Starting phenix.real_space_refine on Fri Sep 11 09:36:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6k42_9912/09_2026/6k42_9912.cif Found real_map, /net/cci-nas-00/data/ceres_data/6k42_9912/09_2026/6k42_9912.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6k42_9912/09_2026/6k42_9912.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6k42_9912/09_2026/6k42_9912.map" model { file = "/net/cci-nas-00/data/ceres_data/6k42_9912/09_2026/6k42_9912.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6k42_9912/09_2026/6k42_9912.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6k42_9912/09_2026/6k42_9912.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6k42_9912/09_2026/6k42_9912.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 5630 2.51 5 N 1510 2.21 5 O 1618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8816 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1759 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Chain: "B" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2616 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "R" Number of atoms: 2201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2201 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 12, 'TRANS': 257} Chain breaks: 3 Chain: "H" Number of atoms: 1801 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 233, 1793 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Conformer: "B" Number of residues, atoms: 233, 1793 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 bond proxies already assigned to first conformer: 1828 Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'CZX': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N LYS H 236 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS H 236 " occ=0.00 Time building chain proxies: 2.18, per 1000 atoms: 0.25 Number of scatterers: 8816 At special positions: 0 Unit cell: (112.08, 110.679, 128.892, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 58 16.00 O 1618 8.00 N 1510 7.00 C 5630 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 164 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 294.8 milliseconds 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2098 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 13 sheets defined 33.1% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 8 through 33 removed outlier: 4.114A pdb=" N GLU A 14 " --> pdb=" O LYS A 10 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE A 19 " --> pdb=" O ARG A 15 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASP A 20 " --> pdb=" O SER A 16 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU A 23 " --> pdb=" O ILE A 19 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLU A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 216 removed outlier: 3.653A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 255 removed outlier: 3.871A pdb=" N LYS A 248 " --> pdb=" O HIS A 244 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 276 removed outlier: 3.823A pdb=" N GLU A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.527A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE A 303 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP A 309 " --> pdb=" O CYS A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 351 Processing helix chain 'B' and resid 3 through 19 removed outlier: 3.770A pdb=" N ALA B 11 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 22 removed outlier: 4.101A pdb=" N LEU G 15 " --> pdb=" O GLN G 11 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 55 through 59 removed outlier: 3.612A pdb=" N ASN G 59 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 12 through 29 Processing helix chain 'R' and resid 29 through 39 Processing helix chain 'R' and resid 48 through 74 removed outlier: 3.729A pdb=" N LEU R 64 " --> pdb=" O LEU R 60 " (cutoff:3.500A) Proline residue: R 67 - end of helix Processing helix chain 'R' and resid 83 through 116 removed outlier: 4.332A pdb=" N VAL R 87 " --> pdb=" O THR R 83 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N CYS R 96 " --> pdb=" O ASP R 92 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER R 99 " --> pdb=" O PHE R 95 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL R 114 " --> pdb=" O ARG R 110 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ARG R 116 " --> pdb=" O TRP R 112 " (cutoff:3.500A) Processing helix chain 'R' and resid 117 through 122 removed outlier: 3.942A pdb=" N ASN R 121 " --> pdb=" O ALA R 117 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER R 122 " --> pdb=" O LEU R 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 117 through 122' Processing helix chain 'R' and resid 125 through 145 Processing helix chain 'R' and resid 169 through 181 removed outlier: 3.858A pdb=" N LEU R 174 " --> pdb=" O ALA R 170 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA R 175 " --> pdb=" O TRP R 171 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 202 Processing helix chain 'R' and resid 359 through 397 removed outlier: 3.632A pdb=" N THR R 364 " --> pdb=" O ARG R 360 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG R 365 " --> pdb=" O ALA R 361 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS R 367 " --> pdb=" O LEU R 363 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE R 377 " --> pdb=" O LEU R 373 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N PHE R 380 " --> pdb=" O VAL R 376 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL R 381 " --> pdb=" O ILE R 377 " (cutoff:3.500A) Proline residue: R 386 - end of helix removed outlier: 3.877A pdb=" N GLY R 394 " --> pdb=" O SER R 390 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ALA R 395 " --> pdb=" O TYR R 391 " (cutoff:3.500A) Processing helix chain 'R' and resid 406 through 417 removed outlier: 3.813A pdb=" N PHE R 410 " --> pdb=" O GLY R 406 " (cutoff:3.500A) Processing helix chain 'R' and