle pdb=" CA PRO S 75 " pdb=" N PRO S 75 " pdb=" CD PRO S 75 " ideal model delta sigma weight residual 112.00 97.74 14.26 1.40e+00 5.10e-01 1.04e+02 angle pdb=" CA PRO R 226 " pdb=" N PRO R 226 " pdb=" CD PRO R 226 " ideal model delta sigma weight residual 112.00 100.12 11.88 1.40e+00 5.10e-01 7.20e+01 angle pdb=" N PRO R 268 " pdb=" CD PRO R 268 " pdb=" CG PRO R 268 " ideal model delta sigma weight residual 103.20 95.71 7.49 1.50e+00 4.44e-01 2.49e+01 ... (remaining 11364 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.75: 4174 16.75 - 33.49: 557 33.49 - 50.24: 183 50.24 - 66.99: 24 66.99 - 83.74: 10 Dihedral angle restraints: 4948 sinusoidal: 1793 harmonic: 3155 Sorted by residual: dihedral pdb=" CB CYS S 147 " pdb=" SG CYS S 147 " pdb=" SG CYS S 217 " pdb=" CB CYS S 217 " ideal model delta sinusoidal sigma weight residual 93.00 165.29 -72.29 1 1.00e+01 1.00e-02 6.68e+01 dihedral pdb=" CA SER B 334 " pdb=" C SER B 334 " pdb=" N PHE B 335 " pdb=" CA PHE B 335 " ideal model delta harmonic sigma weight residual -180.00 -156.98 -23.02 0 5.00e+00 4.00e-02 2.12e+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 180.00 161.25 18.75 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 4945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1054 0.056 - 0.112: 220 0.112 - 0.168: 17 0.168 - 0.224: 4 0.224 - 0.280: 1 Chirality restraints: 1296 Sorted by residual: chirality pdb=" CA PRO R 271 " pdb=" N PRO R 271 " pdb=" C PRO R 271 " pdb=" CB PRO R 271 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CA THR R 255 " pdb=" N THR R 255 " pdb=" C THR R 255 " pdb=" CB THR R 255 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CB ILE S 58 " pdb=" CA ILE S 58 " pdb=" CG1 ILE S 58 " pdb=" CG2 ILE S 58 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.90e-01 ... (remaining 1293 not shown) Planarity restraints: 1437 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP R 267 " -0.126 5.00e-02 4.00e+02 1.75e-01 4.87e+01 pdb=" N PRO R 268 " 0.301 5.00e-02 4.00e+02 pdb=" CA PRO R 268 " -0.092 5.00e-02 4.00e+02 pdb=" CD PRO R 268 " -0.083 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " 0.099 5.00e-02 4.00e+02 1.40e-01 3.12e+01 pdb=" N PRO S 75 " -0.241 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " 0.069 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " 0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET R 270 " -0.074 5.00e-02 4.00e+02 1.02e-01 1.67e+01 pdb=" N PRO R 271 " 0.176 5.00e-02 4.00e+02 pdb=" CA PRO R 271 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO R 271 " -0.056 5.00e-02 4.00e+02 ... (remaining 1434 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 212 2.69 - 3.24: 7695 3.24 - 3.80: 13427 3.80 - 4.35: 16816 4.35 - 4.90: 29017 Nonbonded interactions: 67167 Sorted by model distance: nonbonded pdb=" ND1 HIS R 126 " pdb=" NE2 HIS R 126 " model vdw 2.141 2.560 nonbonded pdb=" O MET A 18 " pdb=" ND2 ASN A 22 " model vdw 2.200 3.120 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.272 3.040 nonbonded pdb=" OG1 THR B 86 " pdb=" OD1 ASN B 88 " model vdw 2.274 3.040 nonbonded pdb=" OD1 ASN R 133 " pdb=" OG SER R 286 " model vdw 2.277 3.040 ... (remaining 67162 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: 1.390 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: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 23.170 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 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 0.171 8415 Z= 0.281 Angle : 0.751 16.527 11369 Z= 0.407 Chirality : 0.045 0.280 1296 Planarity : 0.009 0.175 1437 Dihedral : 16.983 83.736 2936 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.36 % Allowed : 29.33 % Favored : 70.