Starting phenix.real_space_refine on Fri Jul 19 20:05:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8trm_41583/07_2024/8trm_41583_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8trm_41583/07_2024/8trm_41583.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8trm_41583/07_2024/8trm_41583.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8trm_41583/07_2024/8trm_41583.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8trm_41583/07_2024/8trm_41583_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8trm_41583/07_2024/8trm_41583_neut.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.359 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 3 5.21 5 S 57 5.16 5 C 5544 2.51 5 N 1470 2.21 5 O 1734 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 25": "OD1" <-> "OD2" Residue "A GLU 73": "OE1" <-> "OE2" Residue "A ASP 82": "OD1" <-> "OD2" Residue "A GLU 101": "OE1" <-> "OE2" Residue "A GLU 168": "OE1" <-> "OE2" Residue "A GLU 206": "OE1" <-> "OE2" Residue "A ASP 212": "OD1" <-> "OD2" Residue "A ASP 223": "OD1" <-> "OD2" Residue "A ASP 245": "OD1" <-> "OD2" Residue "A ASP 293": "OD1" <-> "OD2" Residue "A GLU 362": "OE1" <-> "OE2" Residue "A ASP 364": "OD1" <-> "OD2" Residue "B ASP 25": "OD1" <-> "OD2" Residue "B GLU 73": "OE1" <-> "OE2" Residue "B ASP 82": "OD1" <-> "OD2" Residue "B GLU 101": "OE1" <-> "OE2" Residue "B GLU 168": "OE1" <-> "OE2" Residue "B GLU 206": "OE1" <-> "OE2" Residue "B ASP 212": "OD1" <-> "OD2" Residue "B ASP 223": "OD1" <-> "OD2" Residue "B ASP 245": "OD1" <-> "OD2" Residue "B ASP 293": "OD1" <-> "OD2" Residue "B GLU 362": "OE1" <-> "OE2" Residue "B ASP 364": "OD1" <-> "OD2" Residue "C ASP 25": "OD1" <-> "OD2" Residue "C GLU 73": "OE1" <-> "OE2" Residue "C ASP 82": "OD1" <-> "OD2" Residue "C GLU 101": "OE1" <-> "OE2" Residue "C GLU 168": "OE1" <-> "OE2" Residue "C GLU 206": "OE1" <-> "OE2" Residue "C ASP 212": "OD1" <-> "OD2" Residue "C ASP 223": "OD1" <-> "OD2" Residue "C ASP 245": "OD1" <-> "OD2" Residue "C ASP 293": "OD1" <-> "OD2" Residue "C GLU 362": "OE1" <-> "OE2" Residue "C ASP 364": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 8814 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "B" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "C" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Time building chain proxies: 5.03, per 1000 atoms: 0.57 Number of scatterers: 8814 At special positions: 0 Unit cell: (77.464, 99.356, 138.93, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 57 16.00 P 6 15.00 Mg 3 11.99 O 1734 8.00 N 1470 7.00 C 5544 6.00 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: 3.57 Conformation dependent library (CDL) restraints added in 1.6 seconds 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2046 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 18 sheets defined 50.1% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'A' and resid 56 through 62 Processing helix chain 'A' and resid 79 through 93 Processing helix chain 'A' and resid 113 through 127 removed outlier: 4.018A pdb=" N ARG A 117 " --> pdb=" O PRO A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 146 Processing helix chain 'A' and resid 173 through 176 Processing helix chain 'A' and resid 182 through 194 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 203 through 218 Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 253 through 258 Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 264 through 269 Processing helix chain 'A' and resid 274 through 285 Processing helix chain 'A' and resid 290 through 297 Processing helix chain 'A' and resid 302 through 306 removed outlier: 3.575A pdb=" N THR A 305 " --> pdb=" O GLY A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 322 Processing helix chain 'A' and resid 335 through 337 No H-bonds generated for 'chain 'A' and resid 335 through 337' Processing helix chain 'A' and resid 338 through 349 Processing helix chain 'A' and resid 350 through 356 removed outlier: 3.540A pdb=" N GLN A 354 " --> pdb=" O SER A 351 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLN A 355 " --> pdb=" O THR A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 367 Processing helix chain 'A' and resid 369 through 375 removed outlier: 4.113A pdb=" N ARG A 373 " --> pdb=" O SER A 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 62 Processing helix chain 'B' and resid 79 through 93 Processing helix chain 'B' and resid 113 through 127 removed outlier: 4.019A pdb=" N ARG B 117 " --> pdb=" O PRO B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 146 Processing helix chain 'B' and resid 173 through 176 Processing helix chain 'B' and resid 182 through 194 Processing helix chain 'B' and resid 195 through 198 Processing helix chain 'B' and resid 203 through 218 Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 253 through 258 Processing helix chain 'B' and resid 259 through 263 Processing helix chain 'B' and resid 264 through 