Starting phenix.real_space_refine on Wed Feb 4 13:05:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nxc_49901/02_2026/9nxc_49901.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nxc_49901/02_2026/9nxc_49901.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9nxc_49901/02_2026/9nxc_49901.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nxc_49901/02_2026/9nxc_49901.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nxc_49901/02_2026/9nxc_49901.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nxc_49901/02_2026/9nxc_49901.map" } resolution = 3.51 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= 0.001 sd= 0.013 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 50 5.16 5 C 6865 2.51 5 N 1792 2.21 5 O 1870 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10577 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" Number of atoms: 2595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2595 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 16, 'TRANS': 317} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 2210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2210 Classifications: {'peptide': 286} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 16, 'TRANS': 269} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 2876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2876 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 20, 'TRANS': 350} Chain: "D" Number of atoms: 2896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2896 Classifications: {'peptide': 373} Link IDs: {'PTRANS': 20, 'TRANS': 352} Time building chain proxies: 2.18, per 1000 atoms: 0.21 Number of scatterers: 10577 At special positions: 0 Unit cell: (83.426, 93.338, 142.898, 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 50 16.00 O 1870 8.00 N 1792 7.00 C 6865 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 472.4 milliseconds 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2526 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 10 sheets defined 51.6% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'H' and resid 41 through 51 Processing helix chain 'H' and resid 60 through 79 removed outlier: 3.938A pdb=" N ALA H 64 " --> pdb=" O ARG H 60 " (cutoff:3.500A) Proline residue: H 70 - end of helix removed outlier: 6.084A pdb=" N GLY H 74 " --> pdb=" O PRO H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 92 removed outlier: 3.887A pdb=" N PHE H 91 " --> pdb=" O ILE H 87 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR H 92 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 251 through 255 Processing helix chain 'H' and resid 261 through 267 Processing helix chain 'H' and resid 273 through 307 Processing helix chain 'H' and resid 313 through 327 Proline residue: H 324 - end of helix Processing helix chain 'H' and resid 328 through 340 Processing helix chain 'H' and resid 346 through 355 Processing helix chain 'H' and resid 364 through 395 Proline residue: H 382 - end of helix Processing helix chain 'H' and resid 397 through 407 Processing helix chain 'H' and resid 409 through 417 Processing helix chain 'H' and resid 419 through 439 removed outlier: 4.166A pdb=" N LYS H 424 " --> pdb=" O PRO H 420 " (cutoff:3.500A) Proline residue: H 425 - end of helix Proline residue: H 428 - end of helix Processing helix chain 'H' and resid 440 through 447 Processing helix chain 'H' and resid 466 through 477 Processing helix chain 'H' and resid 478 through 481 removed outlier: 3.501A pdb=" N GLY H 481 " --> pdb=" O GLY H 478 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 478 through 481' Processing helix chain 'H' and resid 483 through 488 Processing helix chain 'H' and resid 489 through 509 removed outlier: 4.385A pdb=" N PHE H 495 " --> pdb=" O ALA H 491 " (cutoff:3.500A) Processing helix chain 'I' and resid 7 through 40 removed outlier: 4.090A pdb=" N ALA I 11 " --> pdb=" O LYS I 7 " (cutoff:3.500A) Proline residue: I 30 - end of helix removed outlier: 3.597A pdb=" N LEU I 39 " --> pdb=" O VAL I 35 " (cutoff:3.500A) Processing helix chain 'I' and resid 56 through 64 Processing helix chain 'I' and resid 80 through 112 removed outlier: 4.764A pdb=" N THR I 105 " --> pdb=" O ALA I 101 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N CYS I 106 " --> pdb=" O LEU I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 130 Processing helix chain 'I' and resid 135 through 149 removed outlier: 3.919A pdb=" N ALA I 139 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N GLU I 149 " --> pdb=" O ASP I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 151 through 155 Processing helix chain 'I' and resid 158 through 167 removed outlier: 3.851A pdb=" N VAL I 162 " --> pdb=" O THR I 158 " (cutoff:3.500A) Processing helix chain 'I' and resid 169 through 184 removed outlier: 4.247A pdb=" N TRP I 175 " --> pdb=" O ALA I 171 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N THR I 176 " --> pdb=" O LEU I 172 " (cutoff:3.500A) Processing helix chain 'I' and resid 187 through 196 Processing helix chain 'I' and resid 198 through 206 Processing helix chain 'I' and resid 208 through 210 No H-bonds generated for 'chain 'I' and resid 208 through 210' Processing helix chain 'I' and resid 211 through 228 Processing helix chain 'I' and resid 230 through 237 Processing helix chain 'I' and resid 247 through 252 removed outlier: 4.137A pdb=" N GLN I 251 " --> pdb=" O VAL I 247 " (cutoff:3.500A) Processing helix chain 'I' and resid 259 through 270 Processing helix chain 'I' and resid 270 through 280 removed outlier: 4.296A pdb=" N ILE I 274 " --> pdb=" O SER I 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 51 removed outlier: 3.898A pdb=" N LYS C 42 " --> pdb=" O SER C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 75 Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'C' and resid 97 through 103 removed outlier: 3.875A pdb=" N ALA C 103 " --> pdb=" O GLY C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 120 removed outlier: 3.854A pdb=" N VAL C 114 " --> pdb=" O ILE