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.25), residues: 1106 helix: 0.18 (0.27), residues: 349 sheet: -1.39 (0.31), residues: 272 loop : -1.34 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP S 47 HIS 0.003 0.001 HIS S 155 PHE 0.035 0.002 PHE S 80 TYR 0.015 0.001 TYR S 178 ARG 0.014 0.001 ARG R 260 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 114 time to evaluate : 0.934 Fit side-chains REVERT: A 197 LYS cc_start: 0.7589 (mttm) cc_final: 0.7110 (mttm) REVERT: A 198 MET cc_start: 0.8127 (mtp) cc_final: 0.7910 (mtp) REVERT: B 292 PHE cc_start: 0.8725 (m-80) cc_final: 0.8401 (m-80) REVERT: S 60 TYR cc_start: 0.8936 (m-80) cc_final: 0.8456 (m-80) outliers start: 3 outliers final: 3 residues processed: 115 average time/residue: 0.2004 time to fit residues: 32.1421 Evaluate side-chains 113 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 110 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain S residue 171 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 155 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 8415 Z= 0.410 Angle : 0.649 13.017 11369 Z= 0.343 Chirality : 0.046 0.221 1296 Planarity : 0.006 0.086 1437 Dihedral : 5.183 52.529 1209 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 5.11 % Allowed : 26.25 % Favored : 68.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.25), residues: 1106 helix: 0.63 (0.28), residues: 355 sheet: -1.52 (0.30), residues: 271 loop : -1.07 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP S 47 HIS 0.006 0.001 HIS R 258 PHE 0.024 0.002 PHE R 250 TYR 0.025 0.002 TYR S 178 ARG 0.005 0.001 ARG R 260 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 111 time to evaluate : 1.022 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.7652 (tpp) cc_final: 0.7402 (tpp) REVERT: A 22 ASN cc_start: 0.7004 (m-40) cc_final: 0.6686 (m110) REVERT: A 197 LYS cc_start: 0.7964 (mttm) cc_final: 0.7755 (mttm) REVERT: A 247 MET cc_start: 0.7888 (OUTLIER) cc_final: 0.7222 (mtp) REVERT: B 45 MET cc_start: 0.8858 (mmt) cc_final: 0.7961 (mmt) REVERT: B 262 MET cc_start: 0.8143 (mmt) cc_final: 0.7844 (mmt) REVERT: B 314 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7471 (ptt180) REVERT: C 62 ARG cc_start: 0.6529 (mtm110) cc_final: 0.6309 (mtm180) REVERT: S 22 CYS cc_start: 0.6372 (t) cc_final: 0.5959 (t) REVERT: S 60 TYR cc_start: 0.8858 (m-80) cc_final: 0.8608 (m-80) REVERT: S 113 GLN cc_start: 0.7687 (tp40) cc_final: 0.7389 (tp-100) outliers start: 43 outliers final: 28 residues processed: 143 average time/residue: 0.1953 time to fit residues: 39.1049 Evaluate side-chains 139 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 109 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 127 VAL Chi-restraints excluded: chain R residue 133 ASN Chi-restraints excluded: chain R residue 174 VAL Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 255 THR Chi-restraints excluded: chain R residue 283 VAL Chi-restraints excluded: chain R residue 296 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 88 SER Chi-restraints excluded: chain S residue 171 GLN Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 82 optimal weight: 40.0000 chunk 67 optimal weight: 50.0000 chunk 27 optimal weight: 0.6980 chunk 99 optimal weight: 50.0000 chunk 107 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 98 optimal weight: 0.0670 chunk 33 optimal weight: 0.1980 chunk 79 optimal weight: 1.9990 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8415 Z= 0.158 Angle : 0.504 8.067 11369 Z= 0.266 Chirality : 0.042 0.160 1296 Planarity : 0.004 0.062 1437 Dihedral : 4.602 48.670 1206 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.56 % Allowed : 27.79 % Favored : 68.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.26), residues: 1106 helix: 1.20 (0.28), residues: 353 sheet: -1.33 (0.29), residues: 292 loop : -0.98 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 47 HIS 0.003 0.001 HIS S 35 PHE 0.013 0.001 PHE R 131 TYR 0.023 0.001 TYR S 178 ARG 0.004 0.000 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 122 time to evaluate : 1.898 Fit side-chains REVERT: A 18 MET cc_start: 0.7558 (tpp) cc_final: 0.7335 (tpp) REVERT: A 22 ASN cc_start: 0.7061 (m-40) cc_final: 0.6677 (m110) REVERT: A 192 LYS cc_start: 0.9117 (ttpp) cc_final: 0.8875 (ttpp) REVERT: A 197 LYS cc_start: 0.8038 (mttm) cc_final: 0.7712 (mttm) REVERT: A 247 MET cc_start: 0.7833 (OUTLIER) cc_final: 0.7156 (mtp) REVERT: B 292 PHE cc_start: 0.8942 (m-10) cc_final: 0.8335 (m-80) REVERT: S 22 CYS cc_start: 0.6304 (t) cc_final: 0.5884 (t) REVERT: S 82 GLN cc_start: 0.7235 (tp-100) cc_final: 