269 Processing helix chain 'B' and resid 274 through 285 Processing helix chain 'B' and resid 290 through 297 Processing helix chain 'B' and resid 302 through 306 removed outlier: 3.575A pdb=" N THR B 305 " --> pdb=" O GLY B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 322 Processing helix chain 'B' and resid 335 through 337 No H-bonds generated for 'chain 'B' and resid 335 through 337' Processing helix chain 'B' and resid 338 through 349 Processing helix chain 'B' and resid 350 through 356 removed outlier: 3.540A pdb=" N GLN B 354 " --> pdb=" O SER B 351 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLN B 355 " --> pdb=" O THR B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 367 Processing helix chain 'B' and resid 369 through 375 removed outlier: 4.113A pdb=" N ARG B 373 " --> pdb=" O SER B 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 62 Processing helix chain 'C' and resid 79 through 93 Processing helix chain 'C' and resid 113 through 127 removed outlier: 4.018A pdb=" N ARG C 117 " --> pdb=" O PRO C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 146 Processing helix chain 'C' and resid 173 through 176 Processing helix chain 'C' and resid 182 through 194 Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 203 through 218 Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 253 through 258 Processing helix chain 'C' and resid 259 through 263 Processing helix chain 'C' and resid 264 through 269 Processing helix chain 'C' and resid 274 through 285 Processing helix chain 'C' and resid 290 through 297 Processing helix chain 'C' and resid 302 through 306 removed outlier: 3.574A pdb=" N THR C 305 " --> pdb=" O GLY C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 322 Processing helix chain 'C' and resid 335 through 337 No H-bonds generated for 'chain 'C' and resid 335 through 337' Processing helix chain 'C' and resid 338 through 349 Processing helix chain 'C' and resid 350 through 356 removed outlier: 3.540A pdb=" N GLN C 354 " --> pdb=" O SER C 351 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN C 355 " --> pdb=" O THR C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 367 Processing helix chain 'C' and resid 369 through 375 removed outlier: 4.113A pdb=" N ARG C 373 " --> pdb=" O SER C 369 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 33 removed outlier: 6.669A pdb=" N LEU A 9 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N THR A 107 " --> pdb=" O LEU A 9 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N VAL A 11 " --> pdb=" O THR A 107 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 72 through 73 Processing sheet with id=AA4, first strand: chain 'A' and resid 170 through 171 Processing sheet with id=AA5, first strand: chain 'A' and resid 170 through 171 removed outlier: 6.832A pdb=" N VAL A 298 " --> pdb=" O VAL A 331 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 239 through 242 Processing sheet with id=AA7, first strand: chain 'B' and resid 30 through 33 removed outlier: 6.669A pdb=" N LEU B 9 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N THR B 107 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N VAL B 11 " --> pdb=" O THR B 107 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AA9, first strand: chain 'B' and resid 72 through 73 Processing sheet with id=AB1, first strand: chain 'B' and resid 170 through 171 Processing sheet with id=AB2, first strand: chain 'B' and resid 170 through 171 removed outlier: 6.832A pdb=" N VAL B 298 " --> pdb=" O VAL B 331 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 239 through 242 Processing sheet with id=AB4, first strand: chain 'C' and resid 30 through 33 removed outlier: 6.669A pdb=" N LEU C 9 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N THR C 107 " --> pdb=" O LEU C 9 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N VAL C 11 " --> pdb=" O THR C 107 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AB6, first strand: chain 'C' and resid 72 through 73 Processing sheet with id=AB7, first strand: chain 'C' and resid 170 through 171 Processing sheet with id=AB8, first strand: chain 'C' and resid 170 through 171 removed outlier: 6.832A pdb=" N VAL C 298 " --> pdb=" O VAL C 331 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 239 through 242 447 hydrogen bonds defined for protein. 1143 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: 3.06 Time building geometry restraints manager: 3.