Starting phenix.real_space_refine on Thu Feb 13 09:18:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6k42_9912/02_2025/6k42_9912.cif Found real_map, /net/cci-nas-00/data/ceres_data/6k42_9912/02_2025/6k42_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_9912/02_2025/6k42_9912.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6k42_9912/02_2025/6k42_9912.map" model { file = "/net/cci-nas-00/data/ceres_data/6k42_9912/02_2025/6k42_9912.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6k42_9912/02_2025/6k42_9912.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 6.77, per 1000 atoms: 0.77 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: 2.53 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 0.90 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: 2.37 Time building geometry restraints manager: 2.67 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: 5108 14.97 - 29.95: 173 29.95 - 44.92: 56 44.92 - 59.89: 8 59.89 - 74.86: 3 Dihedral angle restraints: 5348 sinusoidal: 2102 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 5345 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: 0.000 Normalize map: mean=0, sd=1: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 24.010 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6323 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 9005 Z= 0.383 Angle : 0.823 9.687 12191 Z= 0.478 Chirality : 0.049 0.307 1373 Planarity : 0.007 0.094 1537 Dihedral : 9.237 74.864 3241 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 4.50 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.015 0.001 TRP B 211 HIS 0.010 0.001 HIS R 102 PHE 0.031 0.002 PHE R 369 TYR 0.017 0.002 TYR R 79 ARG 0.005 0.000 ARG B 68 *********************** 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 : 0.959 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: 0.7222 (pp) REVERT: A 49 ILE cc_start: 0.6716 (pt) cc_final: 0.6462 (pt) REVERT: A 50 VAL cc_start: 0.6760 (m) cc_final: 0.6501 (m) REVERT: B 43 ILE cc_start: 0.7437 (mm) cc_final: 0.6307 (mm) REVERT: B 280 LYS cc_start: 0.6658 (tptt) cc_final: 0.6209 (tptm) REVERT: B 313 ASN cc_start: 0.7856 (t0) cc_final: 0.7340 (m-40) REVERT: R 102 HIS cc_start: 0.6568 (m-70) cc_final: 0.5985 (m-70) REVERT: R 414 ILE cc_start: 0.7376 (mm) cc_final: 0.7152 (mm) REVERT: R 429 PHE cc_start: 0.6872 (m-10) cc_final: 0.6657 (m-10) REVERT: H 58 ILE cc_start: 0.8045 (mt) cc_final: 0.7839 (mt) outliers start: 1 outliers final: 1 residues processed: 431 average time/residue: 0.2501 time to fit residues: 140.6486 Evaluate side-chains 283 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 282 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 1.9990 chunk 83 optimal weight: 0.1980 chunk 46 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 56 optimal weight: 0.0070 chunk 44 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 33 optimal weight: 0.1980 chunk 52 optimal weight: 0.5980 chunk 64 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 overall best weight: 0.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 244 HIS A 304 GLN A 346 ASN B 16 ASN B 75 GLN B 239 ASN ** 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.185434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.167394 restraints weight = 22794.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.170239 restraints weight = 24255.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.171181 restraints weight = 16749.233| |-----------------------------------------------------------------------------| r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3867 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3867 r_free = 0.3867 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3867 r_free = 0.3867 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3867 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6761 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9005 Z= 0.184 Angle : 0.619 7.064 12191 Z= 0.332 Chirality : 0.043 0.275 1373 Planarity : 0.005 0.079 1537 Dihedral : 