Starting phenix.real_space_refine on Sun Dec 10 07:02:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dt0_8911/12_2023/6dt0_8911.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dt0_8911/12_2023/6dt0_8911.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dt0_8911/12_2023/6dt0_8911.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dt0_8911/12_2023/6dt0_8911.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dt0_8911/12_2023/6dt0_8911.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dt0_8911/12_2023/6dt0_8911.pdb" } resolution = 3.7 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 ------------------------------------------------------------------------------- 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= 0.007 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 Ca 1 9.91 5 S 18 5.16 5 C 4688 2.51 5 N 1244 2.21 5 O 1182 1.98 5 H 6626 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 13759 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 3448 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 11, 'TRANS': 224} Chain breaks: 4 Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 11, 'ARG:plan': 8, 'ASN:plan1': 1, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 105 Chain: "B" Number of atoms: 3431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 3431 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 11, 'TRANS': 224} Chain breaks: 4 Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 209 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 11, 'ARG:plan': 8, 'ASN:plan1': 1, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 115 Chain: "C" Number of atoms: 3448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 3448 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 11, 'TRANS': 224} Chain breaks: 4 Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 11, 'ARG:plan': 8, 'ASN:plan1': 1, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 105 Chain: "D" Number of atoms: 3431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 3431 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 11, 'TRANS': 224} Chain breaks: 4 Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 209 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 11, 'ARG:plan': 8, 'ASN:plan1': 1, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 115 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.40, per 1000 atoms: 0.47 Number of scatterers: 13759 At special positions: 0 Unit cell: (77.05, 83.95, 139.15, 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) Ca 1 19.99 S 18 16.00 O 1182 8.00 N 1244 7.00 C 4688 6.00 H 6626 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 - 3.50 Amino acid : False - 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: 11.90 Conformation dependent library (CDL) restraints added in 1.5 seconds 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1760 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 6 sheets defined 64.8% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 164 through 176 removed outlier: 3.658A pdb=" N VAL A 168 " --> pdb=" O PRO A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 266 Processing helix chain 'A' and resid 288 through 349 removed outlier: 4.580A pdb=" N ARG A 292 " --> pdb=" O SER A 288 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ARG A 299 " --> pdb=" O TYR A 295 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER A 324 " --> pdb=" O LEU A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 356 Processing helix chain 'A' and resid 357 through 380 removed outlier: 3.537A pdb=" N ASN A 380 " --> pdb=" O PHE A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 405 Processing helix chain 'A' and resid 407 through 432 removed outlier: 3.513A pdb=" N TRP A 411 " --> pdb=" O ASP A 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 176 removed outlier: 4.076A pdb=" N VAL B 168 " --> pdb=" O PRO B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 269 removed outlier: 3.597A pdb=" N PHE B 261 " --> pdb=" O GLU B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 350 removed outlier: 5.990A pdb=" N TYR B 295 " --> pdb=" O ASP B 291 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N MET B 296 " --> pdb=" O ARG B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 356 Processing helix chain 'B' and resid 357 through 380 Processing helix chain 'B' and resid 396 through 405 Processing helix chain 'B' and resid 408 through 432 Processing helix chain 'B' and resid 437 through 441 Processing helix chain 'C' and resid 164 through 176 removed outlier: 3.653A pdb=" N VAL C 168 " --> pdb=" O PRO C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 266 Processing helix chain 'C' and resid 288 through 349 removed outlier: 4.583A pdb=" N ARG C 292 " --> pdb=" O SER C 288 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ARG C 299 " --> pdb=" O TYR C 295 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER C 324 " --> pdb=" O LEU C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 356 Processing helix chain 'C' and resid 357 through 380 removed outlier: 3.542A pdb=" N ASN C 380 " --> pdb=" O PHE C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 405 Processing helix chain 'C' and resid 407 through 432 removed outlier: 3.507A pdb=" N TRP C 411 " --> pdb=" O ASP C 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 176 removed outlier: 4.078A pdb=" N VAL D 168 " --> pdb=" O PRO D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 269 removed outlier: 3.595A pdb=" N PHE D 261 " --> pdb=" O GLU D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 350 removed outlier: 5.984A pdb=" N TYR D 295 " --> pdb=" O ASP D 291 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N MET D 296 " --> pdb=" O ARG D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 356 Processing helix chain 'D' and resid 357 through 380 Processing helix chain 'D' and resid 396 through 405 Processing helix chain 'D' and resid 408 through 432 Processing helix chain 'D' and resid 437 through 441 Processing sheet with id=AA1, first strand: chain 'A' and resid 155 through 159 removed outlier: 4.045A pdb=" N LEU A 111 " --> pdb=" O SER A 285 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET A 282 " --> pdb=" O ILE A 273 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 110 through 113 Processing sheet with id=AA3, first strand: chain 'B' and resid 190 through 193 Processing sheet with id=AA4, first strand: chain 'C' and resid 155 through 159 removed outlier: 4.046A pdb=" N LEU C 111 " --> pdb=" O SER C 285 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET C 282 " --> pdb=" O ILE C 273 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 110 through 113 Processing sheet with id=AA6, first strand: chain 'D' and resid 190 through 193 552 hydrogen bonds defined for protein. 1590 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: 4.68 Time building geometry restraints manager: 12.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6622 1.03 - 1.22: 6 1.22 - 1.42: 3177 1.42 - 1.61: 4117 1.61 - 1.80: 32 Bond restraints: 13954 Sorted by residual: bond pdb=" N ASN B 189 " pdb=" CA ASN B 189 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.23e-02 6.61e+03 6.58e+00 bond pdb=" N GLU D 276 " pdb=" CA GLU D 276 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.30e+00 bond pdb=" N ILE D 280 " pdb=" CA ILE D 280 " ideal model delta sigma weight residual 1.459 1.487 -0.029 1.20e-02 6.94e+03 5.64e+00 bond pdb=" N GLY D 277 " pdb=" CA GLY D 277 " ideal model delta sigma weight residual 1.449 1.478 -0.029 1.45e-02 4.76e+03 3.98e+00 bond pdb=" N TYR D 278 " pdb=" CA TYR D 278 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.23e-02 6.61e+03 3.84e+00 ... (remaining 13949 not shown) Histogram of bond angle deviations from ideal: 99.40 - 106.31: 300 106.31 - 113.22: 15354 113.22 - 120.14: 4588 120.14 - 127.05: 4681 127.05 - 133.96: 137 Bond angle restraints: 25060 Sorted by residual: angle pdb=" CA VAL D 286 " pdb=" C VAL D 286 " pdb=" N PRO D 287 " ideal model delta sigma weight residual 116.57 119.89 -3.32 9.80e-01 1.04e+00 1.15e+01 angle pdb=" CA GLU D 276 " pdb=" C GLU D 276 " pdb=" O GLU D 276 " ideal model delta sigma weight residual 120.55 117.34 3.21 1.06e+00 8.90e-01 9.17e+00 angle pdb=" N ASN D 279 " pdb=" CA ASN D 279 " pdb=" C ASN D 279 " ideal model delta sigma weight residual 111.74 107.83 3.91 1.35e+00 5.49e-01 8.37e+00 angle pdb=" C ILE D 275 " pdb=" N GLU D 276 " pdb=" CA GLU D 276 " ideal model delta sigma weight residual 120.28 124.09 -3.81 1.34e+00 5.57e-01 8.09e+00 angle pdb=" C VAL D 286 " pdb=" CA VAL D 286 " pdb=" CB VAL D 286 " ideal model delta sigma weight residual 109.33 111.93 -2.60 9.80e-01 1.04e+00 7.02e+00 ... (remaining 25055 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.97: 6151 14.97 - 29.95: 206 29.95 - 44.92: 49 44.92 - 59.90: 26 59.90 - 74.87: 8 Dihedral angle restraints: 6440 sinusoidal: 3072 harmonic: 3368 Sorted by residual: dihedral pdb=" CA PHE A 271 " pdb=" C PHE A 271 " pdb=" N ALA A 272 " pdb=" CA ALA A 272 " ideal model delta harmonic sigma weight residual -180.00 -163.31 -16.69 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA PHE C 271 " pdb=" C PHE C 271 " pdb=" N ALA C 272 " pdb=" CA ALA C 272 " ideal model delta harmonic sigma weight residual -180.00 -163.46 -16.54 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA ILE A 159 " pdb=" C ILE A 159 " pdb=" N HIS A 160 " pdb=" CA HIS A 160 " ideal model delta harmonic sigma weight residual 180.00 163.86 16.14 0 5.00e+00 4.00e-02 1.04e+01 ... (remaining 6437 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 902 0.054 - 0.108: 176 0.108 - 0.163: 34 0.163 - 0.217: 2 0.217 - 0.271: 2 Chirality restraints: 1116 Sorted by residual: chirality pdb=" CA LEU D 356 " pdb=" N LEU D 356 " pdb=" C LEU D 356 " pdb=" CB LEU D 356 