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2870 1.34 - 1.46: 1656 1.46 - 1.57: 4339 1.57 - 1.69: 9 1.69 - 1.81: 99 Bond restraints: 8973 Sorted by residual: bond pdb=" N ASP B 212 " pdb=" CA ASP B 212 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.19e-02 7.06e+03 4.76e+00 bond pdb=" N ASP C 212 " pdb=" CA ASP C 212 " ideal model delta sigma weight residual 1.459 1.485 -0.025 1.19e-02 7.06e+03 4.55e+00 bond pdb=" N ASP A 212 " pdb=" CA ASP A 212 " ideal model delta sigma weight residual 1.459 1.485 -0.025 1.19e-02 7.06e+03 4.50e+00 bond pdb=" C4 ADP C 402 " pdb=" C5 ADP C 402 " ideal model delta sigma weight residual 1.490 1.466 0.024 2.00e-02 2.50e+03 1.43e+00 bond pdb=" C4 ADP A 402 " pdb=" C5 ADP A 402 " ideal model delta sigma weight residual 1.490 1.466 0.024 2.00e-02 2.50e+03 1.43e+00 ... (remaining 8968 not shown) Histogram of bond angle deviations from ideal: 99.53 - 106.86: 329 106.86 - 114.19: 5159 114.19 - 121.53: 4541 121.53 - 128.86: 2073 128.86 - 136.19: 60 Bond angle restraints: 12162 Sorted by residual: angle pdb=" N ILE C 290 " pdb=" CA ILE C 290 " pdb=" C ILE C 290 " ideal model delta sigma weight residual 113.42 109.06 4.36 1.17e+00 7.31e-01 1.39e+01 angle pdb=" N ILE B 290 " pdb=" CA ILE B 290 " pdb=" C ILE B 290 " ideal model delta sigma weight residual 113.42 109.06 4.36 1.17e+00 7.31e-01 1.39e+01 angle pdb=" N ILE A 290 " pdb=" CA ILE A 290 " pdb=" C ILE A 290 " ideal model delta sigma weight residual 113.42 109.07 4.35 1.17e+00 7.31e-01 1.38e+01 angle pdb=" CA ILE A 290 " pdb=" C ILE A 290 " pdb=" N ARG A 291 " ideal model delta sigma weight residual 118.90 115.55 3.35 9.40e-01 1.13e+00 1.27e+01 angle pdb=" CA ILE B 290 " pdb=" C ILE B 290 " pdb=" N ARG B 291 " ideal model delta sigma weight residual 118.90 115.58 3.32 9.40e-01 1.13e+00 1.25e+01 ... (remaining 12157 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.62: 5010 28.62 - 57.24: 351 57.24 - 85.86: 36 85.86 - 114.48: 3 114.48 - 143.10: 6 Dihedral angle restraints: 5406 sinusoidal: 2205 harmonic: 3201 Sorted by residual: dihedral pdb=" O1B ADP C 402 " pdb=" O3A ADP C 402 " pdb=" PB ADP C 402 " pdb=" PA ADP C 402 " ideal model delta sinusoidal sigma weight residual -60.00 83.10 -143.10 1 2.00e+01 2.50e-03 4.32e+01 dihedral pdb=" O1B ADP B 402 " pdb=" O3A ADP B 402 " pdb=" PB ADP B 402 " pdb=" PA ADP B 402 " ideal model delta sinusoidal sigma weight residual -60.00 83.07 -143.08 1 2.00e+01 2.50e-03 4.32e+01 dihedral pdb=" O1B ADP A 402 " pdb=" O3A ADP A 402 " pdb=" PB ADP A 402 " pdb=" PA ADP A 402 " ideal model delta sinusoidal sigma weight residual -60.00 83.05 -143.05 1 2.00e+01 2.50e-03 4.32e+01 ... (remaining 5403 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 654 0.027 - 0.053: 378 0.053 - 0.080: 156 0.080 - 0.106: 122 0.106 - 0.133: 34 Chirality restraints: 1344 Sorted by residual: chirality pdb=" CA ILE A 358 " pdb=" N ILE A 358 " pdb=" C ILE A 358 " pdb=" CB ILE A 358 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.41e-01 chirality pdb=" CA ILE B 358 " pdb=" N ILE B 358 " pdb=" C ILE B 358 " pdb=" CB ILE B 358 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA ILE C 358 " pdb=" N ILE C 358 " pdb=" C ILE C 358 " pdb=" CB ILE C 358 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.26e-01 ... (remaining 1341 not shown) Planarity restraints: 1557 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 164 " 0.021 5.00e-02 4.00e+02 3.13e-02 1.57e+00 pdb=" N PRO A 165 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 165 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 165 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 164 " -0.020 5.00e-02 4.00e+02 3.11e-02 1.54e+00 pdb=" N PRO B 165 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO B 165 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 165 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 164 " -0.020 5.00e-02 4.00e+02 3.09e-02 1.53e+00 pdb=" N PRO C 165 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO C 165 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 165 " -0.017 5.00e-02 4.00e+02 ... (remaining 1554 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 42 2.51 - 3.11: 5956 3.11 - 3.70: 13252 3.70 - 4.30: 20131 4.30 - 4.90: 32954 Nonbonded interactions: 72335 Sorted by model distance: nonbonded pdb="MG MG A 401 " pdb=" O HOH A 507 " model vdw 1.909 2.170 nonbonded pdb="MG MG B 401 " pdb=" O HOH B 507 " model vdw 1.909 2.170 nonbonded pdb="MG MG C 401 " pdb=" O HOH C 507 " model vdw 1.909 2.170 nonbonded pdb="MG MG A 401 " pdb=" O HOH A 503 " model vdw 1.921 2.170 nonbonded pdb="MG MG C 401 " pdb=" O HOH C 503 " model vdw 1.921 2.170 ... (remaining 72330 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' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 26.980 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8949 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8973 Z= 0.205 Angle : 0.606 7.058 12162 Z= 0.310 Chirality : 0.047 0.133 1344 Planarity : 0.004 0.031 1557 Dihedral : 18.288 143.104 3360 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.68 % Allowed : 15.67 % Favored : 82.65 % 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: 1.52 (0.26), residues: 1107 helix: 0.82 (0.25), residues: 459 sheet: 0.95 (0.37), residues: 186 loop : 1.55 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 80 HIS 0.003 0.001 HIS A 102 PHE 0.007 0.001 PHE C 256 TYR 0.009 0.001 TYR A 