0.6949 (tp-100) REVERT: S 218 MET cc_start: 0.8027 (ttm) cc_final: 0.7806 (ttm) outliers start: 30 outliers final: 19 residues processed: 141 average time/residue: 0.2407 time to fit residues: 47.2178 Evaluate side-chains 133 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain R residue 127 VAL Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 174 VAL Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 88 SER Chi-restraints excluded: chain S residue 171 GLN Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 chunk 105 optimal weight: 7.9990 chunk 94 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 171 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 8415 Z= 0.407 Angle : 0.615 6.596 11369 Z= 0.325 Chirality : 0.046 0.206 1296 Planarity : 0.005 0.062 1437 Dihedral : 4.857 37.234 1206 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 6.53 % Allowed : 27.32 % Favored : 66.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.25), residues: 1106 helix: 1.09 (0.28), residues: 352 sheet: -1.49 (0.29), residues: 286 loop : -0.98 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP S 47 HIS 0.005 0.001 HIS R 258 PHE 0.024 0.002 PHE R 250 TYR 0.023 0.002 TYR S 178 ARG 0.005 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 113 time to evaluate : 1.093 Fit side-chains revert: symmetry clash REVERT: A 22 ASN cc_start: 0.7152 (m-40) cc_final: 0.6726 (m110) REVERT: A 197 LYS cc_start: 0.8021 (mttm) cc_final: 0.7718 (mttm) REVERT: A 247 MET cc_start: 0.7883 (OUTLIER) cc_final: 0.7236 (mtp) REVERT: B 45 MET cc_start: 0.8781 (mmt) cc_final: 0.7928 (mmt) REVERT: B 314 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7422 (ptt180) REVERT: R 139 LEU cc_start: 0.7058 (OUTLIER) cc_final: 0.6740 (mp) REVERT: S 22 CYS cc_start: 0.6263 (t) cc_final: 0.5901 (t) REVERT: S 210 GLU cc_start: 0.6815 (OUTLIER) cc_final: 0.6228 (pp20) REVERT: S 218 MET cc_start: 0.8364 (ttm) cc_final: 0.7861 (ttm) outliers start: 55 outliers final: 38 residues processed: 154 average time/residue: 0.1868 time to fit residues: 40.5093 Evaluate side-chains 152 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 110 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 127 VAL Chi-restraints excluded: chain R residue 133 ASN Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 147 ASP Chi-restraints excluded: chain R residue 174 VAL Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 255 THR Chi-restraints excluded: chain R residue 283 VAL Chi-restraints excluded: chain R residue 296 VAL Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 144 SER Chi-restraints excluded: chain S residue 153 LEU Chi-restraints excluded: chain S residue 171 GLN Chi-restraints excluded: chain S residue 210 GLU Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 0.0070 chunk 1 optimal weight: 3.9990 chunk 78 optimal weight: 0.0980 chunk 43 optimal weight: 5.9990 chunk 89 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8415 Z= 0.171 Angle : 0.509 6.275 11369 Z= 0.267 Chirality : 0.042 0.167 1296 Planarity : 0.004 0.055 1437 Dihedral : 4.440 33.234 1206 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 4.63 % Allowed : 29.33 % Favored : 66.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.26), residues: 1106 helix: 1.27 (0.29), residues: 354 sheet: -1.42 (0.28), residues: 294 loop : -0.85 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 47 HIS 0.003 0.001 HIS R 273 PHE 0.012 0.001 PHE R 254 TYR 0.021 0.001 TYR S 178 ARG 0.006 0.000 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 117 time to evaluate : 0.873 Fit side-chains revert: symmetry clash REVERT: A 22 ASN cc_start: 0.7104 (m-40) cc_final: 0.6681 (m110) REVERT: A 197 LYS cc_start: 0.8011 (mttm) cc_final: 0.7605 (mttm) REVERT: A 247 MET cc_start: 0.7820 (OUTLIER) cc_final: 0.7136 (mtp) REVERT: B 292 PHE cc_start: 0.9067 (m-10) cc_final: 0.8456 (m-80) REVERT: B 314 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7379 (ptt180) REVERT: S 22 CYS cc_start: 0.6240 (t) cc_final: 0.5837 (t) REVERT: S 210 GLU cc_start: 0.6881 (OUTLIER) cc_final: 0.6324 (pp20) REVERT: S 218 MET cc_start: 0.8185 (ttm) cc_final: 0.7768 (ttm) outliers