C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 127 removed outlier: 3.594A pdb=" N LEU C 127 " --> pdb=" O ALA C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 134 Processing helix chain 'C' and resid 135 through 151 Processing helix chain 'C' and resid 159 through 163 removed outlier: 4.053A pdb=" N SER C 162 " --> pdb=" O GLU C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 184 Processing helix chain 'C' and resid 193 through 200 removed outlier: 3.680A pdb=" N ALA C 197 " --> pdb=" O ASP C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 224 Processing helix chain 'C' and resid 227 through 234 Processing helix chain 'C' and resid 348 through 352 Processing helix chain 'D' and resid 40 through 51 Processing helix chain 'D' and resid 91 through 97 Processing helix chain 'D' and resid 97 through 104 Processing helix chain 'D' and resid 106 through 122 Processing helix chain 'D' and resid 135 through 151 Processing helix chain 'D' and resid 160 through 163 removed outlier: 4.398A pdb=" N ASN D 163 " --> pdb=" O PRO D 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 160 through 163' Processing helix chain 'D' and resid 165 through 184 Processing helix chain 'D' and resid 193 through 201 Processing helix chain 'D' and resid 217 through 224 Processing helix chain 'D' and resid 227 through 234 Processing sheet with id=AA1, first strand: chain 'I' and resid 253 through 254 removed outlier: 3.602A pdb=" N ASN I 254 " --> pdb=" O ASN I 257 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 16 through 22 removed outlier: 6.092A pdb=" N VAL C 18 " --> pdb=" O TRP C 13 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N TRP C 13 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N LYS C 20 " --> pdb=" O LYS C 11 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N LYS C 11 " --> pdb=" O LYS C 20 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ASN C 8 " --> pdb=" O ASP C 59 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ASP C 59 " --> pdb=" O ASN C 8 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 77 through 80 removed outlier: 6.074A pdb=" N GLY C 78 " --> pdb=" O LEU C 156 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N PHE C 155 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N VAL C 190 " --> pdb=" O PHE C 155 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LEU C 157 " --> pdb=" O VAL C 190 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N PHE C 31 " --> pdb=" O LYS C 203 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N VAL C 205 " --> pdb=" O PHE C 31 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL C 33 " --> pdb=" O VAL C 205 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N LEU C 207 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL C 35 " --> pdb=" O LEU C 207 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ILE C 204 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N VAL C 215 " --> pdb=" O ILE C 204 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL C 206 " --> pdb=" O ALA C 213 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 61 through 62 removed outlier: 3.564A pdb=" N LYS C 65 " --> pdb=" O ILE C 62 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 265 through 269 removed outlier: 3.504A pdb=" N VAL C 256 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU C 268 " --> pdb=" O VAL C 254 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N GLN C 253 " --> pdb=" O THR C 249 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N THR C 249 " --> pdb=" O GLN C 253 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLN C 255 " --> pdb=" O THR C 247 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS C 245 " --> pdb=" O GLU C 257 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 291 through 292 removed outlier: 5.854A pdb=" N VAL C 304 " --> pdb=" O GLN C 319 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N GLN C 319 " --> pdb=" O VAL C 304 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL C 306 " --> pdb=" O HIS C 317 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN C 331 " --> pdb=" O THR C 314 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 16 through 26 removed outlier: 6.229A pdb=" N VAL D 17 " --> pdb=" O TRP D 13 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N TRP D 13 " --> pdb=" O VAL D 17 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER D 19 " --> pdb=" O LYS D 11 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N VAL D 9 " --> pdb=" O ASP D 21 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ASN D 23 " --> pdb=" O GLN D 7 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N GLN D 7 " --> pdb=" O ASN D 23 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ASP D 25 " --> pdb=" O GLN D 5 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N GLN D 5 " --> pdb=" O ASP D 25 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N VAL D 9 " --> pdb=" O SER D 57 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N SER D 57 " --> pdb=" O VAL D 9 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 77 through 80 removed outlier: 6.319A pdb=" N PHE D 31 " --> pdb=" O LYS D 203 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N VAL D 205 " --> pdb=" O PHE D 31 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL D 33 " --> pdb=" O VAL D 205 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N LEU D 207 " --> pdb=" O VAL D 33 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL D 35 " --> pdb=" O LEU D 207 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE D 204 " --> pdb=" O VAL D 215 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL D 215 " --> pdb=" O ILE D 204 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL D 206 " --> pdb=" O ALA D 213 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 265 through 268 removed outlier: 4.297A pdb=" N ALA D 248 " --> pdb=" O GLN D 255 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLU D 257 " --> pdb=" O VAL D 246 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N VAL D 246 " --> pdb=" O GLU D 257 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N LEU D 354 " --> pdb=" O CYS D 362 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 291 through 292 removed outlier: 5.616A pdb=" N VAL D 304 " --> pdb=" O GLN D 319 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N GLN D 319 " --> pdb=" O VAL D 304 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL D 306 " --> pdb=" O HIS D 317 " (cutoff:3.500A) 529 hydrogen bonds defined for protein. 