295 ARG 0.001 0.000 ARG A 257 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 201 time to evaluate : 0.978 Fit side-chains REVERT: A 177 MET cc_start: 0.9077 (OUTLIER) cc_final: 0.8825 (mtm) REVERT: B 96 ARG cc_start: 0.8115 (mtp85) cc_final: 0.7906 (mtm-85) REVERT: B 168 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8460 (mm-30) REVERT: B 180 ASP cc_start: 0.8056 (OUTLIER) cc_final: 0.7709 (t0) REVERT: B 226 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7429 (mt-10) REVERT: B 229 LYS cc_start: 0.7756 (mtpm) cc_final: 0.7488 (mttm) REVERT: B 287 ASP cc_start: 0.8178 (m-30) cc_final: 0.7974 (m-30) REVERT: B 293 ASP cc_start: 0.8327 (m-30) cc_final: 0.8011 (m-30) REVERT: B 312 GLU cc_start: 0.8495 (mp0) cc_final: 0.8280 (mp0) REVERT: B 329 LYS cc_start: 0.8842 (tmtm) cc_final: 0.8624 (tptp) REVERT: B 354 GLN cc_start: 0.8499 (mm-40) cc_final: 0.8287 (mm-40) REVERT: B 362 GLU cc_start: 0.8475 (mt-10) cc_final: 0.7952 (mt-10) REVERT: C 51 LYS cc_start: 0.7915 (mtmt) cc_final: 0.7681 (mtpt) REVERT: C 84 GLU cc_start: 0.8460 (tt0) cc_final: 0.8251 (tt0) REVERT: C 96 ARG cc_start: 0.7868 (mtp85) cc_final: 0.7640 (mtt-85) REVERT: C 100 GLU cc_start: 0.8090 (pm20) cc_final: 0.7888 (pm20) REVERT: C 122 GLN cc_start: 0.8699 (tt0) cc_final: 0.8487 (tt0) REVERT: C 148 ARG cc_start: 0.8199 (mmm-85) cc_final: 0.7969 (mmt90) REVERT: C 168 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8392 (mt-10) REVERT: C 223 ASP cc_start: 0.8301 (t0) cc_final: 0.7973 (t0) REVERT: C 325 THR cc_start: 0.8732 (m) cc_final: 0.8382 (p) REVERT: C 355 GLN cc_start: 0.8178 (mm110) cc_final: 0.7872 (mp-120) outliers start: 16 outliers final: 4 residues processed: 208 average time/residue: 1.5778 time to fit residues: 344.2860 Evaluate side-chains 189 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 183 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain C residue 180 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.4980 chunk 84 optimal weight: 0.2980 chunk 46 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.8932 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8973 Z= 0.155 Angle : 0.559 6.576 12162 Z= 0.274 Chirality : 0.045 0.135 1344 Planarity : 0.004 0.041 1557 Dihedral : 11.426 143.830 1249 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.26 % Allowed : 14.83 % Favored : 81.91 % 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: 1.84 (0.26), residues: 1107 helix: 1.19 (0.25), residues: 462 sheet: 0.89 (0.37), residues: 186 loop : 1.70 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 80 HIS 0.004 0.001 HIS B 162 PHE 0.008 0.001 PHE B 256 TYR 0.011 0.001 TYR C 295 ARG 0.002 0.000 ARG B 178 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 191 time to evaluate : 1.026 Fit side-chains REVERT: A 73 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7350 (mp0) REVERT: A 96 ARG cc_start: 0.8043 (mtp85) cc_final: 0.7788 (mtm-85) REVERT: A 317 GLU cc_start: 0.9056 (mm-30) cc_final: 0.8815 (mm-30) REVERT: A 329 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8310 (tttm) REVERT: B 29 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.7885 (ptp-170) REVERT: B 58 GLU cc_start: 0.7952 (tt0) cc_final: 0.7700 (tt0) REVERT: B 73 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7171 (mp0) REVERT: B 96 ARG cc_start: 0.8158 (mtp85) cc_final: 0.7935 (mtm-85) REVERT: B 168 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8450 (mm-30) REVERT: B 229 LYS cc_start: 0.7749 (mtpm) cc_final: 0.7473 (mttm) REVERT: B 293 ASP cc_start: 0.8281 (m-30) cc_final: 0.7958 (m-30) REVERT: B 312 GLU cc_start: 0.8516 (mp0) cc_final: 0.8289 (mp0) REVERT: B 329 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8601 (tptp) REVERT: B 354 GLN cc_start: 0.8578 (mm-40) cc_final: 0.8359 (mm-40) REVERT: B 362 GLU cc_start: 0.8469 (mt-10) cc_final: 0.7988 (mt-10) REVERT: C 84 GLU cc_start: 0.8423 (tt0) cc_final: 0.8178 (tt0) REVERT: C 96 ARG cc_start: 0.7882 (mtp85) cc_final: 0.7628 (mtt-85) REVERT: C 122 GLN cc_start: 0.8723 (tt0) cc_final: 0.8504 (tt0) REVERT: C 168 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8484 (mt-10) REVERT: C 223 ASP cc_start: 0.8343 (t0) cc_final: 0.7988 (t0) REVERT: C 325 THR cc_start: 0.8558 (m) cc_final: 0.8267 (p) REVERT: C 355 GLN cc_start: 0.8189 (mm110) cc_final: 0.7879 (mp-120) outliers start: 31 outliers final: 13 residues processed: 204 average time/residue: 1.5860 time to fit residues: 339.4711 Evaluate side-chains 199 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 181 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 329 LYS Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 360 LYS Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 292 LYS Chi-restraints excluded: chain B residue 329 LYS Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 352 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 chunk 83 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 89 