4.672 23.124 1225 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.22), residues: 1095 helix: -0.63 (0.26), residues: 332 sheet: -1.83 (0.30), residues: 249 loop : -2.89 (0.23), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 84 HIS 0.008 0.001 HIS H 155 PHE 0.031 0.002 PHE R 369 TYR 0.020 0.002 TYR H 216 ARG 0.007 0.001 ARG B 314 *********************** 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 327 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 327 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.7125 (tpp) cc_final: 0.6879 (ttm) REVERT: A 227 LEU cc_start: 0.7214 (mt) cc_final: 0.6836 (mt) REVERT: A 246 SER cc_start: 0.8938 (m) cc_final: 0.8541 (m) REVERT: B 68 ARG cc_start: 0.7782 (tpt-90) cc_final: 0.6935 (ttt-90) REVERT: B 211 TRP cc_start: 0.7976 (m100) cc_final: 0.7762 (m100) REVERT: B 280 LYS cc_start: 0.7038 (tptt) cc_final: 0.6565 (tptm) REVERT: B 313 ASN cc_start: 0.7876 (t0) cc_final: 0.7494 (m-40) REVERT: B 322 ASP cc_start: 0.6119 (t0) cc_final: 0.5902 (t0) REVERT: R 414 ILE cc_start: 0.7595 (mm) cc_final: 0.7324 (mm) REVERT: R 418 ASN cc_start: 0.5623 (t0) cc_final: 0.5005 (t0) REVERT: H 93 MET cc_start: 0.5903 (tpp) cc_final: 0.5481 (tpp) outliers start: 0 outliers final: 0 residues processed: 327 average time/residue: 0.2036 time to fit residues: 91.8890 Evaluate side-chains 257 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 16 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 HIS A 304 GLN ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS B 293 ASN R 30 ASN R 102 HIS ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 155 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.171704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.152909 restraints weight = 20965.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.153305 restraints weight = 22714.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.154503 restraints weight = 19361.341| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3682 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3682 r_free = 0.3682 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3682 r_free = 0.3682 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3682 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.5148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 9005 Z= 0.266 Angle : 0.684 8.882 12191 Z= 0.365 Chirality : 0.044 0.243 1373 Planarity : 0.005 0.073 1537 Dihedral : 4.915 21.129 1225 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 0.31 % Allowed : 2.30 % Favored : 97.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.24), residues: 1095 helix: 0.14 (0.28), residues: 337 sheet: -1.64 (0.33), residues: 237 loop : -2.54 (0.24), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP H 111 HIS 0.007 0.002 HIS H 155 PHE 0.030 0.002 PHE R 369 TYR 0.016 0.002 TYR B 59 ARG 0.012 0.001 ARG B 49 *********************** 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 351 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 350 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 ILE cc_start: 0.8507 (pt) cc_final: 0.8204 (mt) REVERT: A 210 LYS cc_start: 0.8479 (mmtt) cc_final: 0.8070 (mmmt) REVERT: A 227 LEU cc_start: 0.7729 (mt) cc_final: 0.7456 (mt) REVERT: A 346 ASN cc_start: 0.8565 (m110) cc_final: 0.8264 (m-40) REVERT: B 75 GLN cc_start: 0.8019 (mm-40) cc_final: 0.7592 (mm-40) REVERT: B 188 MET cc_start: 0.8623 (tpp) cc_final: 0.7944 (mpp) REVERT: B 261 LEU cc_start: 0.8397 (mt) cc_final: 0.8187 (mt) REVERT: B 280 LYS cc_start: 0.6937 (tptt) cc_final: 0.6651 (tmtt) REVERT: B 313 ASN cc_start: 0.8336 (t0) cc_final: 0.8044 (m-40) REVERT: R 25 PHE cc_start: 0.6291 (m-80) cc_final: 0.6087 (m-80) REVERT: R 32 LEU cc_start: 0.7422 (tt) cc_final: 0.6950 (tp) REVERT: R 44 ARG cc_start: 0.8054 (mtt180) cc_final: 0.7464 (mtt-85) REVERT: R 49 LEU cc_start: 0.8940 (mm) cc_final: 0.8687 (mm) REVERT: R 88 TYR cc_start: 0.6777 (t80) cc_final: 0.6498 (t80) REVERT: R 102 HIS cc_start: 0.7556 (m90) cc_final: 0.6967 (m170) REVERT: R 366 GLU