Starting phenix.real_space_refine on Sun Nov 17 17:08:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ux9_42719/11_2024/8ux9_42719_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ux9_42719/11_2024/8ux9_42719.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ux9_42719/11_2024/8ux9_42719.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ux9_42719/11_2024/8ux9_42719.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ux9_42719/11_2024/8ux9_42719_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ux9_42719/11_2024/8ux9_42719_trim.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.017 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 S 21 5.16 5 C 5062 2.51 5 N 1367 2.21 5 O 1327 1.98 5 H 6464 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 14247 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 3810 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 6, 'TRANS': 299} Unresolved non-hydrogen bonds: 354 Unresolved non-hydrogen angles: 434 Unresolved non-hydrogen dihedrals: 280 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 9, 'ASP:plan': 26, 'GLU:plan': 11, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 191 Chain: "B" Number of atoms: 5142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 5142 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 10, 'TRANS': 385} Chain breaks: 4 Unresolved non-hydrogen bonds: 435 Unresolved non-hydrogen angles: 533 Unresolved non-hydrogen dihedrals: 345 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 22, 'PHE:plan': 1, 'GLU:plan': 26, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 275 Chain: "C" Number of atoms: 5233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 5233 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 10, 'TRANS': 391} Chain breaks: 4 Unresolved non-hydrogen bonds: 394 Unresolved non-hydrogen angles: 483 Unresolved non-hydrogen dihedrals: 316 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 21, 'PHE:plan': 4, 'GLU:plan': 27, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 250 Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.09, per 1000 atoms: 0.57 Number of scatterers: 14247 At special positions: 0 Unit cell: (96.048, 145.728, 113.712, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 21 16.00 P 6 15.00 O 1327 8.00 N 1367 7.00 C 5062 6.00 H 6464 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.15 Conformation dependent library (CDL) restraints added in 1.5 seconds 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2114 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 10 sheets defined 54.9% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 8 through 18 Processing helix chain 'A' and resid 28 through 42 removed outlier: 3.569A pdb=" N SER A 32 " --> pdb=" O ARG A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 64 removed outlier: 3.936A pdb=" N LYS A 64 " --> pdb=" O ALA A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 77 Processing helix chain 'A' and resid 120 through 124 Processing helix chain 'A' and resid 127 through 137 removed outlier: 3.820A pdb=" N GLN A 136 " --> pdb=" O ILE A 132 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N PHE A 137 " --> pdb=" O ASP A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 172 removed outlier: 3.614A pdb=" N GLU A 153 " --> pdb=" O GLU A 149 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N SER A 156 " --> pdb=" O SER A 152 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N SER A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA A 160 " --> pdb=" O SER A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 182 removed outlier: 3.915A pdb=" N ALA A 180 " --> pdb=" O GLY A 176 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 224 removed outlier: 3.746A pdb=" N ALA A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) Proline residue: A 221 - end of helix Processing helix chain 'A' and resid 227 through 235 Processing helix chain 'A' and resid 236 through 260 removed outlier: 4.518A pdb=" N GLU A 258 " --> pdb=" O TYR A 254 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ASP A 259 " --> pdb=" O VAL A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 272 Processing helix chain 'A' and resid 275 through 290 Processing helix chain 'A' and resid 300 through 307 Processing helix chain 'B' and resid 15 through 17 No H-bonds generated for 'chain 'B' and resid 15 through 17' Processing helix chain 'B' and resid 38 through 51 Processing helix chain 'B' and resid 53 through 60 removed outlier: 3.627A pdb=" N ALA B 58 " --> pdb=" O ILE B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 112 Processing helix chain 'B' and resid 126 through 138 Processing helix chain 'B' and resid 152 through 158 Processing helix chain 'B' and resid 176 through 189 Processing helix chain 'B' and resid 199 through 237 Processing helix chain 'B' and resid 252 through 264 removed outlier: 3.562A pdb=" N SER B 264 " --> pdb=" O ILE B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 269 removed outlier: 3.693A pdb=" N GLY B 269 " --> pdb=" O ILE B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 288 Processing helix chain 'B' and resid 298 through 319 Processing helix chain 'B' and resid 319 through 331 Processing helix chain 'B' and resid 362 through 366 Processing helix chain 'B' and resid 367 through 381 Processing helix chain 'B' and resid 399 through 412 removed outlier: 3.538A pdb=" N ASP B 405 " --> pdb=" O ASP B 401 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N LEU B 407 " --> pdb=" O GLN B 403 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N LYS B 408 " --> pdb=" O GLU B 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 52 Processing helix chain 'C' and resid 55 through 60 removed outlier: 3.600A pdb=" N ALA C 58 " --> pdb=" O ILE C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 112 Processing helix chain 'C' and resid 125 through 139 Processing helix chain 'C' and resid 151 through 159 Processing helix chain 'C' and resid 178 through 188 Processing helix chain 'C' and resid 199 through 238 removed outlier: 3.513A pdb=" N PHE