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 ASN C 13 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8986 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8973 Z= 0.324 Angle : 0.640 7.575 12162 Z= 0.320 Chirality : 0.049 0.140 1344 Planarity : 0.005 0.042 1557 Dihedral : 11.588 153.739 1239 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 4.00 % Allowed : 14.83 % Favored : 81.18 % 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: 1.69 (0.25), residues: 1107 helix: 1.06 (0.25), residues: 462 sheet: 0.90 (0.36), residues: 201 loop : 1.61 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP A 341 HIS 0.005 0.002 HIS B 162 PHE 0.012 0.002 PHE B 263 TYR 0.011 0.002 TYR C 295 ARG 0.004 0.001 ARG C 291 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 185 time to evaluate : 1.098 Fit side-chains REVERT: A 96 ARG cc_start: 0.8036 (mtp85) cc_final: 0.7787 (mtm-85) REVERT: A 329 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8296 (tttm) REVERT: B 58 GLU cc_start: 0.8031 (tt0) cc_final: 0.7787 (tt0) REVERT: B 73 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7255 (mp0) REVERT: B 177 MET cc_start: 0.9234 (mmm) cc_final: 0.8782 (mtp) REVERT: B 229 LYS cc_start: 0.7780 (mtpm) cc_final: 0.7434 (mttt) REVERT: B 354 GLN cc_start: 0.8715 (mm-40) cc_final: 0.8509 (mm-40) REVERT: B 362 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8034 (mt-10) REVERT: C 73 GLU cc_start: 0.8138 (mp0) cc_final: 0.7888 (mp0) REVERT: C 84 GLU cc_start: 0.8484 (tt0) cc_final: 0.8236 (tt0) REVERT: C 122 GLN cc_start: 0.8804 (tt0) cc_final: 0.8551 (tt0) REVERT: C 223 ASP cc_start: 0.8437 (t0) cc_final: 0.8069 (t0) REVERT: C 325 THR cc_start: 0.8664 (m) cc_final: 0.8402 (p) REVERT: C 355 GLN cc_start: 0.8245 (mm110) cc_final: 0.7898 (mp-120) REVERT: C 373 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.7586 (ptm-80) outliers start: 38 outliers final: 20 residues processed: 205 average time/residue: 1.5391 time to fit residues: 331.4908 Evaluate side-chains 205 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 182 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 329 LYS Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 292 LYS Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 292 LYS Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 373 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 0.5980 chunk 52 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 28 optimal weight: 0.8980 chunk 89 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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: 0.8983 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8973 Z= 0.294 Angle : 0.625 7.321 12162 Z= 0.312 Chirality : 0.048 0.138 1344 Planarity : 0.005 0.042 1557 Dihedral : 11.586 162.973 1239 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 4.31 % Allowed : 14.83 % Favored : 80.86 % 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: 1.64 (0.25), residues: 1107 helix: 1.06 (0.25), residues: 462 sheet: 0.85 (0.36), residues: 201 loop : 1.54 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP A 341 HIS 0.004 0.001 HIS A 102 PHE 0.010 0.001 PHE C 256 TYR 0.011 0.001 TYR C 295 ARG 0.006 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 186 time to evaluate : 1.100 Fit side-chains REVERT: A 65 ILE cc_start: 0.9384 (OUTLIER) cc_final: 0.8836 (pp) REVERT: A 216 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8069 (mptp) REVERT: A 329 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8317 (tttm) REVERT: B 58 GLU cc_start: 0.8034 (tt0) cc_final: 0.7757 (tt0) REVERT: B 73 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7305 (mp0) REVERT: B 229 LYS cc_start: 0.7824 (mtpm) cc_final: 0.7489 (mttt) REVERT: B 308 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7655 (tm-30) REVERT: B 335 GLU cc_start: 0.8557 (pm20) cc_final: 0.8350 (pm20) REVERT: B 354 GLN cc_start: 0.8747 (mm-40) cc_final: 0.8439 (mm-40) REVERT: B 362 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8005 (mt-10) REVERT: C 84 GLU cc_start: 0.8477 (tt0) cc_final: 0.8229 (tt0) REVERT: C 122 GLN cc_start: 0.8793 (tt0) cc_final: 0.8542 (tt0) REVERT: C 223 ASP cc_start: 0.8446 (t0) cc_final: 0.8076 (t0) REVERT: C 325 THR cc_start: 0.8695 (m) cc_final: 0.8462 (p) REVERT: C 355 GLN cc_start: 0.8254 (mm110) cc_final: 0.7939 (mp-120) REVERT: C 373 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.7621 (ptm-80) outliers start: 41 outliers final: 21 residues processed: 204 average time/residue: 1.5281 time to fit residues: 327.8173 Evaluate side-chains 208 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 181 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 329 LYS Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 13 ASN Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 292 LYS Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 292 LYS Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 373 