cc_start: 0.5915 (tm-30) cc_final: 0.5695 (tm-30) REVERT: R 414 ILE cc_start: 0.7860 (mm) cc_final: 0.7617 (mm) REVERT: H 82 GLN cc_start: 0.6652 (pm20) cc_final: 0.5698 (mp10) outliers start: 1 outliers final: 1 residues processed: 350 average time/residue: 0.2321 time to fit residues: 107.9387 Evaluate side-chains 263 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 262 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 59 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 23 optimal weight: 0.0470 chunk 55 optimal weight: 0.6980 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN B 16 ASN B 176 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 = 0.3821 r_free = 0.3821 target = 0.166615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.146656 restraints weight = 27009.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.147983 restraints weight = 32311.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.150297 restraints weight = 21917.957| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3620 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3620 r_free = 0.3620 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3620 r_free = 0.3620 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3620 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.6047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9005 Z= 0.238 Angle : 0.659 7.317 12191 Z= 0.349 Chirality : 0.045 0.245 1373 Planarity : 0.004 0.063 1537 Dihedral : 4.803 19.682 1225 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.21 % Allowed : 1.78 % Favored : 98.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.24), residues: 1095 helix: 0.38 (0.28), residues: 331 sheet: -1.45 (0.31), residues: 263 loop : -2.48 (0.24), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 111 HIS 0.006 0.001 HIS B 183 PHE 0.027 0.002 PHE R 369 TYR 0.014 0.002 TYR R 416 ARG 0.006 0.001 ARG H 18 *********************** 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 328 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 328 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 227 LEU cc_start: 0.7809 (mt) cc_final: 0.7344 (mt) REVERT: A 346 ASN cc_start: 0.8406 (m110) cc_final: 0.8138 (m110) REVERT: B 86 THR cc_start: 0.8034 (p) cc_final: 0.7747 (p) REVERT: B 88 ASN cc_start: 0.8694 (m-40) cc_final: 0.8152 (m-40) REVERT: B 175 GLN cc_start: 0.7964 (pm20) cc_final: 0.7735 (pm20) REVERT: B 258 ASP cc_start: 0.7378 (t70) cc_final: 0.6955 (t70) REVERT: B 280 LYS cc_start: 0.7157 (tptt) cc_final: 0.6881 (tmtt) REVERT: B 313 ASN cc_start: 0.8486 (t0) cc_final: 0.8143 (m-40) REVERT: B 322 ASP cc_start: 0.6843 (t0) cc_final: 0.6638 (t0) REVERT: R 44 ARG cc_start: 0.8367 (mtt180) cc_final: 0.7644 (mtt-85) REVERT: R 88 TYR cc_start: 0.6819 (t80) cc_final: 0.6598 (t80) REVERT: R 370 THR cc_start: 0.7286 (p) cc_final: 0.7036 (t) REVERT: R 377 ILE cc_start: 0.8067 (tp) cc_final: 0.7787 (tp) REVERT: R 414 ILE cc_start: 0.7843 (mm) cc_final: 0.7541 (mm) REVERT: R 427 THR cc_start: 0.8718 (p) cc_final: 0.8467 (p) REVERT: H 82 GLN cc_start: 0.6443 (pm20) cc_final: 0.5416 (mp10) REVERT: H 225 LEU cc_start: 0.8461 (mp) cc_final: 0.8138 (mm) REVERT: H 232 LYS cc_start: 0.8072 (ptmt) cc_final: 0.7765 (ptmm) outliers start: 0 outliers final: 0 residues processed: 328 average time/residue: 0.2217 time to fit residues: 97.9171 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 : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 56 optimal weight: 0.8980 chunk 43 optimal weight: 0.4980 chunk 106 optimal weight: 2.9990 chunk 72 optimal weight: 0.4980 chunk 13 optimal weight: 0.0970 chunk 75 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN A 304 GLN B 16 ASN ** 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 H 155 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.166397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.147911 restraints weight = 25167.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.148223 restraints weight = 25237.