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA LEU B 356 " pdb=" N LEU B 356 " pdb=" C LEU B 356 " pdb=" CB LEU B 356 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA LEU C 356 " pdb=" N LEU C 356 " pdb=" C LEU C 356 " pdb=" CB LEU C 356 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.87e-01 ... (remaining 1113 not shown) Planarity restraints: 2120 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 376 " 0.005 2.00e-02 2.50e+03 1.38e-02 5.69e+00 pdb=" CG PHE D 376 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE D 376 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE D 376 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE D 376 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE D 376 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE D 376 " -0.002 2.00e-02 2.50e+03 pdb=" HD1 PHE D 376 " -0.024 2.00e-02 2.50e+03 pdb=" HD2 PHE D 376 " -0.023 2.00e-02 2.50e+03 pdb=" HE1 PHE D 376 " 0.008 2.00e-02 2.50e+03 pdb=" HE2 PHE D 376 " 0.007 2.00e-02 2.50e+03 pdb=" HZ PHE D 376 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 376 " -0.005 2.00e-02 2.50e+03 1.33e-02 5.28e+00 pdb=" CG PHE B 376 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE B 376 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE B 376 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE B 376 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 376 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 376 " 0.001 2.00e-02 2.50e+03 pdb=" HD1 PHE B 376 " 0.024 2.00e-02 2.50e+03 pdb=" HD2 PHE B 376 " 0.022 2.00e-02 2.50e+03 pdb=" HE1 PHE B 376 " -0.008 2.00e-02 2.50e+03 pdb=" HE2 PHE B 376 " -0.006 2.00e-02 2.50e+03 pdb=" HZ PHE B 376 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 436 " -0.005 2.00e-02 2.50e+03 1.02e-02 4.15e+00 pdb=" CG TRP C 436 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP C 436 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP C 436 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP C 436 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP C 436 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 436 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 436 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 436 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 436 " -0.003 2.00e-02 2.50e+03 pdb=" HD1 TRP C 436 " -0.025 2.00e-02 2.50e+03 pdb=" HE1 TRP C 436 " 0.011 2.00e-02 2.50e+03 pdb=" HE3 TRP C 436 " -0.005 2.00e-02 2.50e+03 pdb=" HZ2 TRP C 436 " -0.001 2.00e-02 2.50e+03 pdb=" HZ3 TRP C 436 " 0.002 2.00e-02 2.50e+03 pdb=" HH2 TRP C 436 " -0.006 2.00e-02 2.50e+03 ... (remaining 2117 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.01: 63 2.01 - 2.66: 17594 2.66 - 3.30: 37878 3.30 - 3.95: 44248 3.95 - 4.60: 70523 Nonbonded interactions: 170306 Sorted by model distance: nonbonded pdb=" O GLY C 365 " pdb=" HG1 THR C 368 " model vdw 1.359 1.850 nonbonded pdb=" O GLY A 365 " pdb=" HG1 THR A 368 " model vdw 1.360 1.850 nonbonded pdb=" HG1 THR D 114 " pdb=" O LEU D 118 " model vdw 1.381 1.850 nonbonded pdb=" HG1 THR B 114 " pdb=" O LEU B 118 " model vdw 1.382 1.850 nonbonded pdb=" O ALA A 364 " pdb=" HG1 THR A 367 " model vdw 1.475 1.850 ... (remaining 170301 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 107 or (resid 108 and (name N or name CA or name C or name \ O or name CB or name CG or name CD or name H or name HA or name HB2 or name HB3 \ or name HG2 or name HG3)) or resid 109 or (resid 110 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 H or name H \ A or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3)) or r \ esid 111 through 311 or (resid 312 and (name N or name CA or name C or name O or \ name CB or name CG or name CD or name H or name HA or name HB2 or name HB3 or n \ ame HG2 or name HG3)) or resid 313 through 326 or (resid 327 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 328 through \ 412 or (resid 413 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 414 through 430 or (resid 431 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 432 through 436 or \ (resid 437 and (name N or name CA or name C or name O or name CB or name H or n \ ame HA )) or resid 438 through 439 or (resid 440 through 441 and (name N or name \ CA or name C or name O or name CB or name H or name HA )))) selection = (chain 'B' and (resid 107 through 124 or (resid 125 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 126 through 250 or (r \ esid 251 and (name N or name CA or name C or name O or name CB or name CG or nam \ e CD or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3)) or r \ esid 252 through 256 or (resid 257 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 258 through 298 or (resid 299 and (nam \ e N or name CA or name C or name O or name CB or name CG or name CD or name NE o \ r name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 \ or name HD3)) or resid 300 through 302 or (resid 303 and (name N or name CA or n \ ame C or