C 238 " --> pdb=" O PHE C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 262 removed outlier: 3.515A pdb=" N ALA C 261 " --> pdb=" O GLY C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 287 Processing helix chain 'C' and resid 299 through 319 removed outlier: 3.818A pdb=" N VAL C 303 " --> pdb=" O GLY C 299 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N TYR C 304 " --> pdb=" O ALA C 300 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE C 319 " --> pdb=" O GLN C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 331 Processing helix chain 'C' and resid 362 through 366 Processing helix chain 'C' and resid 367 through 381 Processing helix chain 'C' and resid 399 through 413 removed outlier: 3.623A pdb=" N ASP C 405 " --> pdb=" O ASP C 401 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N LEU C 407 " --> pdb=" O GLN C 403 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N LYS C 408 " --> pdb=" O GLU C 404 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN C 413 " --> pdb=" O ARG C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 434 No H-bonds generated for 'chain 'C' and resid 432 through 434' Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 7 removed outlier: 6.280A pdb=" N TYR A 6 " --> pdb=" O LYS A 56 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 51 removed outlier: 6.290A pdb=" N ARG A 22 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N LEU A 86 " --> pdb=" O ARG A 22 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LEU A 24 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N TYR A 114 " --> pdb=" O ILE A 83 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N PHE A 85 " --> pdb=" O TYR A 114 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 94 through 95 Processing sheet with id=AA4, first strand: chain 'A' and resid 187 through 189 Processing sheet with id=AA5, first strand: chain 'B' and resid 18 through 23 removed outlier: 5.391A pdb=" N TYR B 18 " --> pdb=" O LYS B 13 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR B 68 " --> pdb=" O SER B 7 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ILE B 9 " --> pdb=" O LYS B 66 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LYS B 66 " --> pdb=" O ILE B 9 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N LEU B 11 " --> pdb=" O GLU B 64 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N GLU B 64 " --> pdb=" O LEU B 11 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 145 through 148 removed outlier: 6.393A pdb=" N SER B 146 " --> pdb=" O LEU B 390 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ASP B 392 " --> pdb=" O SER B 146 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N PHE B 148 " --> pdb=" O ASP B 392 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N VAL B 389 " --> pdb=" O ILE B 420 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N CYS B 422 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ILE B 391 " --> pdb=" O CYS B 422 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ILE B 437 " --> pdb=" O LEU B 28 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N VAL B 30 " --> pdb=" O ILE B 437 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 338 through 341 Processing sheet with id=AA8, first strand: chain 'C' and resid 97 through 101 removed outlier: 3.756A pdb=" N LYS C 13 " --> pdb=" O TYR C 18 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N TYR C 18 " --> pdb=" O LYS C 13 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 147 through 148 removed outlier: 6.451A pdb=" N VAL C 389 " --> pdb=" O ILE C 420 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N CYS C 422 " --> pdb=" O VAL C 389 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ILE C 391 " --> pdb=" O CYS C 422 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ASN C 29 " --> pdb=" O VAL C 421 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ILE C 437 " --> pdb=" O LEU C 28 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N VAL C 30 " --> pdb=" O ILE C 437 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 337 through 341 480 hydrogen bonds defined for protein. 1368 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: 5.49 Time building geometry restraints manager: 4.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.06: 6461 1.06 - 1.28: 1197 1.28 - 1.50: 3574 1.50 - 1.73: 3138 1.73 - 1.95: 37 Bond restraints: 14407 Sorted by residual: bond pdb=" N SER A 3 " pdb=" CA SER A 3 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.82e+00 bond pdb=" N ILE B 3 " pdb=" CA ILE B 3 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.80e+00 bond pdb=" N ILE C 3 " pdb=" CA ILE C 3 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.72e+00 bond pdb=" N ILE B 3 " pdb=" H ILE B 3 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.22e+00 bond pdb=" N SER A 3 " pdb=" H SER A 3 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.22e+00 ... (remaining 14402 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.10: 25564 7.10 - 14.19: 0 14.19 - 21.29: 0 21.29 - 28.39: 0 28.39 - 35.48: 15 Bond angle restraints: 25579 Sorted by residual: angle pdb=" C LYS C 267 " pdb=" CA LYS C 267 " pdb=" HA LYS C 267 " ideal model delta sigma weight residual 109.00 73.52 35.48 3.00e+00 1.11e-01 1.40e+02 angle pdb=" CB LYS A 40 " pdb=" CA LYS A 40 " pdb=" HA LYS A 40 " ideal model delta sigma weight residual 109.00 73.63 35.37 3.00e+00 1.11e-01 1.39e+02 angle pdb=" C LEU B 414 " pdb=" CA LEU B 414 " pdb=" HA LEU B 414 " ideal model delta sigma weight residual 109.00 73.92 35.08 3.00e+00 1.11e-01 1.37e+02 angle pdb=" N TYR C 271 " pdb=" CA TYR C 271 " pdb=" HA TYR C 271 " ideal model delta sigma weight residual 110.00 74.94 35.06 3.00e+00 1.11e-01 1.37e+02 angle pdb=" N TYR A 253 " pdb=" CA TYR A 253 " pdb=" HA TYR A 253 " ideal model delta sigma weight residual 110.00 74.96 35.04 3.00e+00 1.11e-01 1.36e+02 ... (remaining 25574 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.66: 6778 28.66 - 57.32: 342 57.32 - 85.97: 18 85.97 - 114.63: 1 114.63 - 143.29: 1 Dihedral angle restraints: 7140 sinusoidal: 3295 harmonic: 