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.150155 restraints weight = 20121.556| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3614 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3614 r_free = 0.3614 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3614 r_free = 0.3614 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3614 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.6516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9005 Z= 0.199 Angle : 0.639 7.284 12191 Z= 0.336 Chirality : 0.044 0.255 1373 Planarity : 0.004 0.064 1537 Dihedral : 4.669 19.972 1225 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.24), residues: 1095 helix: 0.58 (0.28), residues: 334 sheet: -1.41 (0.32), residues: 254 loop : -2.30 (0.25), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP H 111 HIS 0.004 0.001 HIS B 183 PHE 0.024 0.002 PHE R 369 TYR 0.012 0.002 TYR A 302 ARG 0.007 0.001 ARG B 68 *********************** 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 309 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 308 time to evaluate : 1.080 Fit side-chains revert: symmetry clash REVERT: A 346 ASN cc_start: 0.8477 (m110) cc_final: 0.8111 (m-40) REVERT: B 86 THR cc_start: 0.8427 (p) cc_final: 0.8026 (p) REVERT: B 88 ASN cc_start: 0.8732 (m-40) cc_final: 0.8275 (m-40) REVERT: B 175 GLN cc_start: 0.8154 (pm20) cc_final: 0.7739 (pm20) REVERT: B 280 LYS cc_start: 0.7016 (tptt) cc_final: 0.6800 (tmtt) REVERT: B 313 ASN cc_start: 0.8466 (t0) cc_final: 0.8210 (m-40) REVERT: B 322 ASP cc_start: 0.6746 (t0) cc_final: 0.6512 (t0) REVERT: R 44 ARG cc_start: 0.8412 (mtt180) cc_final: 0.8090 (mtt180) REVERT: R 370 THR cc_start: 0.7571 (p) cc_final: 0.7334 (t) REVERT: R 377 ILE cc_start: 0.8267 (tp) cc_final: 0.7896 (tp) REVERT: R 407 LEU cc_start: 0.6919 (mt) cc_final: 0.6672 (mt) REVERT: R 414 ILE cc_start: 0.7796 (mm) cc_final: 0.7397 (mm) REVERT: R 427 THR cc_start: 0.8501 (p) cc_final: 0.8245 (p) REVERT: H 82 GLN cc_start: 0.6425 (pm20) cc_final: 0.5572 (mp10) REVERT: H 189 ASP cc_start: 0.7468 (t0) cc_final: 0.7221 (t0) REVERT: H 225 LEU cc_start: 0.8564 (mp) cc_final: 0.8211 (mm) REVERT: H 232 LYS cc_start: 0.8046 (ptmt) cc_final: 0.7827 (ptmm) outliers start: 1 outliers final: 0 residues processed: 309 average time/residue: 0.2177 time to fit residues: 90.6787 Evaluate side-chains 244 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 2 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 109 optimal weight: 0.2980 chunk 57 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 108 optimal weight: 0.6980 chunk 103 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.162491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.144355 restraints weight = 23783.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.143520 restraints weight = 24691.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.146024 restraints weight = 20829.549| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3577 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3577 r_free = 0.3577 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 = 0.3577 r_free = 0.3577 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3577 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.6923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9005 Z= 0.219 Angle : 0.657 7.277 12191 Z= 0.343 Chirality : 0.045 0.227 1373 Planarity : 0.004 0.056 1537 Dihedral : 4.714 19.202 1225 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 0.21 % Allowed : 1.