resid 417 through 429 Proline residue: R 423 - end of helix removed outlier: 3.745A pdb=" N TYR R 426 " --> pdb=" O ASN R 422 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N THR R 427 " --> pdb=" O PRO R 423 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE R 428 " --> pdb=" O VAL R 424 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N PHE R 429 " --> pdb=" O ILE R 425 " (cutoff:3.500A) Processing helix chain 'R' and resid 430 through 442 Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 190 removed outlier: 3.800A pdb=" N CYS A 224 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N HIS A 322 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU A 268 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 51 removed outlier: 3.840A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 61 through 62 removed outlier: 3.527A pdb=" N HIS B 62 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.168A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 7.114A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 190 through 192 removed outlier: 4.099A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.736A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 277 Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AB1, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.621A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 128 through 130 removed outlier: 3.642A pdb=" N ARG H 148 " --> pdb=" O THR H 129 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 135 through 136 removed outlier: 6.109A pdb=" N VAL H 135 " --> pdb=" O GLU H 234 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N TRP H 164 " --> pdb=" O LEU H 176 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 191 through 196 339 hydrogen bonds defined for protein. 966 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: 1.45 Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2622 1.34 - 1.46: 1721 1.46 - 1.58: 4582 1.58 - 1.70: 1 1.70 - 1.82: 79 Bond restraints: 9005 Sorted by residual: bond pdb=" C09 CZX R 501 " pdb=" C12 CZX R 501 " ideal model delta sigma weight residual 1.385 1.529 -0.144 2.00e-02 2.50e+03 5.17e+01 bond pdb=" C11 CZX R 501 " pdb=" C12 CZX R 501 " ideal model delta sigma weight residual 1.386 1.528 -0.142 2.00e-02 2.50e+03 5.07e+01 bond pdb=" C08 CZX R 501 " pdb=" C11 CZX R 501 " ideal model delta sigma weight residual 1.392 1.528 -0.136 2.00e-02 2.50e+03 4.62e+01 bond pdb=" C04 CZX R 501 " pdb=" C09 CZX R 501 " ideal model delta sigma weight residual 1.393 1.526 -0.133 2.00e-02 2.50e+03 4.41e+01 bond pdb=" C04 CZX R 501 " pdb=" C05 CZX R 501 " ideal model delta sigma weight residual 1.403 1.530 -0.127 2.00e-02 2.50e+03 4.01e+01 ... (remaining 9000 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 11801 1.94 - 3.87: 316 3.87 - 5.81: 45 5.81 - 7.75: 20 7.75 - 9.69: 9 Bond angle restraints: 12191 Sorted by residual: angle pdb=" N ILE R 396 " pdb=" CA ILE R 396 " pdb=" C ILE R 396 " ideal model delta sigma weight residual 110.82 101.31 9.51 9.70e-01 1.06e+00 9.61e+01 angle pdb=" C ASN H 157 " pdb=" N GLY H 158 " pdb=" CA GLY H 158 " ideal model delta sigma weight residual 121.70 131.39 -9.69 1.80e+00 3.09e-01 2.90e+01 angle pdb=" C TYR R 79 " pdb=" N PHE R 80 " pdb=" CA PHE R 80 " ideal model delta sigma weight residual 121.54 130.87 -9.33 1.91e+00 2.74e-01 2.39e+01 angle pdb=" C PHE R 80 " pdb=" N ARG R 81 " pdb=" CA ARG R 81 " ideal model delta sigma weight residual 121.54 130.81 -9.27 1.91e+00 2.74e-01 2.35e+01 angle pdb=" CA ALA R 395 " pdb=" C ALA R 395 " pdb=" N ILE R 396 " ideal model delta sigma weight residual 118.81 113.25 5.56 1.15e+00 7.56e-01 2.34e+01 ... (remaining 12186 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.97: 5104 14.97 - 29.95: 169 29.95 - 44.92: 56 44.92 - 59.89: 8 59.89 - 74.86: 3 Dihedral angle restraints: 5340 sinusoidal: 2094 harmonic: 3246 Sorted by residual: dihedral pdb=" CA PRO R 146 " pdb=" C PRO R 146 " pdb=" N PRO R 147 " pdb=" CA PRO R 147 " ideal model delta harmonic sigma weight residual 180.00 155.62 24.38 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA ILE A 19 " pdb=" C ILE A 19 " pdb=" N ASP A 20 " pdb=" CA ASP A 20 " ideal model delta harmonic sigma weight residual 180.00 159.00 21.00 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 59.10 33.90 1 1.00e+01 1.00e-02 1.63e+01 ... (remaining 5337 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1139 0.061 - 0.123: 198 0.123 - 0.184: 32 0.184 - 0.246: 2 0.246 - 0.307: 2 Chirality restraints: 1373 Sorted by residual: chirality pdb=" CA ILE R 396 " pdb=" N ILE R 396 " pdb=" C ILE R 396 " pdb=" CB ILE R 396 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" C03 CZX R 501 " pdb=" C04 CZX R 501 " pdb=" C06 CZX R 501 " pdb=" C07 CZX R 501 " both_signs ideal model delta sigma weight residual False -2.47 -2.76 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CA CYS R 397 " pdb=" N CYS R 397 " pdb=" C CYS R 397 " pdb=" CB CYS R 397 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 1370 not shown) Planarity restraints: 1537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO R 146 " 0.063 5.00e-02 4.00e+02 9.39e-02 1.41e+01 pdb=" N PRO R 147 " -0.162 5.00e-02 4.00e+02 pdb=" CA PRO R 147 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO R 147 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 340 " -0.012 2.00e-02 2.50e+03 2.42e-02 5.85e+00 pdb=" C THR A 340 " 0.042 2.00e-02 2.50e+03 pdb=" O THR A 340 " -0.016 2.00e-02 2.50e+03 pdb=" N ASP A 341 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA R 395 " 0.011 2.00e-02 2.50e+03 2.40e-02 5.78e+00 pdb=" C ALA R 395 " -0.042 2.00e-02 2.50e+03 pdb=" O ALA R 395 " 0.016 2.00e-02 2.50e+03 pdb=" N ILE R 396 " 0.014 2.00e-02 2.50e+03 ... (remaining 1534 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2380 2.81 - 3.33: 7240 3.33 - 3.86: 13758 3.86 - 4.38: 15383 4.38 - 4.90: 