1518 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: 1.73 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2254 1.33 - 1.45: 2301 1.45 - 1.57: 6166 1.57 - 1.69: 1 1.69 - 1.81: 90 Bond restraints: 10812 Sorted by residual: bond pdb=" CB PRO I 132 " pdb=" CG PRO I 132 " ideal model delta sigma weight residual 1.492 1.640 -0.148 5.00e-02 4.00e+02 8.80e+00 bond pdb=" N VAL H 68 " pdb=" CA VAL H 68 " ideal model delta sigma weight residual 1.460 1.495 -0.036 1.21e-02 6.83e+03 8.75e+00 bond pdb=" N MET C 260 " pdb=" CA MET C 260 " ideal model delta sigma weight residual 1.453 1.486 -0.033 1.16e-02 7.43e+03 7.89e+00 bond pdb=" N ASN H 439 " pdb=" CA ASN H 439 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.10e-02 8.26e+03 7.69e+00 bond pdb=" N GLU I 229 " pdb=" CA GLU I 229 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.27e-02 6.20e+03 7.07e+00 ... (remaining 10807 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 14512 2.55 - 5.11: 171 5.11 - 7.66: 22 7.66 - 10.21: 2 10.21 - 12.76: 2 Bond angle restraints: 14709 Sorted by residual: angle pdb=" CA PRO I 132 " pdb=" N PRO I 132 " pdb=" CD PRO I 132 " ideal model delta sigma weight residual 112.00 104.06 7.94 1.40e+00 5.10e-01 3.22e+01 angle pdb=" C THR I 46 " pdb=" CA THR I 46 " pdb=" CB THR I 46 " ideal model delta sigma weight residual 115.79 110.35 5.44 1.19e+00 7.06e-01 2.09e+01 angle pdb=" C GLN I 129 " pdb=" N MET I 130 " pdb=" CA MET I 130 " ideal model delta sigma weight residual 122.56 116.00 6.56 1.72e+00 3.38e-01 1.45e+01 angle pdb=" C PHE H 438 " pdb=" N ASN H 439 " pdb=" CA ASN H 439 " ideal model delta sigma weight residual 122.83 116.97 5.86 1.54e+00 4.22e-01 1.45e+01 angle pdb=" CA LEU H 501 " pdb=" CB LEU H 501 " pdb=" CG LEU H 501 " ideal model delta sigma weight residual 116.30 129.06 -12.76 3.50e+00 8.16e-02 1.33e+01 ... (remaining 14704 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 5518 17.62 - 35.25: 662 35.25 - 52.87: 188 52.87 - 70.49: 47 70.49 - 88.12: 15 Dihedral angle restraints: 6430 sinusoidal: 2511 harmonic: 3919 Sorted by residual: dihedral pdb=" CA GLY H 451 " pdb=" C GLY H 451 " pdb=" N PRO H 452 " pdb=" CA PRO H 452 " ideal model delta harmonic sigma weight residual -180.00 -158.30 -21.70 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA SER H 51 " pdb=" C SER H 51 " pdb=" N ALA H 52 " pdb=" CA ALA H 52 " ideal model delta harmonic sigma weight residual 180.00 158.55 21.45 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA MET I 130 " pdb=" C MET I 130 " pdb=" N PHE I 131 " pdb=" CA PHE I 131 " ideal model delta harmonic sigma weight residual 180.00 159.43 20.57 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 6427 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1314 0.048 - 0.096: 301 0.096 - 0.144: 94 0.144 - 0.192: 6 0.192 - 0.240: 2 Chirality restraints: 1717 Sorted by residual: chirality pdb=" CB ILE H 444 " pdb=" CA ILE H 444 " pdb=" CG1 ILE H 444 " pdb=" CG2 ILE H 444 " both_signs ideal model delta sigma weight residual False 2.64 2.88 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA ILE I 227 " pdb=" N ILE I 227 " pdb=" C ILE I 227 " pdb=" CB ILE I 227 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.52e-01 chirality pdb=" CA PRO I 231 " pdb=" N PRO I 231 " pdb=" C PRO I 231 " pdb=" CB PRO I 231 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.06e-01 ... (remaining 1714 not shown) Planarity restraints: 1869 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA I 226 " -0.012 2.00e-02 2.50e+03 2.54e-02 6.45e+00 pdb=" C ALA I 226 " 0.044 2.00e-02 2.50e+03 pdb=" O ALA I 226 " -0.017 2.00e-02 2.50e+03 pdb=" N ILE I 227 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE I 131 " -0.043 5.00e-02 4.00e+02 6.17e-02 6.09e+00 pdb=" N PRO I 132 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO I 132 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO I 132 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 320 " -0.035 5.00e-02 4.00e+02 5.42e-02 4.70e+00 pdb=" N PRO D 321 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO D 321 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 321 " -0.030 5.00e-02 4.00e+02 ... (remaining 1866 not shown) Histogram of nonbonded interaction distances: 1.06 - 1.83: 7 1.83 - 2.60: 81 2.60 - 3.36: 14220 3.36 - 4.13: 24989 4.13 - 4.90: 45439 Nonbonded interactions: 84736 Sorted by model distance: nonbonded pdb=" O TRP H 246 " pdb=" CD GLU H 249 " model vdw 1.062 3.270 nonbonded pdb=" O TRP H 246 " pdb=" OE2 GLU H 249 " model vdw 1.235 3.040 nonbonded pdb=" O TRP H 246 " pdb=" OE1 GLU H 249 " model vdw 1.314 3.040 nonbonded pdb=" CH2 TRP H 246 " pdb=" OD1 ASP H 248 " model vdw 1.377 3.340 nonbonded pdb=" CZ3 TRP H 246 " pdb=" CE LYS H 250 " model vdw 1.463 3.740 ... (remaining 84731 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 Found NCS groups: ncs_group { reference = chain 'C' selection = (chain 'D' and resid 2 through 372) } 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 group one per residue 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: 1.880 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.380 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 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 : 0.004 0.148 10812 Z= 0.196 Angle : 0.690 12.763 14709 Z= 0.378 Chirality : 0.045 0.240 1717 Planarity : 0.005 0.062 1869 Dihedral : 17.377 88.117 3904 Min Nonbonded Distance : 1.062 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.47 % Favored : 94.46 % Rotamer: Outliers : 0.53 % Allowed : 23.64 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.23), residues: 