start: 39 outliers final: 26 residues processed: 146 average time/residue: 0.1929 time to fit residues: 39.5889 Evaluate side-chains 143 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 114 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 127 VAL Chi-restraints excluded: chain R residue 133 ASN Chi-restraints excluded: chain R residue 174 VAL Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 144 SER Chi-restraints excluded: chain S residue 153 LEU Chi-restraints excluded: chain S residue 210 GLU Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 222 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 61 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 105 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 48 optimal weight: 0.2980 chunk 8 optimal weight: 0.6980 chunk 34 optimal weight: 0.1980 chunk 55 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8415 Z= 0.220 Angle : 0.527 10.398 11369 Z= 0.275 Chirality : 0.043 0.164 1296 Planarity : 0.004 0.061 1437 Dihedral : 4.199 30.040 1203 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 5.58 % Allowed : 28.74 % Favored : 65.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.26), residues: 1106 helix: 1.29 (0.29), residues: 354 sheet: -1.39 (0.29), residues: 294 loop : -0.82 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP S 47 HIS 0.003 0.001 HIS R 273 PHE 0.015 0.001 PHE R 131 TYR 0.021 0.001 TYR S 178 ARG 0.006 0.000 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 118 time to evaluate : 1.120 Fit side-chains revert: symmetry clash REVERT: A 22 ASN cc_start: 0.7132 (m-40) cc_final: 0.6666 (m110) REVERT: A 197 LYS cc_start: 0.7982 (mttm) cc_final: 0.7627 (mttm) REVERT: A 247 MET cc_start: 0.7836 (OUTLIER) cc_final: 0.7172 (mtp) REVERT: A 309 ASP cc_start: 0.7513 (t0) cc_final: 0.6905 (t0) REVERT: B 45 MET cc_start: 0.8622 (mmt) cc_final: 0.7784 (mmt) REVERT: B 292 PHE cc_start: 0.9093 (m-10) cc_final: 0.8530 (m-80) REVERT: B 314 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7355 (ptt180) REVERT: S 22 CYS cc_start: 0.6233 (t) cc_final: 0.5843 (t) REVERT: S 210 GLU cc_start: 0.6911 (OUTLIER) cc_final: 0.6343 (pp20) REVERT: S 218 MET cc_start: 0.8334 (ttm) cc_final: 0.7818 (ttm) outliers start: 47 outliers final: 36 residues processed: 150 average time/residue: 0.1808 time to fit residues: 38.5302 Evaluate side-chains 154 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 115 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 127 VAL Chi-restraints excluded: chain R residue 133 ASN Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 230 HIS Chi-restraints excluded: chain R residue 296 VAL Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 144 SER Chi-restraints excluded: chain S residue 153 LEU Chi-restraints excluded: chain S residue 171 GLN Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 210 GLU Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 0.7980 chunk 60 optimal weight: 8.9990 chunk 77 optimal weight: 0.9980 chunk 59 optimal weight: 0.0070 chunk 88 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 chunk 105 optimal weight: 7.9990 chunk 65 optimal weight: 0.5980 chunk 64 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8415 Z= 0.144 Angle : 0.495 10.185 11369 Z= 0.257 Chirality : 0.041 0.159 1296 Planarity : 0.004 0.058 1437 Dihedral : 3.982 27.605 1203 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 4.51 % Allowed : 30.17 % Favored : 65.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.26), residues: 1106 helix: 1.45 (0.29), residues: 354 sheet: -1.25 (0.29), residues: 290 loop : -0.81 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP S 164 HIS 0.004 0.001 HIS S 35 PHE 0.009 0.001 PHE S 27 TYR 0.020 0.001 TYR S 178 ARG 0.007 0.000 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 121 time to evaluate : 0.924 Fit side-chains revert: symmetry clash REVERT: A 197 LYS cc_start: 0.7943 (mttm) cc_final: 0.7596 (mttm) REVERT: A 247 MET cc_start: 0.7801 (OUTLIER) cc_final: 0.7146 (mtp) REVERT: A 309 ASP cc_start: 0.7488 (t0) cc_final: 0.6890 (t0) REVERT: B 45 MET cc_start: 0.8431 (mmt) cc_final: 0.7610 (mmt) REVERT: B 130 