27036 Nonbonded interactions: 65797 Sorted by model distance: nonbonded pdb=" OG SER R 69 " pdb=" OH TYR R 88 " model vdw 2.288 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.302 3.040 nonbonded pdb=" O PRO R 423 " pdb=" OG1 THR R 427 " model vdw 2.323 3.040 nonbonded pdb=" O LEU B 30 " pdb=" OG1 THR B 34 " model vdw 2.343 3.040 nonbonded pdb=" O CYS R 397 " pdb=" N CYS R 401 " model vdw 2.345 3.120 ... (remaining 65792 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 0.010 Normalize map: mean=0, sd=1: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 9.370 Find NCS groups from input model: 0.050 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: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6300 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.144 9008 Z= 0.269 Angle : 0.823 9.687 12197 Z= 0.478 Chirality : 0.049 0.307 1373 Planarity : 0.007 0.094 1537 Dihedral : 9.197 74.864 3233 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.31 % Allowed : 1.78 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.19 % 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: -4.37 (0.19), residues: 1095 helix: -2.64 (0.19), residues: 340 sheet: -2.22 (0.30), residues: 242 loop : -3.42 (0.21), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 68 TYR 0.017 0.002 TYR R 79 PHE 0.031 0.002 PHE R 369 TRP 0.015 0.001 TRP B 211 HIS 0.010 0.001 HIS R 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.27 ( 9005) covalent geometry : angle 0.82290 / 0.48 (12191) SS BOND : bond 0.00189 / 0.09 ( 3) SS BOND : angle 1.11556 / 0.45 ( 6) hydrogen bonds : bond 0.16614 / 10.50 ( 339) hydrogen bonds : angle 7.06261 / 4.92 ( 966) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 431 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ILE cc_start: 0.7535 (pp) cc_final: 0.7228 (pp) REVERT: A 49 ILE cc_start: 0.6715 (pt) cc_final: 0.6464 (pt) REVERT: A 50 VAL cc_start: 0.6760 (m) cc_final: 0.6497 (m) REVERT: B 43 ILE cc_start: 0.7437 (mm) cc_final: 0.6312 (mm) REVERT: B 153 ASP cc_start: 0.6922 (p0) cc_final: 0.6720 (p0) REVERT: B 280 LYS cc_start: 0.6658 (tptt) cc_final: 0.6202 (tptm) REVERT: B 313 ASN cc_start: 0.7856 (t0) cc_final: 0.7341 (m-40) REVERT: R 102 HIS cc_start: 0.6568 (m-70) cc_final: 0.5991 (m-70) REVERT: R 414 ILE cc_start: 0.7376 (mm) cc_final: 0.7144 (mm) REVERT: R 429 PHE cc_start: 0.6872 (m-10) cc_final: 0.6649 (m-10) REVERT: H 58 ILE cc_start: 0.8045 (mt) cc_final: 0.7842 (mt) outliers start: 1 outliers final: 1 residues processed: 431 average time/residue: 0.1062 time to fit residues: 60.7518 Evaluate side-chains 282 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 281 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 0.0980 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.0980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.4980 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 GLN A 244 HIS A 304 GLN A 346 ASN B 16 ASN B 75 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN B 311 HIS R 30 ASN R 121 ASN ** R 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 418 ASN H 155 HIS H 159 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.181938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.163283 restraints weight = 23119.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.163738 restraints weight = 22778.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.165683 restraints weight = 18217.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.166467 restraints weight = 11353.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.167528 restraints weight = 10497.509| |-----------------------------------------------------------------------------| r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3814 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3814 r_free = 0.3814 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3814 r_free = 0.3814 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3814 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9008 Z= 0.153 Angle : 0.637 6.926 12197 Z= 0.340 Chirality : 0.044 0.275 1373 Planarity : 0.005 0.080 1537 Dihedral : 4.696 22.590 1217 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.21 % Allowed : 2.20 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.19 % 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: -2.89 (0.22), residues: 1095 helix: -0.57 (0.26), residues: 337 sheet: -1.78 (0.31), residues: 247 loop : -2.97 (0.23), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 314 TYR 0.016 0.002 TYR H 216 PHE 0.032 0.003 PHE R 369 TRP 0.019 0.002 TRP R 84 HIS 0.008 0.001 HIS H 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 ( 9005) covalent geometry : angle 0.63659 / 0.34 (12191) SS BOND : bond 0.00285 / 0.14 ( 3) SS BOND : angle 1.48226 / 0.59 ( 6) hydrogen bonds : bond 0.03835 / 2.56 ( 339) hydrogen bonds : angle 5.11897 / 3.61 ( 966) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 332 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 VAL cc_start: 0.7108 (m) cc_final: 0.6509 (m) REVERT: A 198 MET cc_start: 0.7051 (tpp) cc_final: 0.6785 (ttm) REVERT: A 227 LEU cc_start: 0.7399 (mt) cc_final: 0.6998 (mt) REVERT: A 246 SER cc_start: 0.9011 (m) cc_final: 0.8587 (m) REVERT: A 346 ASN cc_start: 0.8890 (m-40) cc_final: 0.8502 (m-40) REVERT: B 57 LYS cc_start: 0.6723 (mttt) cc_final: 0.6501 (mttm) REVERT: B 68 ARG cc_start: 0.7976 (tpt-90) cc_final: 0.7080 (ttt-90) REVERT: B 280 LYS cc_start: 0.7204 (tptt) cc_final: 0.6692 (tptm) REVERT: B 313 ASN cc_start: 0.7985 (t0) cc_final: 0.7642 (m-40) REVERT: B 322 ASP cc_start: 0.6466 (t0) cc_final: 0.6167 (t0) REVERT: R 65 ILE cc_start: 0.7873 (mm) cc_final: 0.7625 (tt) REVERT: R 414 ILE cc_start: 0.7593 (mm) cc_final: 0.7338 (mm) REVERT: R 418 ASN cc_start: 0.5703 (t0) cc_final: 0.5089 (t0) REVERT: H 39 GLN cc_start: 0.6233 (tp40) cc_final: 0.5883 (tt0) REVERT: H 96 CYS cc_start: 0.4077 (p) cc_final: 0.3876 (p) outliers start: 0 outliers final: 0 residues processed: 332 average time/residue: 0.0828 time to fit residues: 38.6291 Evaluate side-chains 261 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 261 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 81 optimal weight: 0.6980 chunk 84 optimal weight: 0.0270 chunk 70 optimal weight: 0.3980 chunk 97 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN B 75 GLN B 220 GLN B 239 ASN ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN R 30 ASN R 362 GLN ** R 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 155 HIS ** H 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.176442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.157729 restraints weight = 26107.