1354 helix: 1.28 (0.21), residues: 609 sheet: -0.49 (0.37), residues: 197 loop : -1.54 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 324 TYR 0.020 0.001 TYR C 222 PHE 0.022 0.001 PHE I 14 TRP 0.026 0.001 TRP I 260 HIS 0.007 0.001 HIS C 192 Details of bonding type rmsd covalent geometry : bond 0.00373 (10812) covalent geometry : angle 0.69036 (14709) hydrogen bonds : bond 0.15834 ( 529) hydrogen bonds : angle 6.28299 ( 1518) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 199 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 70 PRO cc_start: 0.8335 (Cg_exo) cc_final: 0.7874 (Cg_endo) REVERT: H 464 THR cc_start: 0.8321 (p) cc_final: 0.8075 (p) REVERT: I 108 TYR cc_start: 0.9076 (t80) cc_final: 0.8648 (t80) REVERT: I 123 LYS cc_start: 0.8091 (pttt) cc_final: 0.7878 (tmtt) REVERT: C 238 LYS cc_start: 0.8690 (mmmm) cc_final: 0.8203 (mmmm) REVERT: D 281 MET cc_start: 0.8394 (mmm) cc_final: 0.8161 (mmm) outliers start: 6 outliers final: 2 residues processed: 203 average time/residue: 0.1101 time to fit residues: 30.1073 Evaluate side-chains 131 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 129 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 248 ASP Chi-restraints excluded: chain H residue 249 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 7.9990 chunk 55 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 376 ASN I 157 ASN I 250 GLN C 8 ASN ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.091087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.071988 restraints weight = 27806.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.074699 restraints weight = 14757.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.076503 restraints weight = 9865.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.077517 restraints weight = 7588.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.078408 restraints weight = 6451.968| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10812 Z= 0.152 Angle : 0.647 11.696 14709 Z= 0.328 Chirality : 0.045 0.160 1717 Planarity : 0.005 0.061 1869 Dihedral : 5.017 73.004 1464 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.58 % Allowed : 22.40 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.23), residues: 1354 helix: 1.43 (0.21), residues: 621 sheet: -0.32 (0.36), residues: 203 loop : -1.32 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 104 TYR 0.019 0.002 TYR D 222 PHE 0.025 0.001 PHE I 44 TRP 0.016 0.001 TRP H 246 HIS 0.006 0.001 HIS C 192 Details of bonding type rmsd covalent geometry : bond 0.00346 (10812) covalent geometry : angle 0.64703 (14709) hydrogen bonds : bond 0.04380 ( 529) hydrogen bonds : angle 4.97479 ( 1518) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 137 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 406 ASP cc_start: 0.8246 (m-30) cc_final: 0.7975 (m-30) REVERT: H 445 GLN cc_start: 0.8486 (tp-100) cc_final: 0.8055 (tp40) REVERT: I 68 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7338 (mm-30) REVERT: I 189 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8088 (mp0) REVERT: I 282 GLN cc_start: 0.7808 (OUTLIER) cc_final: 0.7546 (tm-30) REVERT: D 20 LYS cc_start: 0.8787 (tptt) cc_final: 0.8546 (tttm) outliers start: 29 outliers final: 17 residues processed: 161 average time/residue: 0.0834 time to fit residues: 19.4307 Evaluate side-chains 150 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 85 CYS Chi-restraints excluded: chain H residue 249 GLU Chi-restraints excluded: chain I residue 3 MET Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 189 GLU Chi-restraints excluded: chain I residue 227 ILE Chi-restraints excluded: chain I residue 245 LEU Chi-restraints excluded: chain I residue 260 TRP Chi-restraints excluded: chain I residue 282 GLN Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain D residue 194 GLN Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 345 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 61 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 108 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 54 optimal weight: 0.3980 chunk 66 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 71 optimal weight: 0.0970 chunk 37 optimal weight: 6.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 157 ASN ** D 122 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 = 0.3504 r_free = 0.3504 target = 0.094401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.075800 restraints weight = 26989.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.078506 restraints weight = 14143.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.080316 restraints weight = 9420.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.081528 restraints weight = 7238.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.082228 restraints weight = 6072.725| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10812 Z= 0.120 Angle : 0.586 10.801 14709 Z= 0.295 Chirality : 0.044 0.150 1717 Planarity : 0.005 0.051 1869 Dihedral : 4.591 55.660 1462 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.93 % Allowed : 21.60 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.23), residues: 1354 helix: 1.54 (0.21), residues: 621 sheet: -0.09 (0.36), residues: 200 loop : -1.28 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 178 TYR 0.020 0.002 TYR I 108 PHE 0.023 0.001 PHE I 44 TRP 0.012 0.001 TRP I 75 HIS 0.006 0.001 HIS C 192 Details of bonding type rmsd covalent geometry : bond 0.00263 (10812) covalent geometry : angle 0.58584 (14709) hydrogen bonds : bond 0.03981 ( 529) hydrogen bonds : angle 4.70436 ( 1518) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 137 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 445 GLN cc_start: 0.8426 (tp-100) cc_final: 0.8132 (tp40) REVERT: I 108 TYR cc_start: 0.8995 (t80) cc_final: 0.8699 (t80) REVERT: I 282 GLN cc_start: 0.7677 (OUTLIER) cc_final: 0.7468 (tm-30) REVERT: D 281 MET cc_start: 0.8889 (mmm) cc_final: 0.8532 (mmm) outliers start: 33 outliers final: 20 residues processed: 162 average time/residue: 0.0885 time to