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.24), residues: 1095 helix: 0.57 (0.28), residues: 338 sheet: -1.27 (0.32), residues: 255 loop : -2.35 (0.25), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 111 HIS 0.004 0.001 HIS B 183 PHE 0.025 0.002 PHE R 369 TYR 0.021 0.002 TYR R 416 ARG 0.005 0.001 ARG B 68 *********************** 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 306 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 306 time to evaluate : 0.978 Fit side-chains revert: symmetry clash REVERT: A 346 ASN cc_start: 0.8402 (m110) cc_final: 0.8047 (m-40) REVERT: B 86 THR cc_start: 0.8558 (p) cc_final: 0.8114 (p) REVERT: B 88 ASN cc_start: 0.8804 (m-40) cc_final: 0.8285 (m-40) REVERT: B 280 LYS cc_start: 0.7152 (tptt) cc_final: 0.6907 (tmtt) REVERT: B 322 ASP cc_start: 0.6833 (t0) cc_final: 0.6604 (t0) REVERT: R 98 SER cc_start: 0.8813 (p) cc_final: 0.7926 (p) REVERT: R 102 HIS cc_start: 0.7880 (m170) cc_final: 0.7262 (m90) REVERT: R 377 ILE cc_start: 0.8347 (tp) cc_final: 0.7943 (tp) REVERT: R 414 ILE cc_start: 0.7850 (mm) cc_final: 0.7461 (mm) REVERT: R 427 THR cc_start: 0.8618 (p) cc_final: 0.8376 (p) REVERT: H 82 GLN cc_start: 0.6339 (pm20) cc_final: 0.5471 (mp10) REVERT: H 93 MET cc_start: 0.6572 (tpp) cc_final: 0.6115 (tpp) REVERT: H 95 TYR cc_start: 0.6480 (m-10) cc_final: 0.6275 (m-10) REVERT: H 138 THR cc_start: 0.6949 (t) cc_final: 0.6532 (m) REVERT: H 189 ASP cc_start: 0.7492 (t0) cc_final: 0.7276 (t0) REVERT: H 232 LYS cc_start: 0.8038 (ptmt) cc_final: 0.7836 (ptmm) outliers start: 0 outliers final: 0 residues processed: 306 average time/residue: 0.2105 time to fit residues: 87.5932 Evaluate side-chains 265 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 56 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 97 optimal weight: 0.4980 chunk 52 optimal weight: 3.9990 chunk 109 optimal weight: 8.9990 chunk 76 optimal weight: 0.4980 chunk 105 optimal weight: 0.3980 chunk 80 optimal weight: 0.0370 chunk 4 optimal weight: 0.0040 overall best weight: 0.2870 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN A 304 GLN G 11 GLN R 30 ASN ** R 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.166040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.148477 restraints weight = 16656.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.149714 restraints weight = 17476.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.149736 restraints weight = 12176.721| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3621 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3621 r_free = 0.3621 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3621 r_free = 0.3621 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3621 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.7022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9005 Z= 0.172 Angle : 0.631 7.842 12191 Z= 0.328 Chirality : 0.044 0.211 1373 Planarity : 0.004 0.063 1537 Dihedral : 4.573 18.811 1225 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.21 % Allowed : 1.78 % Favored : 98.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.25), residues: 1095 helix: 0.75 (0.29), residues: 334 sheet: -1.09 (0.33), residues: 240 loop : -2.30 (0.25), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP H 111 HIS 0.003 0.001 HIS B 183 PHE 0.033 0.002 PHE R 181 TYR 0.019 0.002 TYR H 215 ARG 0.005 0.001 ARG H 168 *********************** 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 314 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 314 time to evaluate : 0.950 Fit side-chains revert: symmetry clash REVERT: B 86 THR cc_start: 0.8515 (p) cc_final: 0.8073 (p) REVERT: B 88 ASN cc_start: 0.8895 (m-40) cc_final: 0.8413 (m-40) REVERT: B 173 THR cc_start: 0.7366 (p) cc_final: 0.7161 (p) REVERT: B 175 GLN cc_start: 0.8266 (pm20) cc_final: 0.7889 (pm20) REVERT: B 220 GLN cc_start: 0.6947 (mt0) cc_final: 0.6722 (mp-120) REVERT: B 258 ASP cc_start: 0.7673 (t70) cc_final: 0.7369 (t0) REVERT: B 280 LYS cc_start: 0.7252 (tptt) cc_final: 0.6966 (tmtt) REVERT: B 322 ASP cc_start: 0.6658 (t0) cc_final: 0.6406 (t0) REVERT: R 54 LEU cc_start: 0.8781 (tt) cc_final: 0.8560 (tp) REVERT: R 98 SER cc_start: 0.8690 (p) cc_final: 0.7911 (p) REVERT: R 102 HIS cc_start: 0.7846 (m170) cc_final: 0.7261 (m90) REVERT: R 148 LEU cc_start: 0.7125 (tp) cc_final: 0.6894 (tp) REVERT: R 377 ILE cc_start: 0.8353 (tp) cc_final: 0.8010 (tp) REVERT: R 414 ILE cc_start: 0.7867 (mm) cc_final: 0.7576 (mm) REVERT: R 422 ASN cc_start: 0.6763 (m-40) cc_final: 0.6418 (m-40) REVERT: H 82 GLN cc_start: 0.6428 (pm20) cc_final: 0.5590 (mp10) REVERT: H 