3845 Sorted by residual: dihedral pdb=" CA GLU A 142 " pdb=" C GLU A 142 " pdb=" N TYR A 143 " pdb=" CA TYR A 143 " ideal model delta harmonic sigma weight residual 180.00 151.97 28.03 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA PHE A 126 " pdb=" C PHE A 126 " pdb=" N ASN A 127 " pdb=" CA ASN A 127 " ideal model delta harmonic sigma weight residual 180.00 157.71 22.29 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" O1B AGS B 501 " pdb=" O3B AGS B 501 " pdb=" PB AGS B 501 " pdb=" PG AGS B 501 " ideal model delta sinusoidal sigma weight residual 68.91 -74.38 143.29 1 3.00e+01 1.11e-03 1.92e+01 ... (remaining 7137 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 1218 0.087 - 0.173: 80 0.173 - 0.260: 0 0.260 - 0.346: 3 0.346 - 0.433: 2 Chirality restraints: 1303 Sorted by residual: chirality pdb=" CA LEU B 414 " pdb=" N LEU B 414 " pdb=" C LEU B 414 " pdb=" CB LEU B 414 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.68e+00 chirality pdb=" CA LYS C 267 " pdb=" N LYS C 267 " pdb=" C LYS C 267 " pdb=" CB LYS C 267 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.98e+00 chirality pdb=" CA TYR A 253 " pdb=" N TYR A 253 " pdb=" C TYR A 253 " pdb=" CB TYR A 253 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.85e+00 ... (remaining 1300 not shown) Planarity restraints: 2434 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 308 " 0.017 2.00e-02 2.50e+03 3.37e-02 1.13e+01 pdb=" C LEU C 308 " -0.058 2.00e-02 2.50e+03 pdb=" O LEU C 308 " 0.022 2.00e-02 2.50e+03 pdb=" N ARG C 309 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 306 " -0.015 2.00e-02 2.50e+03 3.07e-02 9.42e+00 pdb=" C ASP C 306 " 0.053 2.00e-02 2.50e+03 pdb=" O ASP C 306 " -0.020 2.00e-02 2.50e+03 pdb=" N ALA C 307 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 355 " 0.050 5.00e-02 4.00e+02 7.41e-02 8.79e+00 pdb=" N PRO B 356 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO B 356 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 356 " 0.041 5.00e-02 4.00e+02 ... (remaining 2431 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 560 2.17 - 2.78: 25409 2.78 - 3.38: 37617 3.38 - 3.99: 48354 3.99 - 4.60: 75609 Nonbonded interactions: 187549 Sorted by model distance: nonbonded pdb=" OE1 GLU B 433 " pdb=" H GLU B 433 " model vdw 1.558 2.450 nonbonded pdb=" HA TYR A 253 " pdb=" HB3 TYR A 253 " model vdw 1.601 1.952 nonbonded pdb=" HA LYS A 40 " pdb=" HB3 LYS A 40 " model vdw 1.615 1.952 nonbonded pdb=" HA TYR C 271 " pdb=" HB3 TYR C 271 " model vdw 1.622 1.952 nonbonded pdb=" HA LEU B 414 " pdb=" HB2 LEU B 414 " model vdw 1.625 1.952 ... (remaining 187544 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 3 through 6 or (resid 7 through 8 and (name N or name CA o \ r name C or name O or name CB or name H or name HA )) or resid 9 through 73 or ( \ resid 74 and (name N or name CA or name C or name O or name CB or name CG or nam \ e CD or name CE or name NZ or name H or name HA )) or resid 75 through 80 or (re \ sid 81 through 84 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 85 or (resid 86 and (name N or name CA or name C or nam \ e O or name CB or name H or name HA )) or resid 87 through 95 or (resid 96 and ( \ name N or name CA or name C or name O or name CB or name CG or name CD or name C \ E or name NZ or name H or name HA )) or resid 97 through 108 or (resid 109 throu \ gh 126 and (name N or name CA or name C or name O or name CB or name H or name H \ A )) or resid 127 through 159 or (resid 160 through 175 and (name N or name CA o \ r name C or name O or name CB or name H or name HA )) or resid 176 through 212 o \ r (resid 213 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 214 through 222 or (resid 223 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or (resid 224 and (name N or nam \ e CA or name C or name O or name CB or name CG or name CD or name NE or name CZ \ or name NH1 or name NH2 or name H or name HA )) or resid 225 through 226 or (res \ id 227 through 235 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 236 through 254 or (resid 255 through 256 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 257 t \ hrough 266 or (resid 267 through 268 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 269 through 287 or (resid 297 throug \ h 298 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 299 through 301 or (resid 302 and (name N or name CA or name C or n \ ame O or name CB or name H or name HA )) or resid 303 through 335 or (resid 336 \ and (name N or name CA or name C or name O or name CB or name CG or name CD or n \ ame CE or name NZ or name H or name HA )) or resid 337 through 349 or (resid 350 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) o \ r resid 351 through 352 or (resid 353 and (name N or name CA or name C or name O \ or name CB or name CG or name CD1 or name CD2 or name H or name HA )) or (resid \ 354 and (name N or name CA or name C or name O or name CB or name CG or name CD \ or name CE or name NZ or name H or name HA )) or resid 355 through 358 or (resi \ d 359 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 360 through 369 or (resid 370 and (name N or name CA or name C or n \ ame O or name CB or name H or name HA )) or resid 371 through 392 or (resid 393 \ and (name N or name CA or name C or name O or name CB or name CG or name CD or n \ ame OE1 or name OE2 or name H or name HA )) or resid 394 through 396 or (resid 3 \ 97 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 398 through 403 or (resid 404 through 405 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 406 through 407 or (r \ esid 408 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 409 through 411 or (resid 412 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 413 through 432 or (resid 4 \ 33 through 434 and (name N or name CA or name C or name O or name CB or name H o \ r name HA )) or resid 435 through 444 or resid 501)) selection = (chain 'C' and (resid 3 through 7 or (resid 8 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 9 or (resid 10 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 11 th \ rough 