name O or name CB or name CG or name H or name HA or name HB2 or name H \ B3)) or resid 304 through 399 or (resid 400 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 401 through 441)) selection = (chain 'C' and (resid 107 or (resid 108 and (name N or name CA or name C or name \ O or name CB or name CG or name CD or name H or name HA or name HB2 or name HB3 \ or name HG2 or name HG3)) or resid 109 or (resid 110 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 H or name H \ A or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3)) or r \ esid 111 through 311 or (resid 312 and (name N or name CA or name C or name O or \ name CB or name CG or name CD or name H or name HA or name HB2 or name HB3 or n \ ame HG2 or name HG3)) or resid 313 through 326 or (resid 327 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 328 through \ 412 or (resid 413 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 414 through 430 or (resid 431 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 432 through 436 or \ (resid 437 and (name N or name CA or name C or name O or name CB or name H or n \ ame HA )) or resid 438 through 439 or (resid 440 through 441 and (name N or name \ CA or name C or name O or name CB or name H or name HA )))) selection = (chain 'D' and (resid 107 through 124 or (resid 125 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 126 through 250 or (r \ esid 251 and (name N or name CA or name C or name O or name CB or name CG or nam \ e CD or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3)) or r \ esid 252 through 256 or (resid 257 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 258 through 298 or (resid 299 and (nam \ e N or name CA or name C or name O or name CB or name CG or name CD or name NE o \ r name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 \ or name HD3)) or resid 300 through 302 or (resid 303 and (name N or name CA or n \ ame C or name O or name CB or name CG or name H or name HA or name HB2 or name H \ B3)) or resid 304 through 399 or (resid 400 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 401 through 441)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 0.900 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: 0.200 Extract box with map and model: 4.280 Check model and map are aligned: 0.190 Set scattering table: 0.130 Process input model: 46.100 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.050 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 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 0.049 7328 Z= 0.364 Angle : 0.716 6.775 9992 Z= 0.396 Chirality : 0.044 0.271 1116 Planarity : 0.005 0.038 1240 Dihedral : 8.500 74.874 2444 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -1.45 (0.26), residues: 904 helix: -0.03 (0.20), residues: 540 sheet: -2.26 (0.36), residues: 136 loop : -2.04 (0.43), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 436 HIS 0.006 0.002 HIS B 349 PHE 0.022 0.002 PHE D 376 TYR 0.017 0.002 TYR D 373 ARG 0.007 0.001 ARG B 117 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 125 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue MET 303 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue MET 303 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Evaluate side-chains 244 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.5629 time to fit residues: 169.0011 Evaluate side-chains 138 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 1.059 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 27 optimal weight: 0.4980 chunk 43 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 HIS C 398 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7328 Z= 0.217 Angle : 0.541 4.442 9992 Z= 0.290 Chirality : 0.039 0.138 1116 Planarity : 0.005 0.057 1240 Dihedral : 3.931 13.958 1024 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.09 % Allowed : 7.72 % Favored : 90.19 % 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: 0.97 (0.29), residues: 904 helix: 1.99 (0.22), residues: 558 sheet: -1.64 (0.37), residues: 138 loop : -1.38 (0.46), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 436 HIS 0.006 0.001 HIS D 349 PHE 0.011 0.001 PHE C 348 TYR 0.013 0.001 TYR B 373 ARG 0.005 0.000 ARG C 440 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 125 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue MET 303 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue MET 303 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Evaluate side-chains 158 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 145 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 12 residues processed: 154 average time/residue: 0.3584 time to fit residues: 74.6722 Evaluate side-chains 139 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 127 time to evaluate : 1.098 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1453 time to fit residues: 4.4656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 82 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 GLN ** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 398 HIS C 416 GLN ** D 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 398 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.5675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 7328 Z= 0.411 Angle : 0.644 4.801 9992 Z= 0.355 Chirality : 0.041 0.145 1116 Planarity : 0.005 0.028 1240 Dihedral : 4.222 18.872 1024 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.93 % Allowed : 9.49 % Favored : 88.59 % 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: 1.31 (0.29), residues: 904 helix: 2.16 (0.22), residues: 562 sheet: -1.58 (0.36), residues: 154 loop : -0.85 (0.51), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 436 HIS 0.009 0.002 HIS B 349 PHE 0.021 0.002 PHE C 348 TYR 0.017 0.002 TYR B 373 ARG 0.004 0.001 ARG A 170 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 125 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue MET 303 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue MET 303 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Evaluate side-chains 131 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 119 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 129 average time/residue: 0.3974 time to fit residues: 68.4975 Evaluate side-chains 113 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 105 time to evaluate : 1.180 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1680 time to fit residues: 3.6103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 74 optimal weight: 0.5980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 GLN B 326 HIS C 298 GLN ** D 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.5829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7328 Z= 0.198 Angle : 0.503 4.329 9992 Z= 0.265 Chirality : 0.038 0.157 1116 Planarity : 0.003 0.030 1240 Dihedral : 3.669 14.679 1024 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.80 % Allowed : 11.90 % Favored : 87.30 % 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: 2.23 (0.30), residues: 904 helix: 2.91 (0.22), residues: 564 sheet: -0.93 (0.39), residues: 140 loop : -0.99 (0.48), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 HIS 0.003 0.001 HIS B 322 PHE 0.013 0.001 PHE A 376 TYR 0.010 0.001 TYR B 373 ARG 0.003 0.000 ARG A 263 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 125 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue MET 303 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue MET 303 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Evaluate side-chains 128 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 123 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 123 average time/residue: 0.3646 time to fit residues: 61.4235 Evaluate side-chains 113 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 1.074 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 75 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 326 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.6350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 7328 Z= 0.326 Angle : 0.545 4.449 9992 Z= 0.296 Chirality : 0.039 0.136 1116 Planarity : 0.003 0.022 1240 Dihedral : 3.764 15.613 1024 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.48 % Allowed : 13.50 % Favored : 86.01 % 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: 2.41 (0.29), residues: 904 helix: 2.96 (0.22), residues: 566 sheet: -0.73 (0.40), residues: 140 loop : -0.74 (0.48), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 252 HIS 0.007 0.001 HIS D 349 PHE 0.014 0.002 PHE C 348 TYR 0.012 0.001 TYR D 373 ARG 0.003 0.000 ARG C 263 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 125 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue MET 303 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue MET 303 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Evaluate side-chains 111 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 108 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 109 average time/residue: 0.3846 time to fit residues: 57.6870 Evaluate side-chains 109 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 106 time to evaluate : 1.085 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1422 time to fit residues: 2.0975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.6622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7328 Z= 0.244 Angle : 0.506 4.387 9992 Z= 0.269 Chirality : 0.038 0.143 1116 Planarity : 0.003 0.019 1240 Dihedral : 3.613 14.112 1024 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.48 % Allowed : 12.54 % Favored : 86.98 % 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: 2.73 (0.29), residues: 904 helix: 3.18 (0.22), residues: 566 sheet: -0.54 (0.41), residues: 140 loop : -0.59 (0.48), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 436 HIS 0.004 0.001 HIS B 326 PHE 0.011 0.001 PHE A 376 TYR 0.010 0.001 TYR A 373 ARG 0.006 0.000 ARG A 170 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 125 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue MET 303 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue MET 303 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Evaluate side-chains 114 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 111 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 113 average time/residue: 0.3851 time to fit residues: 60.3620 Evaluate side-chains 104 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 101 time to evaluate : 1.177 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1567 time to fit residues: 2.3175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 74 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 88 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.6831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7328 Z= 0.251 Angle : 0.506 4.551 9992 Z= 0.270 Chirality : 0.038 0.139 1116 Planarity : 0.003 0.042 1240 Dihedral : 3.546 14.916 1024 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.29 % Allowed : 11.09 % Favored : 87.62 % 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: 2.95 (0.29), residues: 904 helix: 3.31 (0.21), residues: 566 sheet: -0.37 (0.42), residues: 140 loop : -0.45 (0.48), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 252 HIS 0.004 0.001 HIS B 326 PHE 0.011 0.001 PHE C 348 TYR 0.010 0.001 TYR A 373 ARG 0.006 0.000 ARG C 170 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 125 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue MET 303 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue MET 303 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 105 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 109 average time/residue: 0.3380 time to fit residues: 51.2454 Evaluate side-chains 104 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 101 time to evaluate : 1.166 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1580 time to fit residues: 2.2020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 82 optimal weight: 9.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 GLN C 298 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.7044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 7328 Z= 0.322 Angle : 0.541 4.470 9992 Z= 0.293 Chirality : 0.038 0.138 1116 Planarity : 0.004 0.035 1240 Dihedral : 3.667 14.601 1024 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.48 % Allowed : 13.50 % Favored : 86.01 % 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: 2.91 (0.29), residues: 904 helix: 3.23 (0.21), residues: 566 sheet: -0.31 (0.43), residues: 138 loop : -0.35 (0.48), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.004 0.001 HIS B 326 PHE 0.012 0.002 PHE C 348 TYR 0.011 0.001 TYR B 373 ARG 0.004 0.000 ARG A 170 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 125 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue MET 303 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue MET 303 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Evaluate side-chains 108 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 105 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 107 average time/residue: 0.3438 time to fit residues: 51.2629 Evaluate side-chains 105 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 104 time to evaluate : 1.197 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1476 time to fit residues: 1.7473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 4.9990 chunk 49 optimal weight: 0.3980 chunk 35 optimal weight: 0.4980 chunk 64 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 82 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.7132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7328 Z= 0.163 Angle : 0.484 4.939 9992 Z= 0.253 Chirality : 0.037 0.147 1116 Planarity : 0.003 0.030 1240 Dihedral : 3.444 16.479 1024 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.48 % Allowed : 15.11 % Favored : 84.41 % 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: 3.34 (0.30), residues: 904 helix: 3.54 (0.22), residues: 570 sheet: -0.60 (0.41), residues: 156 loop : 0.35 (0.52), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 340 HIS 0.003 0.001 HIS B 326 PHE 0.011 0.001 PHE C 376 TYR 0.008 0.001 TYR A 373 ARG 0.004 0.000 ARG C 170 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 125 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue MET 303 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue MET 303 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue LEU 400 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue ILE 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue LYS 312 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue THR 350 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 370 is missing expected H atoms. Skipping. Residue MET 403 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue THR 439 is missing expected H atoms. Skipping. Evaluate side-chains 112 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 109 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 111 average time/residue: 0.3495 time to fit residues: 54.9192 Evaluate side-chains 107 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 106 time to evaluate : 1.124 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1937 time to fit residues: 1.6749 ------------------------------------------------------------------------------- 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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.2325 > 50: distance: 144 - 198: 9.949 distance: 159 - 222: 4.263 distance: 175 - 238: 10.643 distance: 179 - 180: 6.183 distance: 179 - 187: 8.326 distance: 180 - 183: 5.714 distance: 180 - 188: 4.506 distance: 181 - 182: 9.090 distance: 181 - 198: 10.675 distance: 182 - 257: 13.395 distance: 183 - 184: 4.896 distance: 183 - 185: 9.911 distance: 183 - 189: 5.296 distance: 184 - 186: 8.968 distance: 184 - 190: 5.300 distance: 184 - 191: 5.790 distance: 185 - 192: 4.965 distance: 185 - 193: 4.711 distance: 185 - 194: 4.367 distance: 186 - 195: 7.090 distance: 186 - 196: 6.440 distance: 186 - 197: 4.886 distance: 198 - 199: 4.095 distance: 198 - 209: 10.520 distance: 199 - 200: 7.477 distance: 199 - 202: 3.109 distance: 199 - 210: 8.826 distance: 200 - 201: 4.363 distance: 200 - 222: 8.550 distance: 201 - 267: 8.575 distance: 202 - 203: 7.566 distance: 202 - 211: 11.521 distance: 202 - 212: 10.480 distance: 203 - 204: 4.866 distance: 204 - 205: 11.285 distance: 204 - 215: 4.817 distance: 204 - 216: 7.769 distance: 205 - 206: 9.655 distance: 205 - 217: 13.970 distance: 206 - 207: 12.594 distance: 206 - 208: 13.187 distance: 207 - 218: 5.676 distance: 207 - 219: 3.100 distance: 208 - 220: 4.303 distance: 208 - 221: 3.873 distance: 222 - 223: 13.419 distance: 222 - 229: 8.700 distance: 223 - 224: 20.045 distance: 223 - 226: 6.383 distance: 223 - 230: 8.756 distance: 224 - 225: 13.226 distance: 224 - 238: 12.770 distance: 225 - 283: 8.152 distance: 226 - 227: 4.209 distance: 226 - 228: 15.223 distance: 226 - 231: 3.689 distance: 227 - 232: 8.960 distance: 227 - 233: 9.455 distance: 227 - 234: 5.775 distance: 228 - 235: 11.559 distance: 228 - 236: 10.501 distance: 228 - 237: 4.415 distance: 238 - 239: 4.759 distance: 238 - 246: 17.138 distance: 239 - 240: 4.659 distance: 239 - 242: 5.957 distance: 239 - 247: 13.780 distance: 240 - 241: 6.641 distance: 240 - 257: 4.689 distance: 241 - 298: 13.913 distance: 242 - 243: 4.947 distance: 242 - 244: 3.675 distance: 242 - 248: 4.542 distance: 243 - 245: 6.153 distance: 243 - 249: 3.066 distance: 243 - 250: 3.340 distance: 244 - 251: 5.468 distance: 244 - 252: 7.456 distance: 244 - 253: 4.140 distance: 245 - 254: 3.093 distance: 245 - 256: 5.035 distance: 257 - 258: 4.304 distance: 257 - 262: 3.698 distance: 258 - 261: 4.898 distance: 258 - 263: 4.677 distance: 259 - 260: 17.654 distance: 259 - 267: 10.616 distance: 261 - 264: 22.908 distance: 261 - 265: 17.525 distance: 261 - 266: 27.504 distance: 267 - 268: 5.132 distance: 267 - 274: 6.916 distance: 268 - 269: 5.439 distance: 268 - 271: 12.171 distance: 268 - 275: 8.931 distance: 269 - 270: 13.369 distance: 269 - 283: 7.380 distance: 271 - 272: 9.117 distance: 271 - 273: 11.126 distance: 271 - 276: 3.250 distance: 272 - 278: 4.000 distance: 272 - 279: 6.928 distance: 273 - 280: 6.496 distance: 273 - 281: 6.285 distance: 283 - 284: 17.527 distance: 283 - 292: 19.294 distance: 284 - 285: 13.072 distance: 284 - 287: 5.258 distance: 284 - 293: 16.976 distance: 285 - 286: 11.397 distance: 285 - 298: 45.605 distance: 287 - 288: 23.014 distance: 287 - 294: 18.819 distance: 287 - 295: 7.053 distance: 288 - 289: 3.990 distance: 288 - 296: 14.856 distance: 288 - 297: 8.183 distance: 289 - 290: 12.688 distance: 289 - 291: 12.725 distance: 298 - 299: 16.513 distance: 298 - 310: 19.976 distance: 299 - 300: 21.333 distance: 299 - 302: 21.424 distance: 299 - 311: 15.951 distance: 300 - 301: 14.597 distance: 300 - 319: 40.027 distance: 302 - 303: 11.646 distance: 302 - 312: 7.677 distance: 302 - 313: 5.916 distance: 303 - 305: 10.676 distance: 304 - 306: 6.178 distance: 304 - 314: 3.154 distance: 305 - 307: 3.737 distance: 305 - 315: 6.525 distance: 306 - 308: 3.436 distance: 307 - 317: 3.908 distance: 308 - 309: 5.989 distance: 309 - 318: 7.579 distance: 319 - 320: 16.625 distance: 319 - 327: 5.487 distance: 320 - 321: 7.482 distance: 320 - 323: 5.277 distance: 320 - 328: 9.378 distance: 321 - 322: 14.463 distance: 321 - 331: 25.339 distance: 323 - 324: 14.248 distance: 323 - 329: 27.579 distance: 323 - 330: 23.475 distance: 324 - 325: 14.099 distance: 324 - 326: 4.309 distance: 331 - 332: 6.972 distance: 331 - 336: 14.138 distance: 332 - 333: 21.106 distance: 332 - 335: 7.889 distance: 332 - 337: 15.863 distance: 333 - 334: 34.754 distance: 333 - 338: 27.519