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.160640 restraints weight = 31906.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.162024 restraints weight = 17740.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.163517 restraints weight = 12071.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.163771 restraints weight = 11136.542| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3777 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3777 r_free = 0.3777 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3777 r_free = 0.3777 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3777 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.4741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9008 Z= 0.144 Angle : 0.614 8.395 12197 Z= 0.326 Chirality : 0.043 0.220 1373 Planarity : 0.005 0.070 1537 Dihedral : 4.648 23.666 1217 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.21 % Allowed : 2.09 % Favored : 97.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.19 % 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: -2.23 (0.24), residues: 1095 helix: 0.19 (0.27), residues: 337 sheet: -1.73 (0.31), residues: 248 loop : -2.54 (0.24), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 49 TYR 0.013 0.002 TYR B 59 PHE 0.028 0.002 PHE R 369 TRP 0.018 0.002 TRP B 211 HIS 0.008 0.002 HIS H 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 9005) covalent geometry : angle 0.61337 / 0.33 (12191) SS BOND : bond 0.00333 / 0.17 ( 3) SS BOND : angle 1.47207 / 0.64 ( 6) hydrogen bonds : bond 0.03576 / 2.36 ( 339) hydrogen bonds : angle 4.89402 / 3.46 ( 966) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 333 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ILE cc_start: 0.8275 (pt) cc_final: 0.8016 (mt) REVERT: B 57 LYS cc_start: 0.7593 (mttt) cc_final: 0.7275 (mttm) REVERT: B 68 ARG cc_start: 0.8097 (tpt-90) cc_final: 0.7567 (ttt-90) REVERT: B 261 LEU cc_start: 0.8178 (mt) cc_final: 0.7866 (mt) REVERT: B 280 LYS cc_start: 0.7040 (tptt) cc_final: 0.6608 (tmtt) REVERT: B 313 ASN cc_start: 0.8089 (t0) cc_final: 0.7855 (m110) REVERT: G 42 GLU cc_start: 0.6196 (pp20) cc_final: 0.5913 (pp20) REVERT: G 62 ARG cc_start: 0.6084 (mtp180) cc_final: 0.5834 (tpp-160) REVERT: R 414 ILE cc_start: 0.7985 (mm) cc_final: 0.7686 (mm) REVERT: H 39 GLN cc_start: 0.6252 (tp40) cc_final: 0.5867 (tt0) REVERT: H 58 ILE cc_start: 0.8159 (mt) cc_final: 0.7927 (mt) REVERT: H 103 TYR cc_start: 0.7230 (t80) cc_final: 0.6967 (t80) outliers start: 0 outliers final: 0 residues processed: 333 average time/residue: 0.0960 time to fit residues: 43.7660 Evaluate side-chains 266 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 17 optimal weight: 0.0030 chunk 82 optimal weight: 1.9990 chunk 22 optimal weight: 0.2980 chunk 14 optimal weight: 0.6980 chunk 10 optimal weight: 0.4980 chunk 61 optimal weight: 0.1980 chunk 6 optimal weight: 0.3980 chunk 42 optimal weight: 0.0370 chunk 9 optimal weight: 0.3980 chunk 62 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 overall best weight: 0.1868 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 GLN A 304 GLN ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 11 GLN R 30 ASN ** R 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 362 GLN R 418 ASN R 422 ASN H 155 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.177555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.158290 restraints weight = 21482.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.158603 restraints weight = 24852.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.160010 restraints weight = 17896.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.160758 restraints weight = 13176.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.161219 restraints weight = 11668.301| |-----------------------------------------------------------------------------| r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3754 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3754 r_free = 0.3754 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3754 r_free = 0.3754 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3754 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.5131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9008 Z= 0.111 Angle : 0.594 7.186 12197 Z= 0.313 Chirality : 0.043 0.269 1373 Planarity : 0.004 0.062 1537 Dihedral : 4.459 23.576 1217 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.31 % Allowed : 1.88 % Favored : 97.