93 MET cc_start: 0.6374 (tpp) cc_final: 0.5992 (tpp) REVERT: H 94 TYR cc_start: 0.4596 (m-10) cc_final: 0.4310 (m-10) REVERT: H 138 THR cc_start: 0.7405 (t) cc_final: 0.6872 (m) outliers start: 0 outliers final: 0 residues processed: 314 average time/residue: 0.2009 time to fit residues: 86.4590 Evaluate side-chains 270 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 5 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 6 optimal weight: 0.0370 chunk 49 optimal weight: 0.9980 chunk 92 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 44 optimal weight: 0.0970 chunk 80 optimal weight: 0.4980 chunk 32 optimal weight: 2.9990 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN 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 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.164784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.146317 restraints weight = 23676.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.148215 restraints weight = 23693.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.149687 restraints weight = 19174.044| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3609 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3609 r_free = 0.3609 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3609 r_free = 0.3609 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3609 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.7212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9005 Z= 0.194 Angle : 0.662 8.227 12191 Z= 0.345 Chirality : 0.044 0.256 1373 Planarity : 0.004 0.060 1537 Dihedral : 4.624 18.975 1225 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.21 % Allowed : 1.15 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.24), residues: 1095 helix: 0.76 (0.28), residues: 334 sheet: -1.10 (0.33), residues: 240 loop : -2.28 (0.24), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP H 111 HIS 0.003 0.001 HIS B 54 PHE 0.026 0.002 PHE R 369 TYR 0.014 0.002 TYR H 223 ARG 0.005 0.001 ARG B 304 *********************** 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 316 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 316 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 346 ASN cc_start: 0.8481 (m110) cc_final: 0.8105 (m-40) REVERT: B 57 LYS cc_start: 0.8019 (mttm) cc_final: 0.7687 (mttm) REVERT: B 86 THR cc_start: 0.8681 (p) cc_final: 0.8245 (p) REVERT: B 88 ASN cc_start: 0.8878 (m-40) cc_final: 0.8372 (m-40) REVERT: B 209 LYS cc_start: 0.7704 (mmtp) cc_final: 0.7452 (mmtp) REVERT: B 280 LYS cc_start: 0.7464 (tptt) cc_final: 0.6909 (tptp) REVERT: B 322 ASP cc_start: 0.6705 (t0) cc_final: 0.6413 (t0) REVERT: R 98 SER cc_start: 0.8721 (p) cc_final: 0.7889 (p) REVERT: R 102 HIS cc_start: 0.7866 (m170) cc_final: 0.7206 (m90) REVERT: R 377 ILE cc_start: 0.8477 (tp) cc_final: 0.8069 (tp) REVERT: R 414 ILE cc_start: 0.7891 (mm) cc_final: 0.7650 (mm) REVERT: H 82 GLN cc_start: 0.6113 (pm20) cc_final: 0.5374 (mp10) REVERT: H 95 TYR cc_start: 0.6571 (m-10) cc_final: 0.6273 (m-10) REVERT: H 138 THR cc_start: 0.7364 (t) cc_final: 0.6808 (m) outliers start: 0 outliers final: 0 residues processed: 316 average time/residue: 0.2219 time to fit residues: 94.2685 Evaluate side-chains 268 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 73 optimal weight: 0.0170 chunk 81 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 91 optimal weight: 0.4980 chunk 102 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.5820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN G 11 GLN R 30 ASN ** R 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.162536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.144288 restraints weight = 17412.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.144573 restraints weight = 18406.