16 or (resid 17 and (name N or name CA or name C or name O or name CB or n \ ame H or name HA )) or resid 18 through 20 or (resid 21 and (name N or name CA o \ r name C or name O or name CB or name H or name HA )) or resid 22 through 25 or \ (resid 26 through 27 and (name N or name CA or name C or name O or name CB or na \ me H or name HA )) or resid 28 through 33 or (resid 34 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 35 through 63 or ( \ resid 64 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 65 or (resid 66 and (name N or name CA or name C or name O or na \ me CB or name H or name HA )) or resid 67 through 84 or (resid 85 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name OE1 or nam \ e NE2 or name H or name HA )) or resid 86 through 88 or (resid 89 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 90 thro \ ugh 93 or (resid 94 and (name N or name CA or name C or name O or name CB or nam \ e H or name HA )) or resid 95 through 98 or (resid 99 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 100 through 105 or \ (resid 106 and (name N or name CA or name C or name O or name CB or name H or na \ me HA )) or resid 107 through 112 or resid 125 through 131 or (resid 132 through \ 133 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 134 through 140 or (resid 141 through 144 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 145 through 153 or \ (resid 154 and (name N or name CA or name C or name O or name CB or name H or na \ me HA )) or resid 155 through 160 or resid 175 through 177 or (resid 178 through \ 179 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 180 through 201 or (resid 202 and (name N or name CA or name C or na \ me O or name CB or name H or name HA )) or resid 203 through 205 or (resid 206 a \ nd (name N or name CA or name C or name O or name CB or name CG or name CD or na \ me NE or name CZ or name NH1 or name NH2 or name H or name HA )) or resid 207 th \ rough 224 or (resid 225 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 226 through 238 or resid 251 through 257 or (resi \ d 258 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 259 or (resid 260 and (name N or name CA or name C or name O or nam \ e CB or name H or name HA )) or resid 261 through 270 or (resid 271 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 272 t \ hrough 304 or (resid 305 through 306 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 307 through 308 or (resid 309 throug \ h 310 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 311 or (resid 312 through 313 and (name N or name CA or name C or n \ ame O or name CB or name H or name HA )) or resid 314 through 319 or (resid 320 \ through 321 and (name N or name CA or name C or name O or name CB or name H or n \ ame HA )) or resid 322 through 323 or (resid 324 and (name N or name CA or name \ C or name O or name CB or name CG or name OD1 or name ND2 or name H or name HA ) \ ) or resid 325 through 326 or (resid 327 and (name N or name CA or name C or nam \ e O or name CB or name H or name HA )) or resid 328 through 343 or (resid 344 th \ rough 348 and (name N or name CA or name C or name O or name CB or name H or nam \ e HA )) or resid 349 through 380 or (resid 381 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 382 through 414 or (resid \ 415 and (name N or name CA or name C or name O or name CB or name H or name HA ) \ ) or resid 416 through 443 or (resid 444 and (name N or name CA or name C or nam \ e O or name CB or name H or name HA )) or resid 501)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.290 Extract box with map and model: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 35.320 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 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 : 0.003 0.070 7943 Z= 0.195 Angle : 0.502 6.855 10856 Z= 0.284 Chirality : 0.046 0.433 1303 Planarity : 0.005 0.074 1367 Dihedral : 16.208 143.291 2520 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.82 % Favored : 94.09 % Rotamer: Outliers : 0.34 % Allowed : 28.04 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.26), residues: 1082 helix: 1.78 (0.22), residues: 546 sheet: -0.37 (0.42), residues: 163 loop : -1.22 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 184 HIS 0.003 0.001 HIS B 32 PHE 0.016 0.001 PHE C 134 TYR 0.009 0.001 TYR B 432 ARG 0.009 0.001 ARG C 78 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 3 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Residue SER 58 is missing expected H atoms. Skipping. Residue LYS 60 is missing expected H atoms. Skipping. Residue MET 62 is missing expected H atoms. Skipping. Residue SER 63 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue SER 75 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue ILE 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LEU 104 is missing expected H atoms. Skipping. Residue SER 106 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue SER 129 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue SER 141 is missing expected H atoms. Skipping. Residue TYR 143 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue TYR 145 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue SER 152 is missing expected H atoms. Skipping. Residue LEU 154 is missing expected H atoms. Skipping. Residue ILE 155 is missing expected H atoms. Skipping. Residue SER 156 is missing expected H atoms. Skipping. Residue SER 157 is missing expected H atoms. Skipping. Residue SER 158 is missing expected H atoms. Skipping. Residue LEU 162 is missing expected H atoms. Skipping. Residue SER 166 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue ILE 172 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue LEU 181 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LYS 195 is missing expected H atoms. Skipping. Residue ILE 197 is missing expected H atoms. Skipping. Residue SER 201 is missing expected H atoms. Skipping. Residue ILE 204 is missing expected H atoms. Skipping. Residue SER 206 is missing expected H atoms. Skipping. Residue VAL 209 is missing expected H