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.24), residues: 1095 helix: 0.59 (0.28), residues: 339 sheet: -1.54 (0.32), residues: 240 loop : -2.43 (0.24), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 98 TYR 0.017 0.001 TYR R 416 PHE 0.026 0.002 PHE R 369 TRP 0.014 0.001 TRP R 84 HIS 0.006 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 ( 9005) covalent geometry : angle 0.59343 / 0.31 (12191) SS BOND : bond 0.00785 / 0.38 ( 3) SS BOND : angle 1.06689 / 0.48 ( 6) hydrogen bonds : bond 0.03275 / 2.15 ( 339) hydrogen bonds : angle 4.72292 / 3.33 ( 966) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 328 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: A 19 ILE cc_start: 0.8331 (pt) cc_final: 0.8082 (mt) REVERT: A 246 SER cc_start: 0.8951 (m) cc_final: 0.8654 (m) REVERT: A 339 VAL cc_start: 0.8913 (t) cc_final: 0.8487 (t) REVERT: B 33 ILE cc_start: 0.7383 (mm) cc_final: 0.7019 (mm) REVERT: B 68 ARG cc_start: 0.8070 (tpt-90) cc_final: 0.7492 (ttt-90) REVERT: B 105 TYR cc_start: 0.7414 (t80) cc_final: 0.7124 (t80) REVERT: B 120 ILE cc_start: 0.7453 (mt) cc_final: 0.7167 (mt) REVERT: B 188 MET cc_start: 0.8268 (tpp) cc_final: 0.7783 (mpp) REVERT: B 280 LYS cc_start: 0.6967 (tptt) cc_final: 0.6633 (tmtt) REVERT: R 98 SER cc_start: 0.8697 (p) cc_final: 0.8397 (p) REVERT: R 102 HIS cc_start: 0.7344 (m-70) cc_final: 0.7055 (m-70) REVERT: R 414 ILE cc_start: 0.7956 (mm) cc_final: 0.7570 (mm) REVERT: R 422 ASN cc_start: 0.6624 (m-40) cc_final: 0.6346 (m110) REVERT: H 103 TYR cc_start: 0.7195 (t80) cc_final: 0.6977 (t80) REVERT: H 127 VAL cc_start: 0.6422 (t) cc_final: 0.5831 (t) outliers start: 1 outliers final: 0 residues processed: 329 average time/residue: 0.0937 time to fit residues: 42.6149 Evaluate side-chains 269 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 65 optimal weight: 4.9990 chunk 27 optimal weight: 0.0010 chunk 22 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 89 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN A 213 HIS A 304 GLN B 16 ASN ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS G 11 GLN R 30 ASN R 121 ASN ** R 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 362 GLN R 418 ASN H 155 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.166917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.149399 restraints weight = 17445.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.150406 restraints weight = 18276.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.150671 restraints weight = 13690.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.150278 restraints weight = 12962.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.150934 restraints weight = 10593.378| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3638 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3638 r_free = 0.3638 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3638 r_free = 0.3638 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3638 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.6027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9008 Z= 0.162 Angle : 0.657 8.146 12197 Z= 0.344 Chirality : 0.045 0.303 1373 Planarity : 0.005 0.061 1537 Dihedral : 4.683 18.856 1217 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.31 % Allowed : 1.88 % Favored : 97.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.24), residues: 1095 helix: 0.61 (0.28), residues: 335 sheet: -1.39 (0.33), residues: 243 loop : -2.32 (0.24), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 38 TYR 0.013 0.002 TYR B 59 PHE 0.024 0.002 PHE R 369 TRP 0.023 0.002 TRP H 111 HIS 0.006 0.002 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 ( 9005) covalent geometry : angle 0.65584 / 0.34 (12191) SS BOND : bond 0.00447 / 0.22 ( 3) SS BOND : angle 1.67303 / 0.73 ( 6) hydrogen bonds : bond 0.03665 / 2.41 ( 339) hydrogen bonds : angle 4.81580 / 3.39 ( 966) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 331 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ILE cc_start: 0.8757 (pt) cc_final: 0.8458 (mt) REVERT: A 210 LYS cc_start: 0.8734 (mmtt) cc_final: 0.8107 (mmmt) REVERT: A 339 VAL cc_start: 0.8822 (t) cc_final: 0.8586 (t) REVERT: B 258 ASP cc_start: 0.7837 (t70) cc_final: 0.7626 (t70) REVERT: B 280 LYS cc_start: 0.7190 (tptt) cc_final: 0.6816 (tmtt) REVERT: R 44 ARG cc_start: 0.8294 (mtt180) cc_final: 0.7522 (mtt-85) REVERT: R 171 TRP cc_start: 0.5379 (p-90) cc_final: 0.5155 (p-90) REVERT: R 414 ILE cc_start: 0.7748 (mm) cc_final: 0.7367 (mm) REVERT: H 34 MET cc_start: 0.8234 (mmp) cc_final: 0.7672 (mmt) REVERT: H 68 PHE cc_start: 0.5317 (m-80) cc_final: 0.4991 (m-80) REVERT: H 82 GLN cc_start: 0.6461 (pm20) cc_final: 0.5950 (pm20) REVERT: H 103 TYR cc_start: 0.7691 (t80) cc_final: 0.7458 (t80) REVERT: H 206 ARG cc_start: 0.7523 (ptt90) cc_final: 0.7248 (mmp80) REVERT: H 225 LEU cc_start: 0.8762 (mt) cc_final: 0.8308 (mm) outliers start: 1 outliers final: 0 residues processed: 332 average time/residue: 0.0940 time to fit residues: 43.0793 Evaluate side-chains 264 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 85 optimal weight: 2.9990 chunk 95 optimal weight: 0.0370 chunk 93 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 70 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS A 204 GLN A 304 GLN ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 11 GLN R 30 ASN ** R 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 155 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.165641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.146816 restraints weight = 20000.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.146339 restraints weight = 20497.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.147760 restraints weight = 16977.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.148385 restraints weight = 12225.