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.145895 restraints weight = 14941.349| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3574 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3574 r_free = 0.3574 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 = 0.3574 r_free = 0.3574 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3574 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.7575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 9005 Z= 0.221 Angle : 0.670 7.208 12191 Z= 0.351 Chirality : 0.045 0.271 1373 Planarity : 0.004 0.062 1537 Dihedral : 4.720 18.556 1225 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 0.21 % Allowed : 1.15 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.24), residues: 1095 helix: 0.68 (0.28), residues: 339 sheet: -1.03 (0.33), residues: 250 loop : -2.37 (0.24), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP H 111 HIS 0.003 0.001 HIS B 62 PHE 0.026 0.002 PHE R 369 TYR 0.029 0.002 TYR R 416 ARG 0.005 0.001 ARG B 68 *********************** 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 311 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 311 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 57 LYS cc_start: 0.8032 (mttm) cc_final: 0.7682 (mttm) REVERT: B 86 THR cc_start: 0.8687 (p) cc_final: 0.7653 (t) REVERT: B 88 ASN cc_start: 0.8965 (m-40) cc_final: 0.8322 (m-40) REVERT: B 188 MET cc_start: 0.8532 (mmm) cc_final: 0.8317 (mmm) REVERT: B 209 LYS cc_start: 0.7718 (mmtp) cc_final: 0.7485 (mmtp) REVERT: B 280 LYS cc_start: 0.7446 (tptt) cc_final: 0.6857 (tptm) REVERT: B 322 ASP cc_start: 0.6669 (t0) cc_final: 0.6388 (t0) REVERT: G 42 GLU cc_start: 0.6263 (pp20) cc_final: 0.6062 (pp20) REVERT: R 63 THR cc_start: 0.8654 (p) cc_final: 0.8450 (p) REVERT: R 98 SER cc_start: 0.8859 (p) cc_final: 0.7923 (p) REVERT: R 102 HIS cc_start: 0.7888 (m170) cc_final: 0.7234 (m90) REVERT: R 131 CYS cc_start: 0.8606 (m) cc_final: 0.8282 (m) REVERT: R 377 ILE cc_start: 0.8639 (tp) cc_final: 0.8202 (tp) REVERT: R 414 ILE cc_start: 0.7975 (mm) cc_final: 0.7685 (mm) REVERT: H 57 THR cc_start: 0.8173 (m) cc_final: 0.7854 (m) REVERT: H 93 MET cc_start: 0.6444 (tpp) cc_final: 0.5185 (ttt) REVERT: H 95 TYR cc_start: 0.6495 (m-10) cc_final: 0.6279 (m-10) REVERT: H 115 THR cc_start: 0.7997 (p) cc_final: 0.7768 (p) REVERT: H 138 THR cc_start: 0.7276 (t) cc_final: 0.6775 (m) REVERT: H 224 PRO cc_start: 0.8427 (Cg_exo) cc_final: 0.8225 (Cg_endo) outliers start: 0 outliers final: 0 residues processed: 311 average time/residue: 0.2206 time to fit residues: 92.8473 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 : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 53 optimal weight: 0.0870 chunk 41 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 27 optimal weight: 0.0370 chunk 64 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 104 optimal weight: 0.0060 overall best weight: 0.3252 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN A 331 ASN G 11 GLN R 30 ASN H 39 GLN ** H 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.163985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.144854 restraints weight = 25195.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.146043 restraints weight = 26768.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.147786 restraints weight = 21411.148| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3595 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3595 r_free = 0.3595 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 = 0.3595 r_free = 0.3595 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3595 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.7701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9005 Z= 0.189 Angle : 0.673 11.753 12191 Z= 0.350 Chirality : 0.044 0.276 1373 Planarity : 0.004 0.060 1537 Dihedral : 4.619 18.384 1225 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.21 % Allowed : 0.42 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.25), residues: 1095 helix: 0.83 (0.29), residues: 338 sheet: -0.99 (0.33), residues: 246 loop : -2.19 (0.24), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP H 111 HIS 0.004 0.001 HIS H 155 PHE 0.027 0.002 PHE R 369 TYR 0.020 0.002 TYR R 416 ARG 0.004 0.001 ARG H 168 ********************** 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 304 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 0.950 Fit side-chains REVERT: B 57 LYS cc_start: 0.8026 (mttm) cc_final: 0.7803 (mttm) REVERT: B 88 ASN cc_start: 0.8835 (m-40) cc_final: 0.8601 (m-40) REVERT: B 217 MET cc_start: 0.7380 (ttt) cc_final: 0.7144 (ttt) REVERT: B 280 LYS cc_start: 0.7275 (tptt) cc_final: 0.6971 (tmtt) REVERT: B 322 ASP cc_start: 0.6882 (t0) cc_final: 0.6663 (t0) REVERT: G 42 GLU cc_start: 0.6406 (pp20) cc_final: 0.6173 (pp20) REVERT: R 98 SER cc_start: 0.8747 (p) cc_final: 0.7930 (p) REVERT: R 102 HIS cc_start: 0.7806 (m170) cc_final: 0.7201 (m90) REVERT: R 377 ILE cc_start: 0.8480 (tp) cc_final: 0.8010 (tp) REVERT: R 414 ILE cc_start: 0.8023 (mm) cc_final: 0.7572 (mm) REVERT: H 93 MET cc_start: 0.6448 (tpp) cc_final: 0.5220 (ttt) REVERT: H 115 THR cc_start: 0.7978 (p) cc_final: 0.7735 (p) REVERT: H 138 THR cc_start: 0.7336 (t) cc_final: 0.6696 (m) outliers start: 0 outliers final: 0 residues processed: 304 average time/residue: 0.2200 time to fit residues: 90.5472 Evaluate side-chains 259 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.0213 > 50: distance: 28 - 50: 5.228 distance: 33 - 56: 15.688 distance: 41 - 70: 27.858 distance: 45 - 50: 4.504 distance: 50 - 51: 13.873 distance: 51 - 52: 16.138 distance: 51 - 54: 10.331 distance: 52 - 53: 22.361 distance: 52 - 56: 15.366 distance: 54 - 55: 24.288 distance: 56 - 57: 19.813 distance: 57 - 58: 12.760 distance: 57 - 60: 27.676 distance: 58 - 59: 21.677 distance: 58 - 70: 35.332 distance: 60 - 61: 15.070 distance: 61 - 62: 17.728 distance: 61 - 63: 6.884 distance: 62 - 64: 3.147 distance: 63 - 65: 10.737 distance: 63 - 66: 12.854 distance: 64 - 65: 16.236 distance: 65 - 67: 6.626 distance: 66 - 68: 3.548 distance: 67 - 69: 11.097 distance: 68 - 69: 10.564 distance: 70 - 71: 7.177 distance: 71 - 72: 12.007 distance: 71 - 74: 7.455 distance: 72 - 73: 24.736 distance: 72 - 81: 7.211 distance: 73 - 110: 5.941 distance: 74 - 75: 24.271 distance: 75 - 76: 7.681 distance: 75 - 77: 9.668 distance: 76 - 78: 13.821 distance: 77 - 79: 16.820 distance: 78 - 80: 7.496 distance: 79 - 80: 7.689 distance: 81 - 82: 15.793 distance: 81 - 87: 10.009 distance: 82 - 83: 6.084 distance: 82 - 85: 16.264 distance: 83 - 84: 14.492 distance: 83 - 88: 3.186 distance: 84 - 121: 12.814 distance: 85 - 86: 9.824 distance: 86 - 87: 22.820 distance: 88 - 89: 6.739 distance: 89 - 90: 8.428 distance: 89 - 92: 7.236 distance: 90 - 91: 13.746 distance: 90 - 99: 17.630 distance: 91 - 127: 28.065 distance: 92 - 93: 4.843 distance: 93 - 94: 7.725 distance: 93 - 95: 10.441 distance: 94 - 96: 9.176 distance: 96 - 98: 11.625 distance: 97 - 98: 7.121 distance: 99 - 100: 13.385 distance: 100 - 101: 15.728 distance: 100 - 103: 22.277 distance: 101 - 102: 15.546 distance: 101 - 110: 4.543 distance: 102 - 139: 13.706 distance: 103 - 104: 23.138 distance: 104 - 105: 5.862 distance: 104 - 106: 10.209 distance: 105 - 107: 6.881 distance: 106 - 108: 9.352 distance: 108 - 109: 12.750 distance: 111 - 112: 10.829 distance: 111 - 114: 8.443 distance: 112 - 113: 5.812 distance: 112 - 121: 10.946 distance: 113 - 145: 14.044 distance: 114 - 115: 9.419 distance: 115 - 116: 10.146 distance: 115 - 117: 17.026 distance: 116 - 118: 10.719 distance: 117 - 119: 11.202 distance: 118 - 120: 14.875 distance: 119 - 120: 18.896 distance: 121 - 122: 3.922 distance: 122 - 123: 5.317 distance: 122 - 125: 10.058 distance: 123 - 124: 16.637 distance: 123 - 127: 9.605 distance: 125 - 126: 24.994 distance: 127 - 128: 4.250 distance: 128 - 129: 4.940 distance: 128 - 131: 5.925 distance: 129 - 130: 7.342 distance: 129 - 139: 3.503 distance: 131 - 132: 6.531 distance: 132 - 133: 10.130 distance: 132 - 134: 6.939 distance: 133 - 135: 9.087 distance: 134 - 136: 3.331 distance: 135 - 137: 6.401 distance: 136 - 137: 3.432 distance: 137 - 138: 4.993 distance: 139 - 140: 10.463 distance: 140 - 141: 8.165 distance: 140 - 143: 4.647 distance: 141 - 142: 11.517 distance: 141 - 145: 15.600 distance: 142 - 161: 18.617 distance: 143 - 144: 12.184