fit residues: 20.6259 Evaluate side-chains 144 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 65 TRP Chi-restraints excluded: chain H residue 267 VAL Chi-restraints excluded: chain H residue 497 LEU Chi-restraints excluded: chain I residue 3 MET Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 227 ILE Chi-restraints excluded: chain I residue 245 LEU Chi-restraints excluded: chain I residue 252 TYR Chi-restraints excluded: chain I residue 260 TRP Chi-restraints excluded: chain I residue 282 GLN Chi-restraints excluded: chain I residue 286 VAL Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 194 GLN Chi-restraints excluded: chain D residue 345 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 89 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 97 optimal weight: 0.0980 chunk 8 optimal weight: 3.9990 chunk 110 optimal weight: 0.0970 chunk 43 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 30 optimal weight: 0.0270 overall best weight: 1.0238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 317 HIS D 82 GLN D 122 GLN D 163 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.092731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.074183 restraints weight = 27321.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.076846 restraints weight = 14371.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.078639 restraints weight = 9569.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.079792 restraints weight = 7355.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.080436 restraints weight = 6192.150| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10812 Z= 0.133 Angle : 0.585 10.524 14709 Z= 0.294 Chirality : 0.043 0.151 1717 Planarity : 0.004 0.048 1869 Dihedral : 4.048 19.484 1459 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.20 % Allowed : 21.33 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.23), residues: 1354 helix: 1.58 (0.21), residues: 629 sheet: -0.08 (0.36), residues: 209 loop : -1.22 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 324 TYR 0.013 0.001 TYR D 222 PHE 0.021 0.001 PHE I 44 TRP 0.015 0.001 TRP H 246 HIS 0.006 0.001 HIS C 192 Details of bonding type rmsd covalent geometry : bond 0.00303 (10812) covalent geometry : angle 0.58489 (14709) hydrogen bonds : bond 0.03915 ( 529) hydrogen bonds : angle 4.59968 ( 1518) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 128 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 70 PRO cc_start: 0.8501 (Cg_exo) cc_final: 0.8113 (Cg_endo) REVERT: I 108 TYR cc_start: 0.9091 (t80) cc_final: 0.8773 (t80) REVERT: D 281 MET cc_start: 0.8859 (mmm) cc_final: 0.8500 (mmm) outliers start: 36 outliers final: 23 residues processed: 155 average time/residue: 0.0816 time to fit residues: 18.8324 Evaluate side-chains 144 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 65 TRP Chi-restraints excluded: chain H residue 267 VAL Chi-restraints excluded: chain H residue 300 MET Chi-restraints excluded: chain H residue 497 LEU Chi-restraints excluded: chain H residue 509 THR Chi-restraints excluded: chain I residue 3 MET Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain I residue 227 ILE Chi-restraints excluded: chain I residue 245 LEU Chi-restraints excluded: chain I residue 252 TYR Chi-restraints excluded: chain I residue 260 TRP Chi-restraints excluded: chain I residue 286 VAL Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 194 GLN Chi-restraints excluded: chain D residue 345 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 125 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 76 optimal weight: 0.0010 chunk 19 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.090646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.071893 restraints weight = 27295.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.074470 restraints weight = 14518.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.076187 restraints weight = 9766.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.077304 restraints weight = 7572.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.078074 restraints weight = 6416.476| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10812 Z= 0.165 Angle : 0.606 8.167 14709 Z= 0.309 Chirality : 0.044 0.152 1717 Planarity : 0.004 0.046 1869 Dihedral : 4.115 20.052 1459 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 3.47 % Allowed : 21.07 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.23), residues: 1354 helix: 1.67 (0.21), residues: 627 sheet: -0.00 (0.36), residues: 209 loop : -1.30 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 266 TYR 0.018 0.002 TYR I 243 PHE 0.025 0.002 PHE I 44 TRP 0.015 0.001 TRP H 246 HIS 0.006 0.001 HIS C 192 Details of bonding type rmsd covalent geometry : bond 0.00385 (10812) covalent geometry : angle 0.60641 (14709) hydrogen bonds : bond 0.04132 ( 529) hydrogen bonds : angle 4.54641 ( 1518) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 130 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 70 PRO cc_start: 0.8638 (Cg_exo) cc_final: 0.8315 (Cg_endo) REVERT: I 12 ARG cc_start: 0.7035 (mtp180) cc_final: 0.6231 (mtm-85) REVERT: I 68 GLU cc_start: 0.7486 (mm-30) cc_final: 0.6658 (mt-10) REVERT: D 281 MET cc_start: 0.8851 (mmm) cc_final: 0.8554 (mmm) outliers start: 39 outliers final: 30 residues processed: 155 average time/residue: 0.0842 time to fit residues: 19.0084 Evaluate side-chains 151 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 121 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 65 TRP Chi-restraints excluded: chain H residue 267 VAL Chi-restraints excluded: chain H residue 300 MET Chi-restraints excluded: chain H residue 349 MET Chi-restraints excluded: chain H residue 509 THR Chi-restraints excluded: chain I residue 3 MET Chi-restraints excluded: chain I residue 15 ILE Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain I residue 121 LEU Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain I residue 227 ILE Chi-restraints excluded: chain I residue 245 LEU Chi-restraints excluded: chain I residue 252 TYR Chi-restraints excluded: chain I residue 260 TRP Chi-restraints excluded: chain I residue 272 LEU Chi-restraints excluded: chain I residue 286 VAL Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 194 GLN Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 345 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 63 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 95 optimal weight: 8.9990 chunk 109 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 445 GLN D 122 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.088193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.069050 restraints weight = 27732.