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.148889 restraints weight = 11282.099| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3613 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3613 r_free = 0.3613 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3613 r_free = 0.3613 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3613 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.6537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9008 Z= 0.141 Angle : 0.639 7.266 12197 Z= 0.335 Chirality : 0.044 0.263 1373 Planarity : 0.004 0.062 1537 Dihedral : 4.683 18.811 1217 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.31 % Allowed : 1.26 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.24), residues: 1095 helix: 0.72 (0.28), residues: 340 sheet: -1.39 (0.32), residues: 253 loop : -2.42 (0.24), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 13 TYR 0.023 0.002 TYR R 416 PHE 0.025 0.002 PHE R 369 TRP 0.019 0.002 TRP R 84 HIS 0.010 0.001 HIS R 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 9005) covalent geometry : angle 0.63811 / 0.33 (12191) SS BOND : bond 0.00826 / 0.40 ( 3) SS BOND : angle 1.52910 / 0.64 ( 6) hydrogen bonds : bond 0.03497 / 2.32 ( 339) hydrogen bonds : angle 4.77138 / 3.36 ( 966) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 312 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 ILE cc_start: 0.8704 (pt) cc_final: 0.8226 (mt) REVERT: A 210 LYS cc_start: 0.8548 (mmtt) cc_final: 0.8212 (mmmt) REVERT: B 68 ARG cc_start: 0.8513 (tpt-90) cc_final: 0.8251 (tpt-90) REVERT: B 86 THR cc_start: 0.8368 (p) cc_final: 0.8056 (p) REVERT: B 88 ASN cc_start: 0.8838 (m-40) cc_final: 0.8400 (m-40) REVERT: B 169 TRP cc_start: 0.8230 (m100) cc_final: 0.8019 (m100) REVERT: B 188 MET cc_start: 0.8915 (tpp) cc_final: 0.8465 (mpp) REVERT: B 280 LYS cc_start: 0.6994 (tptt) cc_final: 0.6736 (tmtt) REVERT: B 322 ASP cc_start: 0.6432 (t0) cc_final: 0.6193 (t0) REVERT: R 102 HIS cc_start: 0.7789 (m-70) cc_final: 0.7222 (m-70) REVERT: R 362 GLN cc_start: 0.5918 (pp30) cc_final: 0.5693 (pp30) REVERT: R 370 THR cc_start: 0.7472 (p) cc_final: 0.7244 (t) REVERT: R 373 LEU cc_start: 0.8292 (mt) cc_final: 0.8047 (mt) REVERT: R 414 ILE cc_start: 0.7878 (mm) cc_final: 0.7564 (mm) REVERT: R 427 THR cc_start: 0.8861 (p) cc_final: 0.8660 (p) REVERT: H 93 MET cc_start: 0.6531 (tpp) cc_final: 0.4603 (ttt) REVERT: H 95 TYR cc_start: 0.7252 (m-80) cc_final: 0.6901 (m-80) REVERT: H 115 THR cc_start: 0.7294 (p) cc_final: 0.6973 (p) REVERT: H 189 ASP cc_start: 0.7473 (t0) cc_final: 0.7248 (t0) REVERT: H 206 ARG cc_start: 0.7434 (ptt90) cc_final: 0.7121 (mmp80) REVERT: H 225 LEU cc_start: 0.8625 (mt) cc_final: 0.8209 (mm) outliers start: 1 outliers final: 0 residues processed: 313 average time/residue: 0.0933 time to fit residues: 40.3325 Evaluate side-chains 274 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 274 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 99 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 51 optimal weight: 0.0670 chunk 62 optimal weight: 0.8980 chunk 79 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 30 optimal weight: 0.1980 chunk 15 optimal weight: 0.0170 chunk 23 optimal weight: 0.0970 overall best weight: 0.2154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 GLN A 244 HIS A 304 GLN ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 11 GLN R 30 ASN R 102 HIS ** R 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 155 HIS H 157 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.169006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.150328 restraints weight = 24063.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.151251 restraints weight = 26641.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.153076 restraints weight = 21798.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.153810 restraints weight = 13221.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.154406 restraints weight = 12634.587| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3668 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3668 r_free = 0.3668 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3668 r_free = 0.3668 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3668 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.6663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9008 Z= 0.114 Angle : 0.620 7.389 12197 Z= 0.323 Chirality : 0.043 0.269 1373 Planarity : 0.004 0.058 1537 Dihedral : 4.495 19.158 1217 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.42 % Allowed : 1.26 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.25), residues: 1095 helix: 0.91 (0.28), residues: 337 sheet: -1.10 (0.32), residues: 250 loop : -2.34 (0.25), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 134 TYR 0.009 0.001 TYR R 196 PHE 0.023 0.002 PHE B 241 TRP 0.019 0.001 TRP R 84 HIS 0.023 0.002 HIS R 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 9005) covalent geometry : angle 0.61918 / 0.32 (12191) SS BOND : bond 0.00297 / 0.15 ( 3) SS BOND : angle 1.39885 / 0.63 ( 6) hydrogen bonds : bond 0.03333 / 2.15 ( 339) hydrogen bonds : angle 4.69472 / 3.29 ( 966) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 304 time to evaluate : 0.271 Fit side-chains REVERT: A 19 ILE cc_start: 0.8613 (pt) cc_final: 0.8338 (mt) REVERT: A 210 LYS cc_start: 0.8599 (mmtt) cc_final: 0.8207 (mmmt) REVERT: B 86 THR cc_start: 0.8421 (p) cc_final: 0.7988 (p) REVERT: B 88 ASN cc_start: 0.8914 (m-40) cc_final: 0.8445 (m-40) REVERT: B 188 MET cc_start: 0.8816 (tpp) cc_final: 0.8399 (mpp) REVERT: B 220 GLN cc_start: 0.7255 (mt0) cc_final: 0.6697 (mp-120) REVERT: B 258 ASP cc_start: 0.7651 (t70) cc_final: 0.7234 (t0) REVERT: B 322 ASP cc_start: 0.6728 (t0) cc_final: 0.6489 (t0) REVERT: R 362 GLN cc_start: 0.5845 (pp30) cc_final: 0.5442 (pp30) REVERT: R 414 ILE cc_start: 0.7856 (mm) cc_final: 0.7523 (mm) REVERT: R 422 ASN cc_start: 0.6436 (m-40) cc_final: 0.5982 (m-40) REVERT: R 427 THR cc_start: 0.8734 (p) cc_final: 0.8475 (p) REVERT: H 81 LEU cc_start: 0.6949 (tt) cc_final: 0.6651 (tt) REVERT: H 93 MET cc_start: 0.6439 (tpp) cc_final: 0.4586 (ttt) REVERT: H 95 TYR cc_start: 0.7204 (m-80) cc_final: 0.6848 (m-80) REVERT: H 138 THR cc_start: 0.6688 (t) cc_final: 0.6230 (m) REVERT: H 206 ARG cc_start: 0.7387 (ptt90) cc_final: 0.7107 (mmp80) outliers start: 2 outliers final: 0 residues processed: 306 average time/residue: 0.0934 time to fit residues: 39.0041 Evaluate side-chains 267 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 18 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 98 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 244 HIS A 304 GLN ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 11 GLN R 30 ASN ** R 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 155 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.162152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.144300 restraints weight = 16724.