Starting phenix.real_space_refine on Sun Apr 5 07:25:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vmn_65192/04_2026/9vmn_65192_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vmn_65192/04_2026/9vmn_65192.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9vmn_65192/04_2026/9vmn_65192.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vmn_65192/04_2026/9vmn_65192.map" model { file = "/net/cci-nas-00/data/ceres_data/9vmn_65192/04_2026/9vmn_65192_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vmn_65192/04_2026/9vmn_65192_neut.cif" } 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= 0.009 sd= 0.560 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 58 5.16 5 C 5568 2.51 5 N 1476 2.21 5 O 1603 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8705 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1798 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 6, 'TRANS': 227} Chain breaks: 1 Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 116 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 7, 'ARG:plan': 6, 'GLN:plan1': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 7} Unresolved non-hydrogen planarities: 95 Chain: "B" Number of atoms: 2491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2491 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 5, 'GLN:plan1': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 78 Chain: "G" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 353 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "R" Number of atoms: 2310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2310 Classifications: {'peptide': 294} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 10, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 36 Chain: "S" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1743 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "R" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'AKG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.88, per 1000 atoms: 0.22 Number of scatterers: 8705 At special positions: 0 Unit cell: (87.98, 119.78, 126.14, 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 58 16.00 O 1603 8.00 N 1476 7.00 C 5568 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 183 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.05 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 396.7 milliseconds 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2164 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 14 sheets defined 39.2% alpha, 24.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 Processing helix chain 'A' and resid 45 through 56 removed outlier: 3.527A pdb=" N ARG A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 216 removed outlier: 3.920A pdb=" N ASN A 216 " --> pdb=" O GLN A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 245 Processing helix chain 'A' and resid 260 through 268 removed outlier: 3.513A pdb=" N VAL A 268 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 277 removed outlier: 4.284A pdb=" N TYR A 276 " --> pdb=" O LYS A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 281 removed outlier: 3.755A pdb=" N ALA A 281 " --> pdb=" O PRO A 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 278 through 281' Processing helix chain 'A' and resid 296 through 316 removed outlier: 3.664A pdb=" N PHE A 310 " --> pdb=" O ILE A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 356 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 12 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'R' and resid 28 through 62 removed outlier: 4.227A pdb=" N LEU R 36 " --> pdb=" O LYS R 32 " (cutoff:3.500A) Proline residue: R 37 - end of helix Proline residue: R 49 - end of helix removed outlier: 3.826A pdb=" N MET R 62 " --> pdb=" O TYR R 58 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 85 removed outlier: 3.707A pdb=" N SER R 85 " --> pdb=" O LEU R 81 " (cutoff:3.500A) Processing helix chain 'R' and resid 85 through 95 removed outlier: 3.539A pdb=" N LEU R 89 " --> pdb=" O SER R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 137 removed outlier: 3.920A pdb=" N LYS R 107 " --> pdb=" O ASP R 103 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N HIS R 114 " --> pdb=" O ARG R 110 " (cutoff:3.500A) Processing helix chain 'R' and resid 142 through 145 Processing helix chain 'R' and