Starting phenix.real_space_refine on Sat Apr 6 19:51:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8trm_41583/04_2024/8trm_41583_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8trm_41583/04_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_41583/04_2024/8trm_41583.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8trm_41583/04_2024/8trm_41583.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8trm_41583/04_2024/8trm_41583_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8trm_41583/04_2024/8trm_41583_updated.pdb" } 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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 5.59, per 1000 atoms: 0.63 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: 3.34 Conformation dependent library (CDL) restraints added in 1.8 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... running ksdssp... Secondary structure from input PDB file: 54 helices and 15 sheets defined 42.9% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.91 Creating SS restraints... Processing helix chain 'A' and resid 57 through 61 Processing helix chain 'A' and resid 63 through 65 No H-bonds generated for 'chain 'A' and resid 63 through 65' Processing helix chain 'A' and resid 80 through 92 Processing helix chain 'A' and resid 114 through 126 Processing helix chain 'A' and resid 138 through 145 Processing helix chain 'A' and resid 173 through 175 No H-bonds generated for 'chain 'A' and resid 173 through 175' Processing helix chain 'A' and resid 183 through 197 removed outlier: 3.813A pdb=" N HIS A 195 " --> pdb=" O MET A 191 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N GLU A 196 " --> pdb=" O LYS A 192 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ARG A 197 " --> pdb=" O ILE A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 217 Processing helix chain 'A' and resid 224 through 233 Processing helix chain 'A' and resid 253 through 262 removed outlier: 4.382A pdb=" N CYS A 258 " --> pdb=" O ARG A 255 " (cutoff:3.500A) Proline residue: A 259 - end of helix Processing helix chain 'A' and resid 265 through 268 Processing helix chain 'A' and resid 275 through 285 Processing helix chain 'A' and resid 291 through 297 Processing helix chain 'A' and resid 310 through 321 Processing helix chain 'A' and resid 336 through 348 removed outlier: 3.595A pdb=" N SER A 339 " --> pdb=" O ARG A 336 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N VAL A 340 " --> pdb=" O LYS A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 355 removed outlier: 3.923A pdb=" N GLN A 355 " --> pdb=" O THR A 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 352 through 355' Processing helix chain 'A' and resid 360 through 366 Processing helix chain 'A' and resid 368 through 374 removed outlier: 3.646A pdb=" N LYS A 374 " --> pdb=" O VAL A 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 61 Processing helix chain 'B' and resid 63 through 65 No H-bonds generated for 'chain 'B' and resid 63 through 65' Processing helix chain 'B' and resid 80 through 92 Processing helix chain 'B' and resid 114 through 126 Processing helix chain 'B' and resid 138 through 145 Processing helix chain 'B' and resid 173 through 175 No H-bonds generated for 'chain 'B' and resid 173 through 175' Processing helix chain 'B' and resid 183 through 197 removed outlier: 3.812A pdb=" N HIS B 195 " --> pdb=" O MET B 191 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLU B 196 " --> pdb=" O LYS B 192 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ARG B 197 " --> pdb=" O ILE B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 217 Processing helix chain 'B' and resid 224 through 233 Processing helix chain 'B' and resid 253 through 262 removed outlier: 4.381A pdb=" N CYS B 258 " --> pdb=" O ARG B 255 " (cutoff:3.500A) Proline residue: B 259 - end of helix Processing helix chain 'B' and resid 265 through 268 Processing helix chain 'B' and resid 275 through 285 Processing helix chain 'B' and resid 291 through 297 Processing helix chain 'B' and resid 310 through 321 Processing helix chain 'B' and resid 336 through 348 removed outlier: 3.595A pdb=" N SER B 339 " --> pdb=" O ARG B 336 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N VAL B 340 " --> pdb=" O LYS B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 355 removed outlier: 3.924A pdb=" N GLN B 355 " --> pdb=" O THR B 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 352 through 355' Processing helix chain 'B' and resid 360 through 366 Processing helix chain 'B' and resid 368 through 374 removed outlier: 3.645A pdb=" N LYS B 374 " --> pdb=" O VAL B 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 61 Processing helix chain 'C' and resid 63 through 65 No H-bonds generated for 'chain 'C' and resid 63 through 65' Processing helix chain 'C' and resid 80 through 92 Processing helix chain 'C' and resid 114 through 126 Processing helix chain 'C' and resid 138 through 145 Processing helix chain 'C' and resid 173 through 175 No H-bonds generated for 'chain 'C' and resid 173 through 175' Processing helix chain 'C' and resid 183 through 197 removed outlier: 3.813A pdb=" N HIS C 195 " --> pdb=" O MET C 191 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLU C 196 " --> pdb=" O LYS C 192 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ARG C 197 " --> pdb=" O ILE C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 217 Processing helix chain 'C' and resid 224 through 233 Processing helix chain 'C' and resid 253 through 262 removed outlier: 4.381A pdb=" N CYS C 258 " --> pdb=" O ARG C 255 " (cutoff:3.500A) Proline residue: C 259 - end of helix Processing helix chain 'C' and resid 265 through 268 Processing helix chain 'C' and resid 275 through 285 Processing helix chain 'C' and resid 291 through 297 Processing helix chain 'C' and resid 310 through 321 Processing helix chain 'C' and resid 336 through 348 removed outlier: 3.595A pdb=" N SER C 339 " --> pdb=" O ARG C 336 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N VAL C 340 " --> pdb=" O LYS C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 355 removed outlier: 3.925A pdb=" N GLN C 355 " --> pdb=" O THR C 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 352 through 355' Processing helix chain 'C' and resid 360 through 366 Processing helix chain 'C' and resid 368 through 374 removed outlier: 3.646A pdb=" N LYS