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.071611 restraints weight = 14876.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.073336 restraints weight = 10019.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.074476 restraints weight = 7769.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.075173 restraints weight = 6573.456| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 10812 Z= 0.222 Angle : 0.647 9.204 14709 Z= 0.328 Chirality : 0.045 0.157 1717 Planarity : 0.005 0.044 1869 Dihedral : 4.241 21.454 1459 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 4.09 % Allowed : 21.16 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.23), residues: 1354 helix: 1.56 (0.21), residues: 629 sheet: 0.01 (0.37), residues: 205 loop : -1.32 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 266 TYR 0.030 0.002 TYR I 108 PHE 0.025 0.002 PHE I 44 TRP 0.015 0.001 TRP I 260 HIS 0.006 0.001 HIS C 180 Details of bonding type rmsd covalent geometry : bond 0.00518 (10812) covalent geometry : angle 0.64711 (14709) hydrogen bonds : bond 0.04455 ( 529) hydrogen bonds : angle 4.64251 ( 1518) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 126 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 70 PRO cc_start: 0.8759 (Cg_exo) cc_final: 0.8510 (Cg_endo) REVERT: H 99 GLN cc_start: 0.8501 (pm20) cc_final: 0.8122 (pm20) REVERT: H 364 ASP cc_start: 0.8000 (t0) cc_final: 0.7310 (t70) REVERT: H 506 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8730 (tt) REVERT: D 281 MET cc_start: 0.8886 (mmm) cc_final: 0.8538 (mmm) outliers start: 46 outliers final: 30 residues processed: 156 average time/residue: 0.0828 time to fit residues: 19.1625 Evaluate side-chains 156 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 125 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain H residue 85 CYS Chi-restraints excluded: chain H residue 267 VAL Chi-restraints excluded: chain H residue 286 VAL Chi-restraints excluded: chain H residue 349 MET Chi-restraints excluded: chain H residue 490 ILE Chi-restraints excluded: chain H residue 506 LEU Chi-restraints excluded: chain H residue 509 THR Chi-restraints excluded: chain I residue 3 MET Chi-restraints excluded: chain I residue 15 ILE Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain I residue 121 LEU Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain I residue 227 ILE Chi-restraints excluded: chain I residue 252 TYR Chi-restraints excluded: chain I residue 260 TRP Chi-restraints excluded: chain I residue 272 LEU Chi-restraints excluded: chain I residue 286 VAL Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 194 GLN Chi-restraints excluded: chain D residue 247 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 85 optimal weight: 5.9990 chunk 117 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 125 optimal weight: 6.9990 chunk 133 optimal weight: 0.0870 chunk 75 optimal weight: 0.6980 chunk 106 optimal weight: 0.0030 chunk 49 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 107 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 overall best weight: 0.4368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.091519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.072722 restraints weight = 27259.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.075361 restraints weight = 14336.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.077105 restraints weight = 9595.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.078277 restraints weight = 7406.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.078963 restraints weight = 6250.152| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10812 Z= 0.119 Angle : 0.607 10.146 14709 Z= 0.302 Chirality : 0.043 0.156 1717 Planarity : 0.004 0.044 1869 Dihedral : 4.134 19.326 1459 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.84 % Allowed : 22.84 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.24), residues: 1354 helix: 1.74 (0.21), residues: 630 sheet: 0.09 (0.37), residues: 209 loop : -1.33 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 324 TYR 0.020 0.002 TYR I 108 PHE 0.029 0.001 PHE I 44 TRP 0.016 0.001 TRP I 75 HIS 0.005 0.001 HIS C 192 Details of bonding type rmsd covalent geometry : bond 0.00259 (10812) covalent geometry : angle 0.60710 (14709) hydrogen bonds : bond 0.03899 ( 529) hydrogen bonds : angle 4.48810 ( 1518) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 135 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 65 TRP cc_start: 0.8518 (m-90) cc_final: 0.8239 (m-90) REVERT: H 70 PRO cc_start: 0.8644 (Cg_exo) cc_final: 0.8377 (Cg_endo) REVERT: H 104 ARG cc_start: 0.6527 (ttt180) cc_final: 0.6303 (ptm160) REVERT: H 364 ASP cc_start: 0.7817 (t0) cc_final: 0.7115 (t70) REVERT: H 506 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8655 (tt) REVERT: I 12 ARG cc_start: 0.6881 (mtp180) cc_final: 0.5934 (ttm110) REVERT: I 68 GLU cc_start: 0.7479 (mm-30) cc_final: 0.6700 (mt-10) REVERT: I 157 ASN cc_start: 0.8913 (OUTLIER) cc_final: 0.8657 (t0) REVERT: D 90 LEU cc_start: 0.9054 (mt) cc_final: 0.8795 (mp) REVERT: D 281 MET cc_start: 0.8895 (mmm) cc_final: 0.8514 (mmm) outliers start: 32 outliers final: 24 residues processed: 155 average time/residue: 0.0866 time to fit residues: 19.2142 Evaluate side-chains 152 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain H residue 85 CYS Chi-restraints excluded: chain H residue 267 VAL Chi-restraints excluded: chain H residue 503 ILE Chi-restraints excluded: chain H residue 506 LEU Chi-restraints excluded: chain I residue 3 MET Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain I residue 157 ASN Chi-restraints excluded: chain I residue 227 ILE Chi-restraints excluded: chain I residue 260 TRP Chi-restraints excluded: chain I residue 272 LEU Chi-restraints excluded: chain I residue 286 VAL Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain D residue 194 GLN Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 345 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 76 optimal weight: 0.3980 chunk 93 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 94 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 87 optimal weight: 0.3980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.097075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.079051 restraints weight = 28718.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.081704 restraints weight = 14472.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.083417 restraints weight = 9405.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.084511 restraints weight = 7162.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.085165 restraints weight = 6015.929| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10812 Z= 0.125 Angle : 0.618 9.885 14709 Z= 0.307 Chirality : 0.043 0.156 1717 Planarity : 0.004 0.044 1869 Dihedral : 4.053 19.067 1459 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.76 % Allowed : 22.76 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.24), residues: 1354 helix: 1.76 (0.21), residues: 630 sheet: 0.10 (0.37), residues: 207 loop : -1.29 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 112 TYR 0.024 0.001 TYR I 108 PHE 0.030 0.001 PHE I 44 TRP 0.016 0.001 TRP I 75 HIS 0.005 0.001 HIS C 192 Details of bonding type rmsd covalent geometry : bond 0.00283 (10812) covalent geometry : angle 0.61824 (14709) hydrogen bonds : bond 0.03815 ( 529) hydrogen bonds : angle 4.46130 ( 1518) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 130 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 70 PRO cc_start: 0.8555 (Cg_exo) cc_final: 0.8161 (Cg_endo) REVERT: H 104 ARG cc_start: 0.6653 (ttt180) cc_final: 0.6220 (ptm160) REVERT: H 364 ASP cc_start: 0.7806 (t0) cc_final: 0.7005 (t70) REVERT: H 465 ASP cc_start: 0.7801 (m-30) cc_final: 0.7438 (m-30) REVERT: H 506 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8655 (tt) REVERT: I 12 ARG cc_start: 0.6835 (OUTLIER) cc_final: 0.5771 (ttm110) REVERT: I 68 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7397 (mm-30) REVERT: I 123 LYS cc_start: 0.7978 (tttt) cc_final: 0.7416 (mmtp) REVERT: I 239 ASP cc_start: 0.8297 (t0) cc_final: 0.8006 (t0) REVERT: I 269 MET cc_start: 0.8034 (OUTLIER) cc_final: 0.7806 (ttp) REVERT: D 90 LEU cc_start: 0.9184 (mt) cc_final: 0.8869 (mp) REVERT: D 281 MET cc_start: 0.8886 (mmm) cc_final: 0.8451 (mmm) outliers start: 31 outliers final: 25 residues processed: 148 average time/residue: 0.0908 time to fit residues: 19.6787 Evaluate side-chains 152 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 124 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain H residue 85 CYS Chi-restraints excluded: chain H residue 267 VAL Chi-restraints excluded: chain H residue 497 LEU Chi-restraints excluded: chain H residue 506 LEU Chi-restraints excluded: chain I residue 3 MET Chi-restraints excluded: chain I residue 12 ARG Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain I residue 227 ILE Chi-restraints excluded: chain I residue 260 TRP Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain I residue 272 LEU Chi-restraints excluded: chain I residue 286 VAL Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 172 MET Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 194 GLN Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 345 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 71 optimal weight: 2.9990 chunk 114 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 69 optimal weight: 0.0050 chunk 125 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 overall best weight: 1.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 122 GLN ** D 140 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 = 0.3530 r_free = 0.3530 target = 0.092635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.073322 restraints weight = 28302.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.076159 restraints weight = 14156.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.078001 restraints weight = 9248.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.079157 restraints weight = 7051.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.079798 restraints weight = 5940.104| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10812 Z= 0.166 Angle : 0.646 10.704 14709 Z= 0.321 Chirality : 0.045 0.166 1717 Planarity : 0.004 0.043 1869 Dihedral : 4.153 20.251 1459 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.02 % Allowed : 22.76 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.24), residues: 1354 helix: 1.66 (0.21), residues: 631 sheet: 0.12 (0.37), residues: 205 loop : -1.26 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 112 TYR 0.023 0.002 TYR I 108 PHE 0.028 0.002 PHE I 44 TRP 0.018 0.001 TRP I 75 HIS 0.005 0.001 HIS C 192 Details of bonding type rmsd covalent geometry : bond 0.00387 (10812) covalent geometry : angle 0.64575 (14709) hydrogen bonds : bond 0.04176 ( 529) hydrogen bonds : angle 4.54207 ( 1518) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 123 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 65 TRP cc_start: 0.8404 (m-90) cc_final: 0.7918 (m-90) REVERT: H 364 ASP cc_start: 0.7917 (t0) cc_final: 0.7146 (t70) REVERT: H 506 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8618 (tt) REVERT: I 68 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7402 (mm-30) REVERT: I 123 LYS cc_start: 0.8017 (tttt) cc_final: 0.7459 (mmtp) REVERT: I 252 TYR cc_start: 0.8815 (OUTLIER) cc_final: 0.8572 (t80) REVERT: I 269 MET cc_start: 0.8034 (OUTLIER) cc_final: 0.7794 (ttp) REVERT: C 67 MET cc_start: 0.8023 (mmt) cc_final: 0.7806 (mmt) REVERT: D 90 LEU cc_start: 0.9249 (mt) cc_final: 0.8967 (mp) REVERT: D 281 MET cc_start: 0.8879 (mmm) cc_final: 0.8437 (mmm) outliers start: 34 outliers final: 24 residues processed: 148 average time/residue: 0.0884 time to fit residues: 19.2466 Evaluate side-chains 147 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain H residue 85 CYS Chi-restraints excluded: chain H residue 267 VAL Chi-restraints excluded: chain H residue 497 LEU Chi-restraints excluded: chain H residue 506 LEU Chi-restraints excluded: chain H residue 509 THR Chi-restraints excluded: chain I residue 3 MET Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain I residue 227 ILE Chi-restraints excluded: chain I residue 252 TYR Chi-restraints excluded: chain I residue 260 TRP Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain I residue 272 LEU Chi-restraints excluded: chain I residue 286 VAL Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 194 GLN Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 345 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 90 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 5 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 63 optimal weight: 0.2980 chunk 60 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.093239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.074650 restraints weight = 27648.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.077303 restraints weight = 14017.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.079044 restraints weight = 9187.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.080165 restraints weight = 7020.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.080826 restraints weight = 5905.696| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10812 Z= 0.152 Angle : 0.648 10.670 14709 Z= 0.321 Chirality : 0.044 0.177 1717 Planarity : 0.004 0.043 1869 Dihedral : 4.148 20.055 1459 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 2.67 % Allowed : 23.02 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.54 (0.24), residues: 1354 helix: 1.69 (0.21), residues: 630 sheet: 0.18 (0.38), residues: 202 loop : -1.26 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 112 TYR 0.026 0.002 TYR D 84 PHE 0.030 0.001 PHE I 44 TRP 0.019 0.001 TRP I 75 HIS 0.005 0.001 HIS C 192 Details of bonding type rmsd covalent geometry : bond 0.00354 (10812) covalent geometry : angle 0.64837 (14709) hydrogen bonds : bond 0.04025 ( 529) hydrogen bonds : angle 4.51072 ( 1518) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2708 Ramachandran restraints generated. 1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 125 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 65 TRP cc_start: 0.8440 (m-90) cc_final: 0.7866 (m-90) REVERT: H 364 ASP cc_start: 0.7896 (t0) cc_final: 0.7142 (t70) REVERT: H 506 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8621 (tt) REVERT: I 50 TRP cc_start: 0.6451 (p-90) cc_final: 0.6204 (p-90) REVERT: I 123 LYS cc_start: 0.8064 (tttt) cc_final: 0.7489 (mmtp) REVERT: I 238 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.8012 (mpp80) REVERT: I 252 TYR cc_start: 0.8781 (OUTLIER) cc_final: 0.8496 (t80) REVERT: I 269 MET cc_start: 0.7986 (OUTLIER) cc_final: 0.7734 (ttp) REVERT: C 67 MET cc_start: 0.7984 (mmt) cc_final: 0.7767 (mmt) REVERT: D 281 MET cc_start: 0.8886 (mmm) cc_final: 0.8433 (mmm) outliers start: 30 outliers final: 23 residues processed: 145 average time/residue: 0.0933 time to fit residues: 19.9506 Evaluate side-chains 147 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 85 CYS Chi-restraints excluded: chain H residue 267 VAL Chi-restraints excluded: chain H residue 497 LEU Chi-restraints excluded: chain H residue 506 LEU Chi-restraints excluded: chain H residue 509 THR Chi-restraints excluded: chain I residue 3 MET Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain I residue 121 LEU Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain I residue 238 ARG Chi-restraints excluded: chain I residue 252 TYR Chi-restraints excluded: chain I residue 260 TRP Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain I residue 272 LEU Chi-restraints excluded: chain I residue 286 VAL Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 194 GLN Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 345 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 62 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 126 optimal weight: 0.0070 chunk 39 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 overall best weight: 0.7002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.096487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.079031 restraints weight = 28278.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.081614 restraints weight = 14181.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.083310 restraints weight = 9181.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.084208 restraints weight = 6920.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.085044 restraints weight = 5860.274| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10812 Z= 0.126 Angle : 0.638 10.467 14709 Z= 0.314 Chirality : 0.044 0.171 1717 Planarity : 0.004 0.043 1869 Dihedral : 4.133 20.274 1459 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.31 % Allowed : 23.64 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.24), residues: 1354 helix: 1.78 (0.21), residues: 630 sheet: 0.17 (0.37), residues: 207 loop : -1.31 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 104 TYR 0.021 0.001 TYR I 108 PHE 0.030 0.001 PHE I 44 TRP 0.018 0.001 TRP I 75 HIS 0.005 0.001 HIS C 192 Details of bonding type rmsd covalent geometry : bond 0.00285 (10812) covalent geometry : angle 0.63790 (14709) hydrogen bonds : bond 0.03845 ( 529) hydrogen bonds : angle 4.44203 ( 1518) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1548.14 seconds wall clock time: 27 minutes 28.13 seconds (1648.13 seconds total)