resid 146 through 166 removed outlier: 3.840A pdb=" N ALA R 150 " --> pdb=" O LYS R 146 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 169 No H-bonds generated for 'chain 'R' and resid 167 through 169' Processing helix chain 'R' and resid 185 through 189 Processing helix chain 'R' and resid 191 through 207 Processing helix chain 'R' and resid 207 through 227 Processing helix chain 'R' and resid 233 through 254 Processing helix chain 'R' and resid 254 through 270 Processing helix chain 'R' and resid 273 through 293 removed outlier: 3.518A pdb=" N ARG R 288 " --> pdb=" O TYR R 284 " (cutoff:3.500A) Proline residue: R 289 - end of helix Processing helix chain 'R' and resid 293 through 303 Processing helix chain 'R' and resid 306 through 320 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.807A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191 removed outlier: 6.382A pdb=" N LEU A 34 " --> pdb=" O HIS A 197 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N PHE A 199 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N VAL A 201 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N LEU A 38 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA A 220 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52 removed outlier: 5.647A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.987A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.014A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.619A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.877A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.534A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.648A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 174 through 175 Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.796A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.796A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (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: 3.535A pdb=" N GLU S 234 " --> pdb=" O VAL S 135 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) 466 hydrogen bonds defined for protein. 1308 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: 1.51 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 1393 1.28 - 1.41: 2323 1.41 - 1.55: 5078 1.55 - 1.68: 20 1.68 - 1.82: 80 Bond restraints: 8894 Sorted by residual: bond pdb=" C1 AKG R 401 " pdb=" C2 AKG R 401 " ideal model delta sigma weight residual 1.559 1.347 0.212 2.00e-02 2.50e+03 1.12e+02 bond pdb=" CA ARG R 63 " pdb=" C ARG R 63 " ideal model delta sigma weight residual 1.524 1.398 0.126 1.26e-02 6.30e+03 1.00e+02 bond pdb=" CA PRO R 64 " pdb=" C PRO R 64 " ideal model delta sigma weight residual 1.520 1.646 -0.127 1.42e-02 4.96e+03 7.97e+01 bond pdb=" C HIS B 311 " pdb=" O HIS B 311 " ideal model delta sigma weight residual 1.234 1.141 0.093 1.22e-02 6.72e+03 5.84e+01 bond pdb=" N SER R 68 " pdb=" CA SER R 68 " ideal model delta sigma weight residual 1.459 1.369 0.090 1.20e-02 6.94e+03 5.66e+01 ... (remaining 8889 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.56: 12038 4.56 - 9.13: 53 9.13 - 13.69: 8 13.69 - 18.25: 3 18.25 - 22.82: 2 Bond angle restraints: 12104 Sorted by residual: angle pdb=" C ARG R 63 " pdb=" N PRO R 64 " pdb=" CA PRO R 64 " ideal model delta sigma weight residual 119.84 98.93 20.91 1.25e+00 6.40e-01 2.80e+02 angle pdb=" N SER R 68 " pdb=" CA SER R 68 " pdb=" CB SER R 68 " ideal model delta sigma weight residual 110.07 94.08 15.99 1.45e+00 4.76e-01 1.22e+02 angle pdb=" N ARG R 63 " pdb=" CA ARG R 63 " pdb=" C ARG R 63 " ideal model delta sigma weight residual 109.81 132.63 -22.82 2.21e+00 2.05e-01 1.07e+02 angle pdb=" O MET A 53 " pdb=" C MET A 53 " pdb=" N ARG A 54 " ideal model delta sigma weight residual 121.53 107.28 14.25 1.60e+00 3.91e-01 7.94e+01 angle pdb=" O TYR R 58 " pdb=" C TYR R 58 " pdb=" N ILE R 59 " ideal model delta sigma weight residual 122.22 113.91 8.31 1.17e+00 7.31e-01 5.04e+01 ... (remaining 12099 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 4632 17.73 - 35.47: 461 35.47 - 53.20: 103 53.20 - 70.94: 24 70.94 - 88.67: 7 Dihedral angle restraints: 5227 sinusoidal: 1881 harmonic: 3346 Sorted by residual: dihedral pdb=" N ARG R 63 " pdb=" C ARG R 63 " pdb=" CA ARG R 63 " pdb=" CB ARG R 63 " ideal model delta harmonic sigma weight residual 122.80 146.61 -23.81 0 2.50e+00 1.60e-01 9.07e+01 dihedral pdb=" C