atoms. Skipping. Residue SER 211 is missing expected H atoms. Skipping. Residue VAL 219 is missing expected H atoms. Skipping. Residue ILE 224 is missing expected H atoms. Skipping. Residue SER 226 is missing expected H atoms. Skipping. Residue VAL 228 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 255 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue SER 266 is missing expected H atoms. Skipping. Residue SER 267 is missing expected H atoms. Skipping. Residue LEU 274 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue SER 278 is missing expected H atoms. Skipping. Residue SER 286 is missing expected H atoms. Skipping. Residue SER 302 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue ILE 3 is missing expected H atoms. Skipping. Residue THR 5 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue LYS 66 is missing expected H atoms. Skipping. Residue SER 70 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue SER 93 is missing expected H atoms. Skipping. Residue LYS 99 is missing expected H atoms. Skipping. Residue MET 106 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue SER 125 is missing expected H atoms. Skipping. Residue MET 126 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue LYS 136 is missing expected H atoms. Skipping. Residue LYS 142 is missing expected H atoms. Skipping. Residue VAL 143 is missing expected H atoms. Skipping. Residue MET 154 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 179 is missing expected H atoms. Skipping. Residue SER 199 is missing expected H atoms. Skipping. Residue MET 201 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue SER 229 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue SER 235 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue LEU 251 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 260 is missing expected H atoms. Skipping. Residue SER 264 is missing expected H atoms. Skipping. Residue SER 265 is missing expected H atoms. Skipping. Residue ILE 266 is missing expected H atoms. Skipping. Residue TYR 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue ILE 281 is missing expected H atoms. Skipping. Residue SER 283 is missing expected H atoms. Skipping. Residue LEU 284 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue VAL 297 is missing expected H atoms. Skipping. Residue LEU 301 is missing expected H atoms. Skipping. Residue LYS 317 is missing expected H atoms. Skipping. Residue SER 320 is missing expected H atoms. Skipping. Residue SER 327 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue LEU 344 is missing expected H atoms. Skipping. Residue LYS 347 is missing expected H atoms. Skipping. Residue TYR 348 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue SER 361 is missing expected H atoms. Skipping. Residue SER 368 is missing expected H atoms. Skipping. Residue SER 381 is missing expected H atoms. Skipping. Residue LYS 408 is missing expected H atoms. Skipping. Residue SER 415 is missing expected H atoms. Skipping. Residue SER 440 is missing expected H atoms. Skipping. Residue ILE 3 is missing expected H atoms. Skipping. Residue THR 5 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue LYS 66 is missing expected H atoms. Skipping. Residue SER 70 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 81 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue SER 86 is missing expected H atoms. Skipping. Residue SER 93 is missing expected H atoms. Skipping. Residue LYS 96 is missing expected H atoms. Skipping. Residue LYS 99 is missing expected H atoms. Skipping. Residue VAL 109 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue SER 125 is missing expected H atoms. Skipping. Residue MET 126 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue LYS 136 is missing expected H atoms. Skipping. Residue LYS 142 is missing expected H atoms. Skipping. Residue MET 154 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue SER 173 is missing expected H atoms. Skipping. Residue LYS 179 is missing expected H atoms. Skipping. Residue SER 199 is missing expected H atoms. Skipping. Residue MET 201 is missing expected H atoms. Skipping. Residue SER 223 is missing expected H atoms. Skipping. Residue SER 227 is missing expected H atoms. Skipping. Residue SER 229 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue SER 235 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue LEU 251 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue ILE 255 is missing expected H atoms. Skipping. Residue SER 264 is missing expected H atoms. Skipping. Residue SER 265 is missing expected H atoms. Skipping. Residue ILE 266 is missing expected H atoms. Skipping. Residue LYS 267 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue ILE 281 is missing expected H atoms. Skipping. Residue SER 283 is missing expected H atoms. Skipping. Residue LEU 284 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue VAL 297 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue LEU 301 is missing expected H atoms. Skipping. Residue VAL 302 is missing expected H atoms. Skipping. Residue LYS 317 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue LYS 336 is missing expected H atoms. Skipping. Residue LYS 347 is missing expected H atoms. Skipping. Residue TYR 348 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue LEU 353 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue SER 359 is missing expected H atoms. Skipping. Residue SER 361 is missing expected H atoms. Skipping. Residue SER 368 is missing expected H atoms. Skipping. Residue SER 397 is missing expected H atoms. Skipping. Residue LYS 408 is missing expected H atoms. Skipping. Residue SER 412 is missing expected H atoms. Skipping. Residue SER 440 is missing expected H atoms. Skipping. Evaluate side-chains 217 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 215 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 TRP cc_start: 0.8795 (m-10) cc_final: 0.8217 (m-10) outliers start: 2 outliers final: 1 residues processed: 216 average time/residue: 0.5546 time to fit residues: 151.7889 Evaluate side-chains 214 