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.144806 restraints weight = 17326.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.145935 restraints weight = 13862.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.145326 restraints weight = 12752.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.145994 restraints weight = 10327.957| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3581 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3581 r_free = 0.3581 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3581 r_free = 0.3581 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3581 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.7153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 9008 Z= 0.176 Angle : 0.713 11.198 12197 Z= 0.371 Chirality : 0.046 0.258 1373 Planarity : 0.004 0.063 1537 Dihedral : 4.868 19.643 1217 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 0.21 % Allowed : 1.68 % Favored : 98.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.24), residues: 1095 helix: 0.83 (0.28), residues: 341 sheet: -1.13 (0.32), residues: 255 loop : -2.43 (0.24), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 98 TYR 0.018 0.002 TYR H 215 PHE 0.029 0.002 PHE R 21 TRP 0.025 0.002 TRP B 211 HIS 0.005 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 ( 9005) covalent geometry : angle 0.71243 / 0.37 (12191) SS BOND : bond 0.00670 / 0.32 ( 3) SS BOND : angle 1.45280 / 0.64 ( 6) hydrogen bonds : bond 0.03764 / 2.47 ( 339) hydrogen bonds : angle 4.94302 / 3.47 ( 966) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 306 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: A 19 ILE cc_start: 0.8791 (pt) cc_final: 0.8311 (mt) REVERT: A 294 ASN cc_start: 0.8451 (m-40) cc_final: 0.8246 (m-40) REVERT: B 61 MET cc_start: 0.8308 (tmm) cc_final: 0.7842 (tpp) REVERT: B 86 THR cc_start: 0.8501 (p) cc_final: 0.8016 (p) REVERT: B 88 ASN cc_start: 0.8770 (m-40) cc_final: 0.8313 (m-40) REVERT: B 188 MET cc_start: 0.8929 (tpp) cc_final: 0.8457 (mpp) REVERT: B 220 GLN cc_start: 0.7296 (mt0) cc_final: 0.6738 (mp-120) REVERT: B 258 ASP cc_start: 0.7724 (t70) cc_final: 0.7188 (t0) REVERT: B 270 ILE cc_start: 0.8323 (mt) cc_final: 0.8024 (tt) REVERT: G 62 ARG cc_start: 0.6468 (tpp-160) cc_final: 0.6219 (tpp-160) REVERT: R 362 GLN cc_start: 0.6008 (pp30) cc_final: 0.5755 (pp30) REVERT: R 377 ILE cc_start: 0.8373 (tp) cc_final: 0.7924 (tp) REVERT: R 414 ILE cc_start: 0.7966 (mm) cc_final: 0.7636 (mm) REVERT: R 427 THR cc_start: 0.8782 (p) cc_final: 0.8551 (p) REVERT: H 93 MET cc_start: 0.6629 (tpp) cc_final: 0.4829 (ttt) REVERT: H 95 TYR cc_start: 0.7265 (m-80) cc_final: 0.6998 (m-80) REVERT: H 115 THR cc_start: 0.7885 (p) cc_final: 0.7628 (p) REVERT: H 138 THR cc_start: 0.7427 (t) cc_final: 0.6878 (m) REVERT: H 206 ARG cc_start: 0.7460 (ptt90) cc_final: 0.7095 (mmp-170) outliers start: 0 outliers final: 0 residues processed: 306 average time/residue: 0.0968 time to fit residues: 40.1699 Evaluate side-chains 271 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 74 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 15 optimal weight: 0.4980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 GLN A 244 HIS A 304 GLN B 266 HIS G 11 GLN R 30 ASN ** R 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.160351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.141850 restraints weight = 23492.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.142850 restraints weight = 26193.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.144426 restraints weight = 20727.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.144778 restraints weight = 12935.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.145370 restraints weight = 12968.633| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3558 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3558 r_free = 0.3558 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3558 r_free = 0.3558 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3558 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.7531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9008 Z= 0.178 Angle : 0.729 12.146 12197 Z= 0.377 Chirality : 0.047 0.262 1373 Planarity : 0.004 0.060 1537 Dihedral : 4.939 19.383 1217 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 0.21 % Allowed : 0.84 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.24), residues: 1095 helix: 0.72 (0.28), residues: 341 sheet: -1.04 (0.32), residues: 254 loop : -2.39 (0.24), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 98 TYR 0.030 0.002 TYR R 416 PHE 0.032 0.002 PHE R 21 TRP 0.028 0.002 TRP R 84 HIS 0.007 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 ( 9005) covalent geometry : angle 0.72866 / 0.38 (12191) SS BOND : bond 0.00407 / 0.20 ( 3) SS BOND : angle 1.51689 / 0.71 ( 6) hydrogen bonds : bond 0.03852 / 2.55 ( 339) hydrogen bonds : angle 4.92480 / 3.45 ( 966) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 305 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ILE cc_start: 0.8835 (pt) cc_final: 0.8445 (mt) REVERT: A 294 ASN cc_start: 0.8417 (m-40) cc_final: 0.8165 (m-40) REVERT: B 57 LYS cc_start: 0.8320 (mttt) cc_final: 0.8092 (mttm) REVERT: B 61 MET cc_start: 0.8350 (tmm) cc_final: 0.7965 (tpp) REVERT: B 86 THR cc_start: 0.8674 (p) cc_final: 0.8130 (p) REVERT: B 88 ASN cc_start: 0.8724 (m-40) cc_final: 0.8242 (m-40) REVERT: R 131 CYS cc_start: 0.8491 (m) cc_final: 0.8176 (m) REVERT: R 362 GLN cc_start: 0.6060 (pp30) cc_final: 0.5847 (pp30) REVERT: R 370 THR cc_start: 0.7729 (p) cc_final: 0.7357 (t) REVERT: R 377 ILE cc_start: 0.8534 (tp) cc_final: 0.8061 (tp) REVERT: R 382 LEU cc_start: 0.8615 (pp) cc_final: 0.8233 (tt) REVERT: R 414 ILE cc_start: 0.8169 (mm) cc_final: 0.7788 (mm) REVERT: R 422 ASN cc_start: 0.6756 (m-40) cc_final: 0.6545 (m-40) REVERT: H 93 MET cc_start: 0.6734 (tpp) cc_final: 0.5367 (ttt) REVERT: H 115 THR cc_start: 0.8023 (p) cc_final: 0.7732 (p) REVERT: H 138 THR cc_start: 0.7383 (t) cc_final: 0.6671 (m) outliers start: 0 outliers final: 0 residues processed: 305 average time/residue: 0.0998 time to fit residues: 41.0945 Evaluate side-chains 266 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 79 optimal weight: 0.6980 chunk 15 optimal weight: 0.4980 chunk 100 optimal weight: 0.0980 chunk 75 optimal weight: 0.7980 chunk 86 optimal weight: 0.1980 chunk 97 optimal weight: 0.0570 chunk 19 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 41 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 overall best weight: 0.2898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 GLN A 304 GLN G 11 GLN R 30 ASN R 168 GLN ** R 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 157 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.163670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.146454 restraints weight = 17072.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.146601 restraints weight = 19271.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.147648 restraints weight = 14782.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.147517 restraints weight = 11459.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.147935 restraints weight = 10257.804| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3597 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3597 r_free = 0.3597 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3597 r_free = 0.3597 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.3597 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.7651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9008 Z= 0.130 Angle : 0.702 9.535 12197 Z= 0.364 Chirality : 0.046 0.273 1373 Planarity : 0.004 0.062 1537 Dihedral : 4.796 18.318 1217 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.21 % Allowed : 0.31 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.25), residues: 1095 helix: 0.82 (0.29), residues: 337 sheet: -0.90 (0.32), residues: 256 loop : -2.29 (0.24), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 98 TYR 0.019 0.002 TYR R 416 PHE 0.027 0.002 PHE R 21 TRP 0.020 0.002 TRP B 211 HIS 0.008 0.001 HIS A 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 9005) covalent geometry : angle 0.70110 / 0.36 (12191) SS BOND : bond 0.00359 / 0.17 ( 3) SS BOND : angle 1.29939 / 0.62 ( 6) hydrogen bonds : bond 0.03536 / 2.32 ( 339) hydrogen bonds : angle 4.76931 / 3.35 ( 966) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ILE cc_start: 0.8744 (pt) cc_final: 0.8457 (mt) REVERT: A 294 ASN cc_start: 0.8322 (m-40) cc_final: 0.8045 (m110) REVERT: B 61 MET cc_start: 0.8361 (tmm) cc_final: 0.7902 (tpp) REVERT: B 86 THR cc_start: 0.8647 (p) cc_final: 0.8198 (p) REVERT: B 88 ASN cc_start: 0.8948 (m-40) cc_final: 0.8535 (m-40) REVERT: B 220 GLN cc_start: 0.7343 (mt0) cc_final: 0.7101 (mp-120) REVERT: R 370 THR cc_start: 0.7726 (p) cc_final: 0.7257 (t) REVERT: R 377 ILE cc_start: 0.8525 (tp) cc_final: 0.8094 (tp) REVERT: R 414 ILE cc_start: 0.7882 (mm) cc_final: 0.7424 (mm) REVERT: R 427 THR cc_start: 0.8729 (p) cc_final: 0.8490 (p) REVERT: H 138 THR cc_start: 0.7276 (t) cc_final: 0.6795 (m) outliers start: 0 outliers final: 0 residues processed: 301 average time/residue: 0.1006 time to fit residues: 40.8503 Evaluate side-chains 262 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 3.9990 chunk 92 optimal weight: 0.4980 chunk 35 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 chunk 15 optimal weight: 0.0060 chunk 108 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 255 ASN A 304 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 11 GLN R 30 ASN ** R 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.159787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.140538 restraints weight = 24840.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.141256 restraints weight = 28415.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.143408 restraints weight = 22129.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.144242 restraints weight = 13196.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.145041 restraints weight = 12319.640| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3562 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3562 r_free = 0.3562 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3562 r_free = 0.3562 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3562 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.7913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9008 Z= 0.156 Angle : 0.713 8.650 12197 Z= 0.370 Chirality : 0.046 0.245 1373 Planarity : 0.004 0.060 1537 Dihedral : 4.883 19.412 1217 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.21 % Allowed : 0.10 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.25), residues: 1095 helix: 0.64 (0.28), residues: 343 sheet: -0.71 (0.33), residues: 250 loop : -2.39 (0.24), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 68 TYR 0.016 0.002 TYR R 416 PHE 0.031 0.002 PHE R 21 TRP 0.025 0.002 TRP B 211 HIS 0.004 0.001 HIS A 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 ( 9005) covalent geometry : angle 0.71293 / 0.37 (12191) SS BOND : bond 0.00374 / 0.18 ( 3) SS BOND : angle 1.27138 / 0.60 ( 6) hydrogen bonds : bond 0.03700 / 2.43 ( 339) hydrogen bonds : angle 4.79830 / 3.36 ( 966) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1771.11 seconds wall clock time: 31 minutes 17.03 seconds (1877.03 seconds total)