ARG R 63 " pdb=" N ARG R 63 " pdb=" CA ARG R 63 " pdb=" CB ARG R 63 " ideal model delta harmonic sigma weight residual -122.60 -144.10 21.50 0 2.50e+00 1.60e-01 7.40e+01 dihedral pdb=" N SER R 68 " pdb=" C SER R 68 " pdb=" CA SER R 68 " pdb=" CB SER R 68 " ideal model delta harmonic sigma weight residual 122.80 105.83 16.97 0 2.50e+00 1.60e-01 4.61e+01 ... (remaining 5224 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.268: 1410 0.268 - 0.536: 3 0.536 - 0.804: 0 0.804 - 1.072: 0 1.072 - 1.340: 1 Chirality restraints: 1414 Sorted by residual: chirality pdb=" CA ARG R 63 " pdb=" N ARG R 63 " pdb=" C ARG R 63 " pdb=" CB ARG R 63 " both_signs ideal model delta sigma weight residual False 2.51 1.17 1.34 2.00e-01 2.50e+01 4.49e+01 chirality pdb=" CA TRP R 65 " pdb=" N TRP R 65 " pdb=" C TRP R 65 " pdb=" CB TRP R 65 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.35e+00 chirality pdb=" CA PHE R 60 " pdb=" N PHE R 60 " pdb=" C PHE R 60 " pdb=" CB PHE R 60 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.90e+00 ... (remaining 1411 not shown) Planarity restraints: 1526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A 53 " 0.055 2.00e-02 2.50e+03 9.97e-02 9.95e+01 pdb=" C MET A 53 " -0.173 2.00e-02 2.50e+03 pdb=" O MET A 53 " 0.059 2.00e-02 2.50e+03 pdb=" N ARG A 54 " 0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 290 " -0.065 5.00e-02 4.00e+02 9.77e-02 1.53e+01 pdb=" N PRO A 291 " 0.169 5.00e-02 4.00e+02 pdb=" CA PRO A 291 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 291 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 311 " -0.034 2.00e-02 2.50e+03 2.93e-02 1.29e+01 pdb=" CG HIS B 311 " 0.059 2.00e-02 2.50e+03 pdb=" ND1 HIS B 311 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 HIS B 311 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 HIS B 311 " -0.020 2.00e-02 2.50e+03 pdb=" NE2 HIS B 311 " -0.005 2.00e-02 2.50e+03 ... (remaining 1523 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 248 2.70 - 3.25: 8343 3.25 - 3.80: 14429 3.80 - 4.35: 19120 4.35 - 4.90: 32047 Nonbonded interactions: 74187 Sorted by model distance: nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.151 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.203 3.040 nonbonded pdb=" O ARG R 63 " pdb=" CA PRO R 64 " model vdw 2.219 2.776 nonbonded pdb=" O ILE R 166 " pdb=" OG1 THR R 169 " model vdw 2.230 3.040 nonbonded pdb=" OH TYR R 118 " pdb=" NH2 ARG R 261 " model vdw 2.238 3.120 ... (remaining 74182 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: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.190 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 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 : 0.012 0.779 8897 Z= 0.962 Angle : 0.971 22.818 12108 Z= 0.557 Chirality : 0.065 1.340 1414 Planarity : 0.007 0.100 1526 Dihedral : 15.602 88.669 3057 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.11 % Allowed : 18.56 % Favored : 81.33 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.24), residues: 1131 helix: 0.84 (0.25), residues: 393 sheet: 0.49 (0.30), residues: 282 loop : -0.72 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 63 TYR 0.031 0.003 TYR A 356 PHE 0.025 0.003 PHE A 189 TRP 0.031 0.003 TRP R 158 HIS 0.022 0.003 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00818 ( 8894) covalent geometry : angle 0.97060 (12104) SS BOND : bond 0.01033 ( 2) SS BOND : angle 1.01115 ( 4) hydrogen bonds : bond 0.13944 ( 462) hydrogen bonds : angle 6.10823 ( 1308) Misc. bond : bond 0.77868 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 120 time to evaluate : 0.419 Fit side-chains REVERT: R 185 ASP cc_start: 0.7359 (OUTLIER) cc_final: 0.7113 (m-30) outliers start: 1 outliers final: 0 residues processed: 120 average time/residue: 0.6980 time to fit residues: 88.3086 Evaluate side-chains 114 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 113 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 185 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN A 261 GLN A 322 HIS B 237 ASN B 268 ASN R 199 ASN R 230 GLN R 237 GLN R 311 GLN S 182 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.050345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2468 r_free = 0.2468 target = 0.045684 restraints weight = 19071.401| |-----------------------------------------------------------------------------| r_work (start): 0.2469 rms_B_bonded: 1.03 r_work: 0.2400 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.2321 rms_B_bonded: 2.36 restraints_weight: 0.2500 r_work (final): 0.2321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.0967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8897 Z= 0.150 Angle : 0.613 7.185 12108 Z= 0.328 Chirality : 0.044 0.219 1414 Planarity : 0.005 0.064 1526 Dihedral : 5.496 74.168 1237 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.87 % Allowed : 15.80 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.87 (0.25), residues: 1131 helix: 1.78 (0.25), residues: 399 sheet: 0.72 (0.31), residues: 277 loop : -0.57 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 241 TYR 0.017 0.002 TYR A 356 PHE 0.020 0.002 PHE A 189 TRP 0.016 0.002 TRP R 197 HIS 0.006 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 8894) covalent geometry : angle 0.61276 (12104) SS BOND : bond 0.00879 ( 2) SS BOND : angle 0.82786 ( 4) hydrogen bonds : bond 0.05223 ( 462) hydrogen bonds : angle 4.84037 ( 1308) Misc. bond : bond 0.00044 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: A 209 ARG cc_start: 0.8784 (ptt-90) cc_final: 0.8530 (ptt180) REVERT: A 355 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8063 (tm-30) outliers start: 26 outliers final: 12 residues processed: 133 average time/residue: 0.6337 time to fit residues: 89.2146 Evaluate side-chains 118 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 322 HIS Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 142 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 112 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 77 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 108 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 HIS B 35 ASN B 237 ASN B 340 ASN R 311 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2583 r_free = 0.2583 target = 0.049777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2453 r_free = 0.2453 target = 0.045128 restraints weight = 19072.179| |-----------------------------------------------------------------------------| r_work (start): 0.2453 rms_B_bonded: 1.04 r_work: 0.2385 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.2308 rms_B_bonded: 2.33 restraints_weight: 0.2500 r_work (final): 0.2308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8970 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8897 Z= 0.148 Angle : 0.589 7.243 12108 Z= 0.314 Chirality : 0.043 0.153 1414 Planarity : 0.005 0.047 1526 Dihedral : 5.317 74.283 1235 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.31 % Allowed : 15.36 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.03 (0.25), residues: 1131 helix: 2.02 (0.25), residues: 399 sheet: 0.62 (0.31), residues: 270 loop : -0.44 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 241 TYR 0.014 0.001 TYR A 30 PHE 0.019 0.002 PHE A 189 TRP 0.014 0.002 TRP A 211 HIS 0.004 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 8894) covalent geometry : angle 0.58854 (12104) SS BOND : bond 0.00860 ( 2) SS BOND : angle 0.74838 ( 4) hydrogen bonds : bond 0.05029 ( 462) hydrogen bonds : angle 4.67977 ( 1308) Misc. bond : bond 0.00020 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 107 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: A 209 ARG cc_start: 0.8782 (ptt-90) cc_final: 0.8500 (ptt180) REVERT: A 355 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8062 (tm-30) REVERT: B 75 GLN cc_start: 0.8768 (mt0) cc_final: 0.8405 (mt0) REVERT: B 234 PHE cc_start: 0.9161 (OUTLIER) cc_final: 0.8236 (m-80) REVERT: B 325 MET cc_start: 0.9412 (mmt) cc_final: 0.9169 (mmt) REVERT: R 62 MET cc_start: 0.9085 (mtp) cc_final: 0.8261 (mtm) outliers start: 30 outliers final: 15 residues processed: 126 average time/residue: 0.6180 time to fit residues: 82.6179 Evaluate side-chains 122 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 322 HIS Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 142 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 26 optimal weight: 0.0970 chunk 1 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 108 optimal weight: 0.3980 chunk 86 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 101 optimal weight: 6.9990 chunk 80 optimal weight: 0.5980 chunk 99 optimal weight: 0.3980 chunk 3 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 HIS B 237 ASN B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.051267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2491 r_free = 0.2491 target = 0.046569 restraints weight = 19474.728| |-----------------------------------------------------------------------------| r_work (start): 0.2492 rms_B_bonded: 1.06 r_work: 0.2424 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.2347 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.2347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8897 Z= 0.113 Angle : 0.532 7.322 12108 Z= 0.283 Chirality : 0.041 0.136 1414 Planarity : 0.004 0.044 1526 Dihedral : 5.096 76.215 1235 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.98 % Allowed : 15.69 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.26 (0.25), residues: 1131 helix: 2.28 (0.25), residues: 401 sheet: 0.75 (0.31), residues: 274 loop : -0.40 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 241 TYR 0.016 0.001 TYR A 304 PHE 0.018 0.001 PHE A 189 TRP 0.013 0.001 TRP A 211 HIS 0.003 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 8894) covalent geometry : angle 0.53205 (12104) SS BOND : bond 0.00687 ( 2) SS BOND : angle 0.75408 ( 4) hydrogen bonds : bond 0.04381 ( 462) hydrogen bonds : angle 4.46230 ( 1308) Misc. bond : bond 0.00006 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 108 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: A 209 ARG cc_start: 0.8679 (ptt-90) cc_final: 0.8379 (ptt180) REVERT: B 10 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8222 (tt0) REVERT: B 234 PHE cc_start: 0.9126 (OUTLIER) cc_final: 0.8231 (m-80) REVERT: R 62 MET cc_start: 0.8956 (mtp) cc_final: 0.8005 (mtm) REVERT: S 162 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8754 (tm) outliers start: 27 outliers final: 13 residues processed: 127 average time/residue: 0.6420 time to fit residues: 86.4226 Evaluate side-chains 120 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 322 HIS Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain S residue 162 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 49 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 25 optimal weight: 0.0980 chunk 59 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 HIS B 36 ASN B 75 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.050772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2478 r_free = 0.2478 target = 0.046069 restraints weight = 19252.495| |-----------------------------------------------------------------------------| r_work (start): 0.2479 rms_B_bonded: 1.05 r_work: 0.2411 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.2334 rms_B_bonded: 2.36 restraints_weight: 0.2500 r_work (final): 0.2334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8953 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8897 Z= 0.126 Angle : 0.544 7.984 12108 Z= 0.288 Chirality : 0.042 0.137 1414 Planarity : 0.004 0.042 1526 Dihedral : 5.085 76.109 1235 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.54 % Allowed : 15.58 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.24 (0.25), residues: 1131 helix: 2.37 (0.25), residues: 402 sheet: 0.66 (0.31), residues: 267 loop : -0.46 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 241 TYR 0.016 0.001 TYR A 304 PHE 0.019 0.001 PHE A 189 TRP 0.013 0.002 TRP A 211 HIS 0.003 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 8894) covalent geometry : angle 0.54350 (12104) SS BOND : bond 0.00882 ( 2) SS BOND : angle 0.76805 ( 4) hydrogen bonds : bond 0.04506 ( 462) hydrogen bonds : angle 4.45054 ( 1308) Misc. bond : bond 0.00000 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 102 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.7937 (ttmt) REVERT: A 355 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8345 (tp30) REVERT: B 234 PHE cc_start: 0.9145 (OUTLIER) cc_final: 0.8341 (m-80) REVERT: R 62 MET cc_start: 0.8911 (mtp) cc_final: 0.8037 (mtm) REVERT: R 248 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8631 (mp) REVERT: S 162 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8759 (tm) outliers start: 32 outliers final: 15 residues processed: 126 average time/residue: 0.6250 time to fit residues: 83.5884 Evaluate side-chains 120 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 322 HIS Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain R residue 248 LEU Chi-restraints excluded: chain R residue 273 SER Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain S residue 162 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 HIS B 36 ASN B 266 HIS B 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.049859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2453 r_free = 0.2453 target = 0.045147 restraints weight = 19197.532| |-----------------------------------------------------------------------------| r_work (start): 0.2453 rms_B_bonded: 1.05 r_work: 0.2384 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.2307 rms_B_bonded: 2.36 restraints_weight: 0.2500 r_work (final): 0.2307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8970 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8897 Z= 0.147 Angle : 0.571 8.127 12108 Z= 0.302 Chirality : 0.043 0.137 1414 Planarity : 0.004 0.043 1526 Dihedral : 5.190 76.254 1235 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.31 % Allowed : 16.46 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.23 (0.25), residues: 1131 helix: 2.35 (0.25), residues: 402 sheet: 0.65 (0.31), residues: 267 loop : -0.45 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 241 TYR 0.013 0.001 TYR A 30 PHE 0.020 0.002 PHE A 189 TRP 0.013 0.002 TRP A 211 HIS 0.004 0.001 HIS S 155 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 8894) covalent geometry : angle 0.57123 (12104) SS BOND : bond 0.00780 ( 2) SS BOND : angle 0.69739 ( 4) hydrogen bonds : bond 0.04810 ( 462) hydrogen bonds : angle 4.51954 ( 1308) Misc. bond : bond 0.00014 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 104 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.7980 (ttmt) REVERT: A 269 LEU cc_start: 0.6125 (OUTLIER) cc_final: 0.5153 (mt) REVERT: B 234 PHE cc_start: 0.9163 (OUTLIER) cc_final: 0.8388 (m-80) REVERT: R 62 MET cc_start: 0.8911 (mtp) cc_final: 0.8099 (mtm) outliers start: 30 outliers final: 19 residues processed: 127 average time/residue: 0.6289 time to fit residues: 84.7415 Evaluate side-chains 122 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 322 HIS Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain R residue 273 SER Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 142 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 33 optimal weight: 0.2980 chunk 57 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 HIS B 36 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.050411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2467 r_free = 0.2467 target = 0.045682 restraints weight = 19333.006| |-----------------------------------------------------------------------------| r_work (start): 0.2468 rms_B_bonded: 1.06 r_work: 0.2399 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.2321 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.2321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8897 Z= 0.129 Angle : 0.547 8.553 12108 Z= 0.289 Chirality : 0.042 0.138 1414 Planarity : 0.004 0.042 1526 Dihedral : 5.139 78.499 1235 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.87 % Allowed : 17.57 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.28 (0.25), residues: 1131 helix: 2.43 (0.25), residues: 401 sheet: 0.71 (0.31), residues: 265 loop : -0.47 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 241 TYR 0.015 0.001 TYR A 304 PHE 0.019 0.001 PHE A 189 TRP 0.013 0.002 TRP A 211 HIS 0.004 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 8894) covalent geometry : angle 0.54691 (12104) SS BOND : bond 0.00734 ( 2) SS BOND : angle 0.66096 ( 4) hydrogen bonds : bond 0.04547 ( 462) hydrogen bonds : angle 4.45601 ( 1308) Misc. bond : bond 0.00013 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.7951 (ttmt) REVERT: B 234 PHE cc_start: 0.9156 (OUTLIER) cc_final: 0.8349 (m-80) REVERT: R 62 MET cc_start: 0.8848 (mtp) cc_final: 0.8019 (mtm) REVERT: S 109 ASP cc_start: 0.8100 (m-30) cc_final: 0.7844 (m-30) outliers start: 26 outliers final: 20 residues processed: 119 average time/residue: 0.6723 time to fit residues: 84.6122 Evaluate side-chains 119 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 322 HIS Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain R residue 273 SER Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 142 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 89 