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 213 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 393 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 ASN B 372 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.0495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 7943 Z= 0.456 Angle : 0.554 6.732 10856 Z= 0.313 Chirality : 0.048 0.434 1303 Planarity : 0.004 0.041 1367 Dihedral : 8.439 142.413 1225 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.64 % Favored : 94.27 % Rotamer: Outliers : 1.52 % Allowed : 27.36 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.26), residues: 1082 helix: 1.77 (0.22), residues: 547 sheet: -0.63 (0.41), residues: 167 loop : -1.45 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 287 HIS 0.005 0.001 HIS A 107 PHE 0.023 0.002 PHE C 134 TYR 0.013 0.002 TYR C 18 ARG 0.005 0.001 ARG C 206 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 3 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Residue SER 58 is missing expected H atoms. Skipping. Residue LYS 60 is missing expected H atoms. Skipping. Residue MET 62 is missing expected H atoms. Skipping. Residue SER 63 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue SER 75 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue ILE 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LEU 104 is missing expected H atoms. Skipping. Residue SER 106 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue SER 129 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue SER 141 is missing expected H atoms. Skipping. Residue TYR 143 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue TYR 145 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue SER 152 is missing expected H atoms. Skipping. Residue LEU 154 is missing expected H atoms. Skipping. Residue ILE 155 is missing expected H atoms. Skipping. Residue SER 156 is missing expected H atoms. Skipping. Residue SER 157 is missing expected H atoms. Skipping. Residue SER 158 is missing expected H atoms. Skipping. Residue LEU 162 is missing expected H atoms. Skipping. Residue SER 166 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue ILE 172 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue LEU 181 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LYS 195 is missing expected H atoms. Skipping. Residue ILE 197 is missing expected H atoms. Skipping. Residue SER 201 is missing expected H atoms. Skipping. Residue ILE 204 is missing expected H atoms. Skipping. Residue SER 206 is missing expected H atoms. Skipping. Residue VAL 209 is missing expected H atoms. Skipping. Residue SER 211 is missing expected H atoms. Skipping. Residue VAL 219 is missing expected H atoms. Skipping. Residue ILE 224 is missing expected H atoms. Skipping. Residue SER 226 is missing expected H atoms. Skipping. Residue VAL 228 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 255 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue SER 266 is missing expected H atoms. Skipping. Residue SER 267 is missing expected H atoms. Skipping. Residue LEU 274 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue SER 278 is missing expected H atoms. Skipping. Residue SER 286 is missing expected H atoms. Skipping. Residue SER 302 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue ILE 3 is missing expected H atoms. Skipping. Residue THR 5 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue LYS 66 is missing expected H atoms. Skipping. Residue SER 70 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue SER 93 is missing expected H atoms. Skipping. Residue LYS 99 is missing expected H atoms. Skipping. Residue MET 106 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue SER 125 is missing expected H atoms. Skipping. Residue MET 126 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue LYS 136 is missing expected H atoms. Skipping. Residue LYS 142 is missing expected H atoms. Skipping. Residue VAL 143 is missing expected H atoms. Skipping. Residue MET 154 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 179 is missing expected H atoms. Skipping. Residue SER 199 is missing expected H atoms. Skipping. Residue MET 201 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue SER 229 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue SER 235 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue LEU 251 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 260 is missing expected H atoms. Skipping. Residue SER 264 is missing expected H atoms. Skipping. Residue SER 265 is missing expected H atoms. Skipping. Residue ILE 266 is missing expected H atoms. Skipping. Residue TYR 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue ILE 281 is missing expected H atoms. Skipping. Residue SER 283 is missing expected H atoms. Skipping. Residue LEU 284 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue VAL 297 is missing expected H atoms. Skipping. Residue LEU 301 is missing expected H atoms. Skipping. Residue LYS 317 is missing expected H atoms. Skipping. Residue SER 320 is missing expected H atoms. Skipping. Residue SER 327 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue LEU 344 is missing expected H atoms. Skipping. Residue LYS 347 is missing expected H atoms. Skipping. Residue TYR 348 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue SER 361 is missing expected H atoms. Skipping. Residue SER 368 is missing expected H atoms. Skipping. Residue SER 381 is missing expected H atoms. Skipping. Residue LYS 408 is missing expected H atoms. Skipping. Residue SER 415 is missing expected H atoms. Skipping. Residue SER 440 is missing expected H atoms. Skipping. Residue ILE 3 is missing expected H atoms. Skipping. Residue THR 5 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue LYS 66 is missing expected H atoms. Skipping. Residue SER 70 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 81 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue SER 86 is missing expected H atoms. Skipping. Residue SER 93 is missing expected H atoms. Skipping. Residue LYS 96 is missing expected H atoms. Skipping. Residue LYS 99 