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 0 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 96 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8991 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8973 Z= 0.329 Angle : 0.646 7.576 12162 Z= 0.323 Chirality : 0.049 0.140 1344 Planarity : 0.005 0.040 1557 Dihedral : 11.688 165.429 1239 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 4.21 % Allowed : 15.04 % Favored : 80.76 % 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: 1.61 (0.25), residues: 1107 helix: 1.03 (0.25), residues: 462 sheet: 0.85 (0.36), residues: 201 loop : 1.53 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP A 341 HIS 0.005 0.001 HIS C 174 PHE 0.011 0.002 PHE B 256 TYR 0.011 0.002 TYR C 295 ARG 0.006 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 182 time to evaluate : 1.037 Fit side-chains REVERT: A 65 ILE cc_start: 0.9385 (OUTLIER) cc_final: 0.8839 (pp) REVERT: A 73 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7349 (mp0) REVERT: A 329 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8289 (tttm) REVERT: B 58 GLU cc_start: 0.8057 (tt0) cc_final: 0.7814 (tt0) REVERT: B 73 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7333 (mp0) REVERT: B 229 LYS cc_start: 0.7838 (mtpm) cc_final: 0.7501 (mttt) REVERT: B 292 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8139 (tmmt) REVERT: B 308 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7673 (tm-30) REVERT: B 335 GLU cc_start: 0.8556 (pm20) cc_final: 0.8348 (pm20) REVERT: B 354 GLN cc_start: 0.8720 (mm-40) cc_final: 0.8422 (mm-40) REVERT: C 84 GLU cc_start: 0.8510 (tt0) cc_final: 0.8284 (tt0) REVERT: C 223 ASP cc_start: 0.8455 (t0) cc_final: 0.8078 (t0) REVERT: C 355 GLN cc_start: 0.8260 (mm110) cc_final: 0.7953 (mp-120) REVERT: C 373 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.7688 (ptm-80) outliers start: 40 outliers final: 21 residues processed: 199 average time/residue: 1.5238 time to fit residues: 319.1605 Evaluate side-chains 206 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 178 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 329 LYS Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 292 LYS Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 292 LYS Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 373 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 89 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.8956 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8973 Z= 0.181 Angle : 0.574 7.307 12162 Z= 0.281 Chirality : 0.045 0.134 1344 Planarity : 0.004 0.036 1557 Dihedral : 11.410 174.603 1239 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.58 % Allowed : 15.88 % Favored : 80.55 % 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: 1.85 (0.26), residues: 1107 helix: 1.28 (0.25), residues: 462 sheet: 0.91 (0.37), residues: 201 loop : 1.63 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 80 HIS 0.003 0.001 HIS A 162 PHE 0.009 0.001 PHE B 256 TYR 0.010 0.001 TYR B 295 ARG 0.007 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 185 time to evaluate : 1.105 Fit side-chains REVERT: A 65 ILE cc_start: 0.9376 (OUTLIER) cc_final: 0.8813 (pp) REVERT: A 96 ARG cc_start: 0.8049 (mtp85) cc_final: 0.7785 (mtm-85) REVERT: A 216 LYS cc_start: 0.8583 (mptp) cc_final: 0.8354 (mppt) REVERT: A 329 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8322 (tttm) REVERT: B 58 GLU cc_start: 0.7945 (tt0) cc_final: 0.7695 (tt0) REVERT: B 73 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7314 (mp0) REVERT: B 229 LYS cc_start: 0.7784 (mtpm) cc_final: 0.7449 (mttt) REVERT: B 293 ASP cc_start: 0.8296 (m-30) cc_final: 0.7998 (m-30) REVERT: B 308 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7627 (tm-30) REVERT: B 362 GLU cc_start: 0.8469 (mt-10) cc_final: 0.7845 (mt-10) REVERT: C 84 GLU cc_start: 0.8470 (tt0) cc_final: 0.8248 (tt0) REVERT: C 223 ASP cc_start: 0.8376 (t0) cc_final: 0.8021 (t0) REVERT: C 229 LYS cc_start: 0.8193 (mtpp) cc_final: 0.7858 (mtmt) REVERT: C 355 GLN cc_start: 0.8240 (mm110) cc_final: 0.7928 (mp-120) outliers start: 34 outliers final: 23 residues processed: 195 average time/residue: 1.4904 time to fit residues: 305.8051 Evaluate side-chains 204 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 177 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 329 LYS Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 13 ASN Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 292 LYS Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 292 LYS Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 366 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 63 optimal weight: 0.0970 chunk 32 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8960 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8973 Z= 0.201 Angle : 0.581 7.347 12162 Z= 0.284 Chirality : 0.046 0.136 1344 Planarity : 0.004 0.034 1557 Dihedral : 11.361 179.724 1239 