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 106 optimal weight: 0.4980 chunk 55 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 HIS R 91 HIS R 237 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2554 r_free = 0.2554 target = 0.048676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2422 r_free = 0.2422 target = 0.043997 restraints weight = 19129.859| |-----------------------------------------------------------------------------| r_work (start): 0.2422 rms_B_bonded: 1.04 r_work: 0.2352 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.2275 rms_B_bonded: 2.31 restraints_weight: 0.2500 r_work (final): 0.2275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8991 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8897 Z= 0.184 Angle : 0.616 8.468 12108 Z= 0.326 Chirality : 0.044 0.141 1414 Planarity : 0.005 0.043 1526 Dihedral : 5.387 78.595 1235 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.31 % Allowed : 17.46 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.14 (0.25), residues: 1131 helix: 2.23 (0.25), residues: 401 sheet: 0.64 (0.31), residues: 265 loop : -0.47 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 241 TYR 0.017 0.002 TYR A 304 PHE 0.020 0.002 PHE A 189 TRP 0.013 0.002 TRP A 211 HIS 0.007 0.002 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 8894) covalent geometry : angle 0.61610 (12104) SS BOND : bond 0.00881 ( 2) SS BOND : angle 0.66312 ( 4) hydrogen bonds : bond 0.05261 ( 462) hydrogen bonds : angle 4.64732 ( 1308) Misc. bond : bond 0.00026 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 99 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8070 (ttmt) REVERT: A 269 LEU cc_start: 0.6019 (OUTLIER) cc_final: 0.5097 (mt) REVERT: A 295 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8262 (mt-10) REVERT: B 234 PHE cc_start: 0.9176 (OUTLIER) cc_final: 0.8367 (m-80) REVERT: R 62 MET cc_start: 0.8912 (mtp) cc_final: 0.8181 (mtm) REVERT: S 109 ASP cc_start: 0.8259 (m-30) cc_final: 0.8029 (m-30) outliers start: 30 outliers final: 19 residues processed: 123 average time/residue: 0.6376 time to fit residues: 83.2300 Evaluate side-chains 120 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 180 LYS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 273 SER Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 93 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 25 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 79 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 73 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 HIS R 237 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.050134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2460 r_free = 0.2460 target = 0.045427 restraints weight = 19225.481| |-----------------------------------------------------------------------------| r_work (start): 0.2460 rms_B_bonded: 1.05 r_work: 0.2391 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.2314 rms_B_bonded: 2.36 restraints_weight: 0.2500 r_work (final): 0.2314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8966 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8897 Z= 0.131 Angle : 0.554 8.822 12108 Z= 0.292 Chirality : 0.042 0.137 1414 Planarity : 0.004 0.043 1526 Dihedral : 5.222 82.419 1235 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.54 % Allowed : 18.12 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.25 (0.25), residues: 1131 helix: 2.39 (0.25), residues: 401 sheet: 0.67 (0.31), residues: 267 loop : -0.46 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 241 TYR 0.015 0.001 TYR A 304 PHE 0.019 0.001 PHE A 189 TRP 0.013 0.002 TRP A 211 HIS 0.004 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 8894) covalent geometry : angle 0.55428 (12104) SS BOND : bond 0.00767 ( 2) SS BOND : angle 0.67438 ( 4) hydrogen bonds : bond 0.04582 ( 462) hydrogen bonds : angle 4.47767 ( 1308) Misc. bond : bond 0.00016 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8016 (ttmt) REVERT: A 269 LEU cc_start: 0.6211 (OUTLIER) cc_final: 0.5482 (mt) REVERT: A 295 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8202 (mt-10) REVERT: B 234 PHE cc_start: 0.9154 (OUTLIER) cc_final: 0.8368 (m-80) REVERT: R 62 MET cc_start: 0.8815 (mtp) cc_final: 0.7980 (mtm) REVERT: S 109 ASP cc_start: 0.8161 (m-30) cc_final: 0.7908 (m-30) outliers start: 23 outliers final: 17 residues processed: 116 average time/residue: 0.6816 time to fit residues: 83.5695 Evaluate side-chains 115 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 180 LYS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain R residue 273 SER Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 93 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 79 optimal weight: 0.2980 chunk 41 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 44 optimal weight: 0.0970 chunk 17 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 chunk 20 optimal weight: 0.1980 chunk 76 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 HIS R 230 GLN R 237 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.052050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2511 r_free = 0.2511 target = 0.047340 restraints weight = 19263.194| |-----------------------------------------------------------------------------| r_work (start): 0.2512 rms_B_bonded: 1.06 r_work: 0.2445 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.2368 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work (final): 0.2368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8897 Z= 0.104 Angle : 0.510 8.383 12108 Z= 0.269 Chirality : 0.041 0.144 1414 Planarity : 0.004 0.043 1526 Dihedral : 5.020 85.636 1235 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.32 % Allowed : 18.67 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.43 (0.25), residues: 1131 helix: 2.57 (0.25), residues: 402 sheet: 0.78 (0.31), residues: 272 loop : -0.43 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG R 241 TYR 0.014 0.001 TYR A 304 PHE 0.017 0.001 PHE A 189 TRP 0.012 0.001 TRP A 211 HIS 0.004 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 8894) covalent geometry : angle 0.51011 (12104) SS BOND : bond 0.00641 ( 2) SS BOND : angle 0.71602 ( 4) hydrogen bonds : bond 0.03988 ( 462) hydrogen bonds : angle 4.27719 ( 1308) Misc. bond : bond 0.00005 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: B 186 ASP cc_start: 0.8392 (m-30) cc_final: 0.8118 (m-30) REVERT: B 234 PHE cc_start: 0.9124 (OUTLIER) cc_final: 0.8454 (m-80) REVERT: R 62 MET cc_start: 0.8672 (mtp) cc_final: 0.8067 (mtt) REVERT: S 109 ASP cc_start: 0.8141 (m-30) cc_final: 0.7876 (m-30) outliers start: 21 outliers final: 15 residues processed: 120 average time/residue: 0.7127 time to fit residues: 90.1001 Evaluate side-chains 114 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 273 SER Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 93 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 61 optimal weight: 0.0470 chunk 17 optimal weight: 1.9990 chunk 53 optimal weight: 0.2980 chunk 56 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 14 optimal weight: 0.0370 chunk 37 optimal weight: 5.9990 chunk 86 optimal weight: 0.5980 overall best weight: 0.3356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 HIS B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.052467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2523 r_free = 0.2523 target = 0.047780 restraints weight = 19063.453| |-----------------------------------------------------------------------------| r_work (start): 0.2526 rms_B_bonded: 1.06 r_work: 0.2459 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.2383 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work (final): 0.2383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8897 Z= 0.102 Angle : 0.507 8.271 12108 Z= 0.266 Chirality : 0.041 0.143 1414 Planarity : 0.004 0.048 1526 Dihedral : 4.949 86.537 1235 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.88 % Allowed : 19.12 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.49 (0.25), residues: 1131 helix: 2.68 (0.25), residues: 402 sheet: 0.86 (0.31), residues: 264 loop : -0.46 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG R 241 TYR 0.014 0.001 TYR A 304 PHE 0.016 0.001 PHE A 189 TRP 0.012 0.001 TRP A 211 HIS 0.003 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00213 ( 8894) covalent geometry : angle 0.50710 (12104) SS BOND : bond 0.00604 ( 2) SS BOND : angle 0.72528 ( 4) hydrogen bonds : bond 0.03918 ( 462) hydrogen bonds : angle 4.21029 ( 1308) Misc. bond : bond 0.00009 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3087.63 seconds wall clock time: 53 minutes 29.35 seconds (3209.35 seconds total)