is missing expected H atoms. Skipping. Residue VAL 109 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue SER 125 is missing expected H atoms. Skipping. Residue MET 126 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue LYS 136 is missing expected H atoms. Skipping. Residue LYS 142 is missing expected H atoms. Skipping. Residue MET 154 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue SER 173 is missing expected H atoms. Skipping. Residue LYS 179 is missing expected H atoms. Skipping. Residue SER 199 is missing expected H atoms. Skipping. Residue MET 201 is missing expected H atoms. Skipping. Residue SER 223 is missing expected H atoms. Skipping. Residue SER 227 is missing expected H atoms. Skipping. Residue SER 229 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue SER 235 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue LEU 251 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue ILE 255 is missing expected H atoms. Skipping. Residue SER 264 is missing expected H atoms. Skipping. Residue SER 265 is missing expected H atoms. Skipping. Residue ILE 266 is missing expected H atoms. Skipping. Residue LYS 267 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue ILE 281 is missing expected H atoms. Skipping. Residue SER 283 is missing expected H atoms. Skipping. Residue LEU 284 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue VAL 297 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue LEU 301 is missing expected H atoms. Skipping. Residue VAL 302 is missing expected H atoms. Skipping. Residue LYS 317 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue LYS 336 is missing expected H atoms. Skipping. Residue LYS 347 is missing expected H atoms. Skipping. Residue TYR 348 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue LEU 353 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue SER 359 is missing expected H atoms. Skipping. Residue SER 361 is missing expected H atoms. Skipping. Residue SER 368 is missing expected H atoms. Skipping. Residue SER 397 is missing expected H atoms. Skipping. Residue LYS 408 is missing expected H atoms. Skipping. Residue SER 412 is missing expected H atoms. Skipping. Residue SER 440 is missing expected H atoms. Skipping. Evaluate side-chains 221 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 212 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 360 TRP cc_start: 0.8213 (m100) cc_final: 0.7963 (m100) REVERT: C 4 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7383 (mtt90) outliers start: 9 outliers final: 6 residues processed: 215 average time/residue: 0.5330 time to fit residues: 144.7168 Evaluate side-chains 219 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 212 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 138 ASN Chi-restraints excluded: chain B residue 158 TRP Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain C residue 4 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 chunk 98 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.0562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7943 Z= 0.298 Angle : 0.513 6.830 10856 Z= 0.288 Chirality : 0.046 0.434 1303 Planarity : 0.003 0.035 1367 Dihedral : 8.103 144.889 1222 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.71 % Favored : 95.19 % Rotamer: Outliers : 1.35 % Allowed : 27.70 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.27), residues: 1082 helix: 1.94 (0.22), residues: 548 sheet: -0.52 (0.42), residues: 162 loop : -1.46 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 287 HIS 0.003 0.001 HIS A 107 PHE 0.018 0.001 PHE C 134 TYR 0.010 0.001 TYR C 18 ARG 0.002 0.000 ARG A 92 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 3 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Residue SER 58 is missing expected H atoms. Skipping. Residue LYS 60 is missing expected H atoms. Skipping. Residue MET 62 is missing expected H atoms. Skipping. Residue SER 63 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue SER 75 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue ILE 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LEU 104 is missing expected H atoms. Skipping. Residue SER 106 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue SER 129 is missing expected H atoms. Skipping. Residue SER 139 is missing expected H atoms. Skipping. Residue SER 141 is missing expected H atoms. Skipping. Residue TYR 143 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue TYR 145 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue SER 152 is missing expected H atoms. Skipping. Residue LEU 154 is missing expected H atoms. Skipping. Residue ILE 155 is missing expected H atoms. Skipping. Residue SER 156 is missing expected H atoms. Skipping. Residue SER 157 is missing expected H atoms. Skipping. Residue SER 158 is missing expected H atoms. Skipping. Residue LEU 162 is missing expected H atoms. Skipping. Residue SER 166 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue ILE 172 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue LEU 181 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LYS 195 is missing expected H atoms. Skipping. Residue ILE 197 is missing expected H atoms. Skipping. Residue SER 201 is missing expected H atoms. Skipping. Residue ILE 204 is missing expected H atoms. Skipping. Residue SER 206 is missing expected H atoms. Skipping. Residue VAL 209 is missing expected H atoms. Skipping. Residue SER 211 is missing expected H atoms. Skipping. Residue VAL 219 is missing expected H atoms. Skipping. Residue ILE 224 is missing expected H atoms. Skipping. Residue SER 226 is missing expected H atoms. Skipping. Residue VAL 228 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 255 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue SER 266 is missing expected H atoms. Skipping. Residue SER 267 is missing expected H atoms. Skipping. Residue LEU 274 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue SER 278 is missing expected H atoms. Skipping. Residue SER 286 is missing expected H atoms. Skipping. Residue SER 302 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue ILE 3 is missing expected H atoms. Skipping. Residue THR 5 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue LYS 66 is missing expected H atoms. Skipping. Residue SER 70 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue SER 93 is missing expected H atoms. Skipping. Residue LYS 99 is missing expected H atoms. Skipping. Residue MET 106 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue SER 125 is missing expected H atoms. Skipping. Residue MET 126 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue LYS 136 is missing expected H atoms. Skipping. Residue LYS 142 is missing expected H atoms. Skipping. Residue VAL 143 is missing expected H atoms. Skipping. Residue MET 154 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 179 is missing expected H atoms. Skipping. Residue SER 199 is missing expected H atoms. Skipping. Residue MET 201 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue SER 229 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue SER 235 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue LEU 251 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 260 is missing expected H atoms. Skipping. Residue SER 264 is missing expected H atoms. Skipping. Residue SER 265 is missing expected H atoms. Skipping. Residue ILE 266 is missing expected H atoms. Skipping. Residue TYR 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue ILE 281 is missing expected H atoms. Skipping. Residue SER 283 is missing expected H atoms. Skipping. Residue LEU 284 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue VAL 297 is missing expected H atoms. Skipping. Residue LEU 301 is missing expected H atoms. Skipping. Residue LYS 317 is missing expected H atoms. Skipping. Residue SER 320 is missing expected H atoms. Skipping. Residue SER 327 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue LEU 344 is missing expected H atoms. Skipping. Residue LYS 347 is missing expected H atoms. Skipping. Residue TYR 348 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue SER 361 is missing expected H atoms. Skipping. Residue SER 368 is missing expected H atoms. Skipping. Residue SER 381 is missing expected H atoms. Skipping. Residue LYS 408 is missing expected H atoms. Skipping. Residue SER 415 is missing expected H atoms. Skipping. Residue SER 440 is missing expected H atoms. Skipping. Residue ILE 3 is missing expected H atoms. Skipping. Residue THR 5 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue LYS 66 is missing expected H atoms. Skipping. Residue SER 70 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 81 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue SER 86 is missing expected H atoms. Skipping. Residue SER 93 is missing expected H atoms. Skipping. Residue LYS 96 is missing expected H atoms. Skipping. Residue LYS 99 is missing expected H atoms. Skipping. Residue VAL 109 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue SER 125 is missing expected H atoms. Skipping. Residue MET 126 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue LYS 136 is missing expected H atoms. Skipping. Residue LYS 142 is missing expected H atoms. Skipping. Residue MET 154 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue SER 173 is missing expected H atoms. Skipping. Residue LYS 179 is missing expected H atoms. Skipping. Residue SER 199 is missing expected H atoms. Skipping. Residue MET 201 is missing expected H atoms. Skipping. Residue SER 223 is missing expected H atoms. Skipping. Residue SER 227 is missing expected H atoms. Skipping. Residue SER 229 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue SER 235 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue LEU 251 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue ILE 255 is missing expected H atoms. Skipping. Residue SER 264 is missing expected H atoms. Skipping. Residue SER 265 is missing expected H atoms. Skipping. Residue ILE 266 is missing expected H atoms. Skipping. Residue LYS 267 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue ILE 281 is missing expected H atoms. Skipping. Residue SER 283 is missing expected H atoms. Skipping. Residue LEU 284 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue VAL 297 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue LEU 301 is missing expected H atoms. Skipping. Residue VAL 302 is missing expected H atoms. Skipping. Residue LYS 317 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue LYS 336 is missing expected H atoms. Skipping. Residue LYS 347 is missing expected H atoms. Skipping. Residue TYR 348 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue LEU 353 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue SER 359 is missing expected H atoms. Skipping. Residue SER 361 is missing expected H atoms. Skipping. Residue SER 368 is missing expected H atoms. Skipping. Residue SER 397 is missing expected H atoms. Skipping. Residue LYS 408 is missing expected H atoms. Skipping. Residue SER 412 is missing expected H atoms. Skipping. Residue SER 440 is missing expected H atoms. Skipping. Evaluate side-chains 222 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 214 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 TRP cc_start: 0.8894 (m-10) cc_final: 0.8594 (m-10) REVERT: C 144 ARG cc_start: 0.7529 (mtm110) cc_final: 0.7302 (mtm110) REVERT: C 192 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8218 (tt) outliers start: 8 outliers final: 5 residues processed: 217 average time/residue: 0.5379 time to fit residues: 147.0640 Evaluate side-chains 219 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 213 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 138 ASN Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 393 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 66 optimal weight: 0.5980 chunk 99 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 94 optimal weight: 0.0670 chunk 28 optimal weight: 0.1980 chunk 87 optimal weight: 0.1980 overall best weight: 0.3518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.0706 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: