Starting phenix.real_space_refine on Sat Mar 16 04:46:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dt0_8911/03_2024/6dt0_8911.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dt0_8911/03_2024/6dt0_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_8911/03_2024/6dt0_8911.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dt0_8911/03_2024/6dt0_8911.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dt0_8911/03_2024/6dt0_8911.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dt0_8911/03_2024/6dt0_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-dev-5265/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: 6.55, per 1000 atoms: 0.48 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: 10.27 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: 1.06 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: 4.30 Time building geometry restraints manager: 10.63 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: 6225 14.97 - 29.95: 221 29.95 - 44.92: 59 44.92 - 59.90: 123 59.90 - 74.87: 8 Dihedral angle restraints: 6636 sinusoidal: 3268 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 6633 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: 0.000 Normalize map: mean=0, sd=1: 0.910 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: 0.220 Extract box with map and model: 4.230 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 44.610 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.030 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:2.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.000 ------------------------------------------------------------------------------- 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 : 1.098 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: A 189 ASN cc_start: 0.8215 (m-40) cc_final: 0.7959 (p0) REVERT: A 318 ASP cc_start: 0.8516 (m-30) cc_final: 0.8264 (m-30) REVERT: B 116 THR cc_start: 0.8874 (p) cc_final: 0.8434 (t) REVERT: B 125 LEU cc_start: 0.8898 (tp) cc_final: 0.8666 (tt) REVERT: B 173 GLN cc_start: 0.8759 (mt0) cc_final: 0.8505 (mt0) REVERT: C 189 ASN cc_start: 0.8190 (m-40) cc_final: 0.7922 (p0) REVERT: C 318 ASP cc_start: 0.8530 (m-30) cc_final: 0.8278 (m-30) REVERT: D 116 THR cc_start: 0.8880 (p) cc_final: 0.8418 (t) REVERT: D 125 LEU cc_start: 0.8992 (tp) cc_final: 0.8762 (tt) REVERT: D 173 GLN cc_start: 0.8750 (mt0) cc_final: 0.8491 (mt0) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.5487 time to fit residues: 163.6411 Evaluate side-chains 142 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.115 ------------------------------------------------------------------------------- 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: 1.9990 chunk 38 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 27 optimal weight: 0.0050 chunk 43 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 overall best weight: 1.1200 ------------------------------------------------------------------------------- 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: 0.7900 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7328 Z= 0.202 Angle : 0.533 4.373 9992 Z= 0.285 Chirality : 0.039 0.137 1116 Planarity : 0.005 0.064 1240 Dihedral : 3.915 13.705 1024 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.93 % Allowed : 7.56 % Favored : 90.51 % 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: 1.04 (0.29), residues: 904 helix: 1.99 (0.22), residues: 560 sheet: -1.58 (0.38), residues: 138 loop : -1.25 (0.47), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 436 HIS 0.007 0.001 HIS D 349 PHE 0.011 0.001 PHE C 348 TYR 0.014 0.001 TYR B 373 ARG 0.005 0.000 ARG A 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 164 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 152 time to evaluate : 1.092 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 REVERT: A 189 ASN cc_start: 0.8267 (m-40) cc_final: 0.7944 (p0) REVERT: A 318 ASP cc_start: 0.8435 (m-30) cc_final: 0.8097 (m-30) REVERT: A 340 TRP cc_start: 0.8421 (t60) cc_final: 0.8138 (t60) REVERT: B 125 LEU cc_start: 0.8840 (tp) cc_final: 0.8638 (tt) REVERT: C 189 ASN cc_start: 0.8237 (m-40) cc_final: 0.7902 (p0) REVERT: C 318 ASP cc_start: 0.8420 (m-30) cc_final: 0.8074 (m-30) REVERT: C 340 TRP cc_start: 0.8429 (t60) cc_final: 0.8148 (t60) REVERT: D 125 LEU cc_start: 0.8881 (tp) cc_final: 0.8657 (tt) outliers start: 12 outliers final: 11 residues processed: 159 average time/residue: 0.3632 time to fit residues: 79.1250 Evaluate side-chains 140 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 129 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 HIS Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain C residue 315 HIS Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 298 GLN Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 430 VAL 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: 0.7980 chunk 69 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 GLN C 416 GLN D 398 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.5186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 7328 Z= 0.350 Angle : 0.584 5.088 9992 Z= 0.319 Chirality : 0.040 0.148 1116 Planarity : 0.004 0.022 1240 Dihedral : 3.955 16.486 1024 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.38 % Allowed : 8.68 % Favored : 87.94 % 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: 1.61 (0.29), residues: 904 helix: 2.40 (0.22), residues: 560 sheet: -1.17 (0.39), residues: 138 loop : -1.06 (0.47), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 436 HIS 0.007 0.002 HIS D 349 PHE 0.028 0.002 PHE A 289 TYR 0.015 0.001 TYR D 373 ARG 0.004 0.001 ARG B 423 *********************** 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 143 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 122 time to evaluate : 1.060 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: A 189 ASN cc_start: 0.8368 (m-40) cc_final: 0.7916 (p0) REVERT: A 318 ASP cc_start: 0.8310 (m-30) cc_final: 0.7986 (m-30) REVERT: C 189 ASN cc_start: 0.8340 (m-40) cc_final: 0.7886 (p0) REVERT: C 318 ASP cc_start: 0.8327 (m-30) cc_final: 0.7999 (m-30) outliers start: 21 outliers final: 17 residues processed: 141 average time/residue: 0.3459 time to fit residues: 66.8363 Evaluate side-chains 129 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 112 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 249 TRP Chi-restraints excluded: chain A residue 315 HIS Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 249 TRP Chi-restraints excluded: chain C residue 315 HIS Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain D residue 374 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 88 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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: 0.8025 moved from start: 0.5745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 7328 Z= 0.241 Angle : 0.508 4.320 9992 Z= 0.273 Chirality : 0.038 0.138 1116 Planarity : 0.003 0.030 1240 Dihedral : 3.642 14.338 1024 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.38 % Allowed : 10.77 % Favored : 85.85 % 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 (0.29), residues: 904 helix: 2.91 (0.22), residues: 562 sheet: -0.78 (0.40), residues: 140 loop : -1.08 (0.46), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.003 0.001 HIS B 349 PHE 0.011 0.001 PHE C 348 TYR 0.011 0.001 TYR B 373 ARG 0.004 0.000 ARG C 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 141 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 120 time to evaluate : 1.058 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: A 318 ASP cc_start: 0.8379 (m-30) cc_final: 0.8093 (m-30) REVERT: A 373 TYR cc_start: 0.7765 (t80) cc_final: 0.7460 (t80) REVERT: C 318 ASP cc_start: 0.8316 (m-30) cc_final: 0.8014 (m-30) REVERT: C 373 TYR cc_start: 0.7772 (t80) cc_final: 0.7522 (t80) outliers start: 21 outliers final: 16 residues processed: 137 average time/residue: 0.3675 time to fit residues: 67.8240 Evaluate side-chains 131 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 115 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 TRP Chi-restraints excluded: chain A residue 315 HIS Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 258 MET Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain C residue 249 TRP Chi-restraints excluded: chain C residue 315 HIS Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 258 MET Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 430 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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: 0.8042 moved from start: 0.6181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7328 Z= 0.245 Angle : 0.516 4.352 9992 Z= 0.274 Chirality : 0.038 0.128 1116 Planarity : 0.003 0.019 1240 Dihedral : 3.560 13.390 1024 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.38 % Allowed : 11.41 % Favored : 85.21 % 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: 2.62 (0.30), residues: 904 helix: 3.10 (0.22), residues: 568 sheet: -0.54 (0.41), residues: 140 loop : -0.75 (0.48), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.004 0.001 HIS B 326 PHE 0.012 0.001 PHE A 348 TYR 0.010 0.001 TYR D 373 ARG 0.004 0.000 ARG A 170 *********************** 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 147 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 126 time to evaluate : 1.116 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: A 113 THR cc_start: 0.9055 (m) cc_final: 0.8686 (p) REVERT: A 318 ASP cc_start: 0.8310 (m-30) cc_final: 0.8041 (m-30) REVERT: A 340 TRP cc_start: 0.8824 (t60) cc_final: 0.8494 (t60) REVERT: A 373 TYR cc_start: 0.7779 (t80) cc_final: 0.7420 (t80) REVERT: B 120 LYS cc_start: 0.9161 (tttp) cc_final: 0.8859 (ttmm) REVERT: C 113 THR cc_start: 0.9035 (m) cc_final: 0.8715 (p) REVERT: C 263 ARG cc_start: 0.9020 (OUTLIER) cc_final: 0.8677 (mtm110) REVERT: C 318 ASP cc_start: 0.8327 (m-30) cc_final: 0.8053 (m-30) REVERT: C 340 TRP cc_start: 0.8822 (t60) cc_final: 0.8494 (t60) REVERT: C 373 TYR cc_start: 0.7694 (t80) cc_final: 0.7343 (t80) REVERT: D 120 LYS cc_start: 0.9150 (tttp) cc_final: 0.8847 (ttmm) outliers start: 21 outliers final: 14 residues processed: 141 average time/residue: 0.3600 time to fit residues: 68.9224 Evaluate side-chains 135 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 120 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 TRP Chi-restraints excluded: chain A residue 315 HIS Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain C residue 249 TRP Chi-restraints excluded: chain C residue 263 ARG Chi-restraints excluded: chain C residue 315 HIS Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 430 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 85 optimal weight: 0.3980 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 GLN B 398 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.6583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 7328 Z= 0.307 Angle : 0.542 4.561 9992 Z= 0.290 Chirality : 0.038 0.132 1116 Planarity : 0.004 0.045 1240 Dihedral : 3.655 14.186 1024 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.54 % Allowed : 11.25 % Favored : 85.21 % 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: 2.62 (0.29), residues: 904 helix: 3.04 (0.21), residues: 570 sheet: -0.47 (0.42), residues: 138 loop : -0.62 (0.47), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 HIS 0.005 0.001 HIS B 349 PHE 0.013 0.001 PHE A 348 TYR 0.010 0.001 TYR B 373 ARG 0.006 0.000 ARG C 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 139 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 117 time to evaluate : 1.149 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: A 113 THR cc_start: 0.9065 (m) cc_final: 0.8693 (p) REVERT: A 318 ASP cc_start: 0.8204 (m-30) cc_final: 0.7906 (m-30) REVERT: A 340 TRP cc_start: 0.8887 (t60) cc_final: 0.8563 (t60) REVERT: A 373 TYR cc_start: 0.7781 (t80) cc_final: 0.7429 (t80) REVERT: B 120 LYS cc_start: 0.9230 (tttp) cc_final: 0.8743 (ttpt) REVERT: C 113 THR cc_start: 0.9056 (m) cc_final: 0.8734 (p) REVERT: C 318 ASP cc_start: 0.8219 (m-30) cc_final: 0.7919 (m-30) REVERT: C 340 TRP cc_start: 0.8895 (t60) cc_final: 0.8579 (t60) REVERT: C 373 TYR cc_start: 0.7783 (t80) cc_final: 0.7439 (t80) REVERT: D 120 LYS cc_start: 0.9215 (tttp) cc_final: 0.8729 (ttpt) outliers start: 22 outliers final: 18 residues processed: 132 average time/residue: 0.3603 time to fit residues: 65.7974 Evaluate side-chains 132 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 114 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 249 TRP Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 315 HIS Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 249 TRP Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 315 HIS Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 430 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 74 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 88 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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: 0.8036 moved from start: 0.6676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7328 Z= 0.171 Angle : 0.487 4.258 9992 Z= 0.254 Chirality : 0.037 0.138 1116 Planarity : 0.003 0.026 1240 Dihedral : 3.440 14.095 1024 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.05 % Allowed : 10.77 % Favored : 86.17 % 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: 3.03 (0.29), residues: 904 helix: 3.34 (0.22), residues: 568 sheet: -0.36 (0.42), residues: 140 loop : -0.32 (0.48), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 436 HIS 0.004 0.001 HIS B 326 PHE 0.008 0.001 PHE A 348 TYR 0.008 0.001 TYR D 373 ARG 0.006 0.000 ARG C 263 *********************** 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 149 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 130 time to evaluate : 1.040 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: A 318 ASP cc_start: 0.8232 (m-30) cc_final: 0.7938 (m-30) REVERT: A 340 TRP cc_start: 0.8812 (t60) cc_final: 0.8526 (t60) REVERT: A 345 TYR cc_start: 0.8762 (t80) cc_final: 0.8404 (t80) REVERT: B 120 LYS cc_start: 0.9151 (tttp) cc_final: 0.8698 (ttpt) REVERT: C 318 ASP cc_start: 0.8249 (m-30) cc_final: 0.7952 (m-30) REVERT: C 340 TRP cc_start: 0.8817 (t60) cc_final: 0.8483 (t60) REVERT: C 345 TYR cc_start: 0.8768 (t80) cc_final: 0.8412 (t80) REVERT: D 120 LYS cc_start: 0.9159 (tttp) cc_final: 0.8714 (ttpt) outliers start: 19 outliers final: 11 residues processed: 146 average time/residue: 0.3243 time to fit residues: 65.6596 Evaluate side-chains 130 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 119 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 315 HIS Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain C residue 315 HIS Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 430 VAL 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: 2.9990 chunk 56 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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: 0.8056 moved from start: 0.6885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7328 Z= 0.254 Angle : 0.523 4.496 9992 Z= 0.279 Chirality : 0.038 0.170 1116 Planarity : 0.003 0.030 1240 Dihedral : 3.558 16.329 1024 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.57 % Allowed : 13.18 % Favored : 84.24 % 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: 3.09 (0.29), residues: 904 helix: 3.38 (0.21), residues: 570 sheet: -0.29 (0.43), residues: 138 loop : -0.34 (0.48), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 HIS 0.004 0.001 HIS B 326 PHE 0.011 0.001 PHE A 348 TYR 0.008 0.001 TYR D 373 ARG 0.005 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 140 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 124 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 ASP cc_start: 0.8108 (m-30) cc_final: 0.7819 (m-30) REVERT: A 340 TRP cc_start: 0.8963 (t60) cc_final: 0.8554 (t60) REVERT: A 345 TYR cc_start: 0.8725 (t80) cc_final: 0.8394 (t80) REVERT: B 120 LYS cc_start: 0.9213 (tttp) cc_final: 0.8749 (ttpt) REVERT: C 318 ASP cc_start: 0.8128 (m-30) cc_final: 0.7836 (m-30) REVERT: C 340 TRP cc_start: 0.8902 (t60) cc_final: 0.8552 (t60) REVERT: C 345 TYR cc_start: 0.8742 (t80) cc_final: 0.8411 (t80) REVERT: D 120 LYS cc_start: 0.9188 (tttp) cc_final: 0.8735 (ttpt) outliers start: 16 outliers final: 14 residues processed: 135 average time/residue: 0.3220 time to fit residues: 60.1908 Evaluate side-chains 133 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 119 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 315 HIS Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 315 HIS Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 430 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 82 optimal weight: 9.9990 chunk 54 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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: 0.8041 moved from start: 0.7027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7328 Z= 0.201 Angle : 0.503 4.398 9992 Z= 0.264 Chirality : 0.038 0.137 1116 Planarity : 0.003 0.024 1240 Dihedral : 3.442 15.579 1024 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.57 % Allowed : 13.02 % 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: 3.27 (0.30), residues: 904 helix: 3.51 (0.21), residues: 570 sheet: -0.64 (0.40), residues: 154 loop : 0.22 (0.52), residues: 180 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 0.009 0.001 PHE A 348 TYR 0.008 0.001 TYR D 373 ARG 0.005 0.000 ARG A 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 135 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 119 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: A 318 ASP cc_start: 0.8097 (m-30) cc_final: 0.7813 (m-30) REVERT: A 340 TRP cc_start: 0.8985 (t60) cc_final: 0.8552 (t60) REVERT: A 345 TYR cc_start: 0.8731 (t80) cc_final: 0.8404 (t80) REVERT: B 120 LYS cc_start: 0.9192 (tttp) cc_final: 0.8742 (ttpt) REVERT: C 318 ASP cc_start: 0.8117 (m-30) cc_final: 0.7829 (m-30) REVERT: C 340 TRP cc_start: 0.8896 (t60) cc_final: 0.8531 (t60) REVERT: C 345 TYR cc_start: 0.8740 (t80) cc_final: 0.8390 (t80) REVERT: D 120 LYS cc_start: 0.9196 (tttp) cc_final: 0.8744 (ttpt) outliers start: 16 outliers final: 14 residues processed: 133 average time/residue: 0.3430 time to fit residues: 63.0075 Evaluate side-chains 131 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 117 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 315 HIS Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 315 HIS Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 430 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 84 optimal weight: 0.3980 chunk 72 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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: 0.8039 moved from start: 0.7194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7328 Z= 0.198 Angle : 0.500 4.371 9992 Z= 0.264 Chirality : 0.038 0.136 1116 Planarity : 0.003 0.023 1240 Dihedral : 3.392 17.372 1024 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.25 % Allowed : 13.67 % Favored : 84.08 % 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: 3.37 (0.30), residues: 904 helix: 3.57 (0.21), residues: 570 sheet: -0.62 (0.41), residues: 156 loop : 0.34 (0.53), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 HIS 0.004 0.001 HIS D 326 PHE 0.011 0.001 PHE A 348 TYR 0.008 0.001 TYR D 373 ARG 0.005 0.000 ARG A 170 ********************** REFINEMENT MACRO_CYCLE 10 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 135 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 121 time to evaluate : 1.053 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: A 318 ASP cc_start: 0.8092 (m-30) cc_final: 0.7809 (m-30) REVERT: A 340 TRP cc_start: 0.9027 (t60) cc_final: 0.8664 (t60) REVERT: A 344 TYR cc_start: 0.9171 (t80) cc_final: 0.8936 (t80) REVERT: A 345 TYR cc_start: 0.8736 (t80) cc_final: 0.8420 (t80) REVERT: B 120 LYS cc_start: 0.9182 (tttp) cc_final: 0.8822 (ttpt) REVERT: C 318 ASP cc_start: 0.8111 (m-30) cc_final: 0.7824 (m-30) REVERT: C 340 TRP cc_start: 0.8938 (t60) cc_final: 0.8568 (t60) REVERT: C 345 TYR cc_start: 0.8741 (t80) cc_final: 0.8399 (t80) REVERT: D 120 LYS cc_start: 0.9186 (tttp) cc_final: 0.8755 (ttpt) outliers start: 14 outliers final: 13 residues processed: 133 average time/residue: 0.3343 time to fit residues: 61.3320 Evaluate side-chains 132 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 119 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 315 HIS Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 315 HIS Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 430 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 73 optimal weight: 0.4980 chunk 30 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 64 optimal weight: 0.0970 chunk 4 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.096988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.079482 restraints weight = 57861.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.082304 restraints weight = 21448.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.084024 restraints weight = 11525.462| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.7323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7328 Z= 0.264 Angle : 0.525 4.435 9992 Z= 0.280 Chirality : 0.038 0.134 1116 Planarity : 0.003 0.024 1240 Dihedral : 3.448 15.328 1024 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.41 % Allowed : 13.83 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.35 (0.30), residues: 904 helix: 3.52 (0.21), residues: 570 sheet: -0.53 (0.41), residues: 154 loop : 0.34 (0.52), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.005 0.001 HIS B 160 PHE 0.012 0.001 PHE C 348 TYR 0.009 0.001 TYR D 373 ARG 0.005 0.000 ARG A 170 =============================================================================== Job complete usr+sys time: 2946.28 seconds wall clock time: 52 minutes 20.36 seconds (3140.36 seconds total)