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8113 (mm-30) REVERT: B 292 PHE cc_start: 0.9023 (m-10) cc_final: 0.8454 (m-80) REVERT: B 314 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7385 (ptt180) REVERT: S 22 CYS cc_start: 0.6129 (t) cc_final: 0.5750 (t) REVERT: S 218 MET cc_start: 0.8269 (ttm) cc_final: 0.7762 (ttm) outliers start: 38 outliers final: 31 residues processed: 145 average time/residue: 0.1972 time to fit residues: 39.9859 Evaluate side-chains 149 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 116 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 127 VAL Chi-restraints excluded: chain R residue 133 ASN Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 230 HIS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 144 SER Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 153 LEU Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 222 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 71 optimal weight: 0.0010 chunk 51 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 133 ASN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8415 Z= 0.289 Angle : 0.562 10.722 11369 Z= 0.294 Chirality : 0.044 0.177 1296 Planarity : 0.004 0.063 1437 Dihedral : 4.288 30.040 1203 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 6.06 % Allowed : 28.62 % Favored : 65.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.26), residues: 1106 helix: 1.29 (0.29), residues: 353 sheet: -1.33 (0.30), residues: 276 loop : -0.88 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP S 47 HIS 0.007 0.001 HIS B 54 PHE 0.019 0.002 PHE R 250 TYR 0.020 0.002 TYR S 178 ARG 0.008 0.000 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 109 time to evaluate : 0.955 Fit side-chains revert: symmetry clash REVERT: A 22 ASN cc_start: 0.7099 (m-40) cc_final: 0.6695 (m110) REVERT: A 197 LYS cc_start: 0.7974 (mttm) cc_final: 0.7542 (mttm) REVERT: A 247 MET cc_start: 0.7860 (OUTLIER) cc_final: 0.7257 (mtp) REVERT: B 314 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7290 (ptt180) REVERT: R 132 LEU cc_start: 0.4633 (OUTLIER) cc_final: 0.4297 (mp) REVERT: R 136 CYS cc_start: 0.5956 (OUTLIER) cc_final: 0.5714 (p) REVERT: S 22 CYS cc_start: 0.6184 (t) cc_final: 0.5853 (t) REVERT: S 218 MET cc_start: 0.8475 (ttm) cc_final: 0.8058 (ttm) outliers start: 51 outliers final: 38 residues processed: 147 average time/residue: 0.1827 time to fit residues: 38.5153 Evaluate side-chains 147 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 105 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 127 VAL Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 133 ASN Chi-restraints excluded: chain R residue 136 CYS Chi-restraints excluded: chain R residue 147 ASP Chi-restraints excluded: chain R residue 174 VAL Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 296 VAL Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 144 SER Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 222 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.9990 chunk 100 optimal weight: 6.9990 chunk 58 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8415 Z= 0.205 Angle : 0.528 10.500 11369 Z= 0.275 Chirality : 0.042 0.167 1296 Planarity : 0.004 0.056 1437 Dihedral : 4.166 28.655 1203 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 4.99 % Allowed : 29.81 % Favored : 65.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.26), residues: 1106 helix: 1.33 (0.29), residues: 354 sheet: -1.38 (0.29), residues: 284 loop : -0.81 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 47 HIS 0.003 0.001 HIS R 273 PHE 0.013 0.001 PHE R 250 TYR 0.020 0.001 TYR S 178 ARG 0.008 0.000 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 109 time to evaluate : 0.874 Fit side-chains revert: symmetry clash REVERT: A 22 ASN cc_start: 0.7104 (m-40) cc_final: 0.6675 (m110) REVERT: A 197 LYS cc_start: 0.7986 (mttm) cc_final: 0.7549 (mttm) REVERT: A 247 MET cc_start: 0.7843 (OUTLIER) cc_final: 0.7230 (mtp) REVERT: B 45 MET cc_start: 0.8606 (mmt) cc_final: 0.7774 (mmt) REVERT: B 130 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8083 (mm-30) REVERT: B 314 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7272 (ptt180) REVERT: R 132 LEU cc_start: 0.4622 (OUTLIER) cc_final: 0.4379 (mp) REVERT: S 22 CYS cc_start: 0.6202 (t) cc_final: 0.5806 (t) REVERT: S 218 MET cc_start: 0.8411 (ttm) cc_final: 0.7981 (ttm) outliers start: 42 outliers final: 36 residues processed: 138 average time/residue: 0.1838 time to fit residues: 35.8920 Evaluate side-chains 148 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 109 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 127 VAL Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 133 ASN Chi-restraints excluded: chain R residue 174 VAL Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 255 THR Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 144 SER Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 222 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 0.5980 chunk 71 optimal weight: 0.0000 chunk 108 optimal weight: 0.0970 chunk 99 optimal weight: 50.0000 chunk 86 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 overall best weight: 0.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8415 Z= 0.141 Angle : 0.491 10.585 11369 Z= 0.255 Chirality : 0.041 0.155 1296 Planarity : 0.004 0.061 1437 Dihedral : 3.901 26.632 1203 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 4.28 % Allowed : 30.29 % Favored : 65.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.26), residues: 1106 helix: 1.50 (0.29), residues: 354 sheet: -1.30 (0.29), residues: 292 loop : -0.74 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 175 HIS 0.004 0.001 HIS S 35 PHE 0.020 0.001 PHE R 131 TYR 0.019 0.001 TYR S 178 ARG 0.008 0.000 ARG A 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 114 time to evaluate : 0.902 Fit side-chains revert: symmetry clash REVERT: A 22 ASN cc_start: 0.7073 (m-40) cc_final: 0.6667 (m110) REVERT: A 197 LYS cc_start: 0.8004 (mttm) cc_final: 0.7641 (mttm) REVERT: A 247 MET cc_start: 0.7819 (OUTLIER) cc_final: 0.7179 (mtp) REVERT: B 130 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8142 (mm-30) REVERT: B 292 PHE cc_start: 0.9038 (m-10) cc_final: 0.8498 (m-80) REVERT: B 314 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7384 (ptt180) REVERT: R 68 LEU cc_start: 0.7013 (tp) cc_final: 0.6714 (mm) REVERT: R 132 LEU cc_start: 0.4529 (OUTLIER) cc_final: 0.4297 (mp) REVERT: S 22 CYS cc_start: 0.6186 (t) cc_final: 0.5785 (t) REVERT: S 218 MET cc_start: 0.8272 (ttm) cc_final: 0.7829 (ttm) outliers start: 36 outliers final: 32 residues processed: 138 average time/residue: 0.1951 time to fit residues: 38.0889 Evaluate side-chains 142 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 107 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 127 VAL Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 174 VAL Chi-restraints excluded: chain R residue 255 THR Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 144 SER Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 222 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.0570 chunk 86 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 chunk 76 optimal weight: 0.8980 chunk 4 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.9300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 133 ASN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.168762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.123419 restraints weight = 9410.839| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 3.02 r_work: 0.3256 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8415 Z= 0.187 Angle : 0.515 10.795 11369 Z= 0.268 Chirality : 0.042 0.157 1296 Planarity : 0.004 0.060 1437 Dihedral : 3.960 27.645 1203 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 4.99 % Allowed : 29.57 % Favored : 65.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.26), residues: 1106 helix: 1.48 (0.29), residues: 354 sheet: -1.30 (0.29), residues: 294 loop : -0.71 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP S 47 HIS 0.003 0.001 HIS S 35 PHE 0.012 0.001 PHE R 250 TYR 0.020 0.001 TYR S 178 ARG 0.009 0.000 ARG A 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2018.28 seconds wall clock time: 37 minutes 44.18 seconds (2264.18 seconds total)