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.58 % Allowed : 16.09 % Favored : 80.34 % 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: 1.86 (0.26), residues: 1107 helix: 1.30 (0.25), residues: 462 sheet: 0.89 (0.37), residues: 201 loop : 1.62 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 80 HIS 0.004 0.001 HIS A 162 PHE 0.010 0.001 PHE B 256 TYR 0.010 0.001 TYR B 295 ARG 0.007 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 183 time to evaluate : 1.073 Fit side-chains REVERT: A 65 ILE cc_start: 0.9380 (OUTLIER) cc_final: 0.8806 (pp) REVERT: A 73 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7280 (mp0) REVERT: A 96 ARG cc_start: 0.8046 (mtp85) cc_final: 0.7792 (mtm-85) REVERT: A 329 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8308 (tttm) REVERT: B 58 GLU cc_start: 0.7960 (tt0) cc_final: 0.7709 (tt0) REVERT: B 229 LYS cc_start: 0.7786 (mtpm) cc_final: 0.7471 (mttt) REVERT: B 308 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7649 (tm-30) REVERT: B 335 GLU cc_start: 0.8554 (pm20) cc_final: 0.8346 (pm20) REVERT: B 362 GLU cc_start: 0.8454 (mt-10) cc_final: 0.7860 (mt-10) REVERT: C 84 GLU cc_start: 0.8476 (tt0) cc_final: 0.8240 (tt0) REVERT: C 223 ASP cc_start: 0.8400 (t0) cc_final: 0.8031 (t0) REVERT: C 355 GLN cc_start: 0.8257 (mm110) cc_final: 0.7944 (mp-120) outliers start: 34 outliers final: 25 residues processed: 194 average time/residue: 1.5317 time to fit residues: 312.2019 Evaluate side-chains 209 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 180 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 329 LYS Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 13 ASN Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 292 LYS Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 292 LYS Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 329 LYS Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 366 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 97 optimal weight: 0.0470 chunk 102 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.9682 ------------------------------------------------------------------------------- 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: 0.8962 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8973 Z= 0.212 Angle : 0.590 7.994 12162 Z= 0.288 Chirality : 0.046 0.137 1344 Planarity : 0.004 0.041 1557 Dihedral : 11.293 178.048 1239 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.58 % Allowed : 16.40 % Favored : 80.02 % 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: 1.84 (0.26), residues: 1107 helix: 1.29 (0.25), residues: 462 sheet: 0.87 (0.37), residues: 201 loop : 1.62 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 80 HIS 0.004 0.001 HIS A 162 PHE 0.010 0.001 PHE B 256 TYR 0.009 0.001 TYR B 295 ARG 0.010 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 183 time to evaluate : 1.208 Fit side-chains REVERT: A 65 ILE cc_start: 0.9381 (OUTLIER) cc_final: 0.8808 (pp) REVERT: A 73 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7328 (mp0) REVERT: A 96 ARG cc_start: 0.8045 (mtp85) cc_final: 0.7794 (mtm-85) REVERT: A 329 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8290 (tttm) REVERT: B 58 GLU cc_start: 0.7966 (tt0) cc_final: 0.7714 (tt0) REVERT: B 229 LYS cc_start: 0.7773 (mtpm) cc_final: 0.7457 (mttt) REVERT: B 308 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7651 (tm-30) REVERT: B 335 GLU cc_start: 0.8552 (pm20) cc_final: 0.8344 (pm20) REVERT: B 362 GLU cc_start: 0.8445 (mt-10) cc_final: 0.7841 (mt-10) REVERT: C 223 ASP cc_start: 0.8402 (t0) cc_final: 0.8034 (t0) REVERT: C 229 LYS cc_start: 0.8208 (mtpp) cc_final: 0.7882 (mtmt) REVERT: C 355 GLN cc_start: 0.8260 (mm110) cc_final: 0.7948 (mp-120) outliers start: 34 outliers final: 27 residues processed: 194 average time/residue: 1.5298 time to fit residues: 312.2246 Evaluate side-chains 212 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 181 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 329 LYS Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 13 ASN Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 292 LYS Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 292 LYS Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 329 LYS Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 366 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 78 optimal weight: 0.0670 chunk 30 optimal weight: 0.5980 chunk 90 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 chunk 99 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 overall best weight: 0.6320 ------------------------------------------------------------------------------- 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: 0.8941 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8973 Z= 0.160 Angle : 0.563 8.498 12162 Z= 0.271 Chirality : 0.045 0.139 1344 Planarity : 0.004 0.041 1557 Dihedral : 10.889 167.672 1239 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.36 % Allowed : 16.93 % Favored : 79.71 % 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: 1.97 (0.26), residues: 1107 helix: 1.43 (0.25), residues: 462 sheet: 0.88 (0.37), residues: 201 loop : 1.68 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 80 HIS 0.003 0.001 HIS A 162 PHE 0.009 0.001 PHE B 256 TYR 0.009 0.001 TYR B 295 ARG 0.009 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 185 time to evaluate : 1.113 Fit side-chains REVERT: A 58 GLU cc_start: 0.7977 (tt0) cc_final: 0.7770 (tt0) REVERT: A 65 ILE cc_start: 0.9377 (OUTLIER) cc_final: 0.8810 (pp) REVERT: A 96 ARG cc_start: 0.8024 (mtp85) cc_final: 0.7767 (mtm-85) REVERT: A 329 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8302 (tttm) REVERT: B 58 GLU cc_start: 0.7933 (tt0) cc_final: 0.7683 (tt0) REVERT: B 73 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7342 (mp0) REVERT: B 229 LYS cc_start: 0.7759 (mtpm) cc_final: 0.7445 (mttt) REVERT: B 293 ASP cc_start: 0.8308 (m-30) cc_final: 0.7967 (m-30) REVERT: B 362 GLU cc_start: 0.8433 (mt-10) cc_final: 0.7822 (mt-10) REVERT: C 69 LYS cc_start: 0.8949 (mptm) cc_final: 0.8736 (mptp) REVERT: C 223 ASP cc_start: 0.8374 (t0) cc_final: 0.7998 (t0) REVERT: C 229 LYS cc_start: 0.8218 (mtpp) cc_final: 0.7889 (mtmt) REVERT: C 355 GLN cc_start: 0.8247 (mm110) cc_final: 0.7924 (mp-120) outliers start: 32 outliers final: 23 residues processed: 196 average time/residue: 1.6005 time to fit residues: 331.6374 Evaluate side-chains 216 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 190 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 329 LYS Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 13 ASN Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 292 LYS Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 329 LYS Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 366 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.7980 chunk 73 optimal weight: 0.0770 chunk 110 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 88 optimal weight: 0.0980 chunk 9 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8973 Z= 0.140 Angle : 0.554 8.560 12162 Z= 0.264 Chirality : 0.044 0.143 1344 Planarity : 0.004 0.041 1557 Dihedral : 10.381 162.116 1239 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.52 % Allowed : 17.98 % Favored : 79.50 % 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: 2.10 (0.26), residues: 1107 helix: 1.50 (0.25), residues: 465 sheet: 0.92 (0.37), residues: 201 loop : 1.80 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 80 HIS 0.003 0.001 HIS A 162 PHE 0.008 0.001 PHE B 256 TYR 0.008 0.001 TYR B 295 ARG 0.010 0.000 ARG B 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 193 time to evaluate : 1.059 Fit side-chains REVERT: A 58 GLU cc_start: 0.7931 (tt0) cc_final: 0.7702 (tt0) REVERT: A 65 ILE cc_start: 0.9356 (OUTLIER) cc_final: 0.8787 (pp) REVERT: A 329 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8315 (tttm) REVERT: B 58 GLU cc_start: 0.7912 (tt0) cc_final: 0.7668 (tt0) REVERT: B 229 LYS cc_start: 0.7746 (mtpm) cc_final: 0.7436 (mttt) REVERT: B 293 ASP cc_start: 0.8314 (m-30) cc_final: 0.7961 (m-30) REVERT: B 362 GLU cc_start: 0.8442 (mt-10) cc_final: 0.7846 (mt-10) REVERT: C 212 ASP cc_start: 0.8831 (t70) cc_final: 0.8566 (t70) REVERT: C 223 ASP cc_start: 0.8354 (t0) cc_final: 0.7991 (t0) REVERT: C 229 LYS cc_start: 0.8230 (mtpp) cc_final: 0.7899 (mtmt) REVERT: C 355 GLN cc_start: 0.8232 (mm110) cc_final: 0.7907 (mp-120) outliers start: 24 outliers final: 17 residues processed: 202 average time/residue: 1.4741 time to fit residues: 313.6825 Evaluate side-chains 208 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 189 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 329 LYS Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 292 LYS Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 329 LYS Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 366 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN A 93 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.104744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.090173 restraints weight = 9882.348| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 1.34 r_work: 0.2773 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8973 Z= 0.181 Angle : 0.578 8.509 12162 Z= 0.278 Chirality : 0.045 0.152 1344 Planarity : 0.004 0.041 1557 Dihedral : 10.555 171.180 1239 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.52 % Allowed : 17.98 % Favored : 79.50 % 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: 2.02 (0.26), residues: 1107 helix: 1.42 (0.25), residues: 465 sheet: 0.91 (0.37), residues: 201 loop : 1.77 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 80 HIS 0.003 0.001 HIS A 162 PHE 0.009 0.001 PHE B 256 TYR 0.009 0.001 TYR B 295 ARG 0.009 0.000 ARG B 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4960.72 seconds wall clock time: 86 minutes 52.86 seconds (5212.86 seconds total)