C 374 " --> pdb=" O VAL C 371 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 9 through 13 Processing sheet with id= B, first strand: chain 'A' and resid 36 through 39 Processing sheet with id= C, first strand: chain 'A' and resid 104 through 108 Processing sheet with id= D, first strand: chain 'A' and resid 298 through 301 removed outlier: 6.402A pdb=" N ILE A 152 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N SER A 301 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LEU A 154 " --> pdb=" O SER A 301 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 239 through 242 Processing sheet with id= F, first strand: chain 'B' and resid 9 through 13 Processing sheet with id= G, first strand: chain 'B' and resid 36 through 39 Processing sheet with id= H, first strand: chain 'B' and resid 104 through 108 Processing sheet with id= I, first strand: chain 'B' and resid 298 through 301 removed outlier: 6.402A pdb=" N ILE B 152 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N SER B 301 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LEU B 154 " --> pdb=" O SER B 301 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 239 through 242 Processing sheet with id= K, first strand: chain 'C' and resid 9 through 13 Processing sheet with id= L, first strand: chain 'C' and resid 36 through 39 Processing sheet with id= M, first strand: chain 'C' and resid 104 through 108 Processing sheet with id= N, first strand: chain 'C' and resid 298 through 301 removed outlier: 6.403A pdb=" N ILE C 152 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N SER C 301 " --> pdb=" O ILE C 152 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LEU C 154 " --> pdb=" O SER C 301 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 239 through 242 339 hydrogen bonds defined for protein. 828 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.41 Time building geometry restraints manager: 3.66 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: 6061 3.11 - 3.70: 13294 3.70 - 4.30: 20374 4.30 - 4.90: 32972 Nonbonded interactions: 72743 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 72738 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: 3.350 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: 11.870 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 28.010 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.810 ------------------------------------------------------------------------------- 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= 0.207 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 : 0.977 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: 1.6619 time to fit residues: 361.9436 Evaluate side-chains 189 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 183 time to evaluate : 1.081 ------------------------------------------------------------------------------- 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: 2.9990 chunk 84 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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: 0.8992 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8973 Z= 0.325 Angle : 0.640 7.578 12162 Z= 0.319 Chirality : 0.049 0.139 1344 Planarity : 0.005 0.046 1557 Dihedral : 11.888 151.212 1249 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.36 % Allowed : 15.14 % Favored : 81.49 % 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: 1.47 (0.25), residues: 1107 helix: 0.86 (0.25), residues: 453 sheet: 0.69 (0.35), residues: 207 loop : 1.57 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP A 341 HIS 0.005 0.001 HIS B 162 PHE 0.013 0.002 PHE C 256 TYR 0.012 0.002 TYR C 295 ARG 0.004 0.000 ARG C 291 *********************** 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 212 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 180 time to evaluate : 0.924 Fit side-chains REVERT: A 73 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7469 (mp0) REVERT: A 329 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8295 (tttm) REVERT: B 73 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7353 (mp0) REVERT: B 229 LYS cc_start: 0.7686 (mtpm) cc_final: 0.7375 (mttp) REVERT: B 293 ASP cc_start: 0.8303 (m-30) cc_final: 0.8034 (m-30) REVERT: B 329 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8613 (tptp) REVERT: B 354 GLN cc_start: 0.8663 (mm-40) cc_final: 0.8412 (mm-40) REVERT: B 362 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8001 (mt-10) REVERT: C 84 GLU cc_start: 0.8475 (tt0) cc_final: 0.8250 (tt0) REVERT: C 96 ARG cc_start: 0.7926 (mtp85) cc_final: 0.7718 (mtt-85) REVERT: C 122 GLN cc_start: 0.8776 (tt0) cc_final: 0.8551 (tt0) REVERT: C 223 ASP cc_start: 0.8391 (t0) cc_final: 0.8035 (t0) REVERT: C 325 THR cc_start: 0.8713 (m) cc_final: 0.8441 (p) outliers start: 32 outliers final: 15 residues processed: 196 average time/residue: 1.6599 time to fit residues: 341.2731 Evaluate side-chains 191 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 172 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU 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 251 VAL 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 329 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 352 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 0.0970 chunk 109 optimal weight: 0.3980 chunk 89 optimal weight: 7.9990 chunk 34 optimal weight: 0.1980 chunk 81 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.8955 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8973 Z= 0.173 Angle : 0.553 6.662 12162 Z= 0.268 Chirality : 0.045 0.133 1344 Planarity : 0.004 0.035 1557 Dihedral : 11.310 161.180 1240 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.84 % Allowed : 16.51 % Favored : 80.65 % 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: 1.56 (0.25), residues: 1107 helix: 0.87 (0.25), residues: 456 sheet: 0.79 (0.35), residues: 201 loop : 1.65 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 80 HIS 0.003 0.001 HIS B 162 PHE 0.011 0.001 PHE C 256 TYR 0.009 0.001 TYR C 295 ARG 0.005 0.000 ARG B 96 *********************** 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 217 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 190 time to evaluate : 0.982 Fit side-chains REVERT: A 73 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7427 (mp0) REVERT: A 96 ARG cc_start: 0.8019 (mtp85) cc_final: 0.7773 (mtm-85) REVERT: A 317 GLU cc_start: 0.9047 (mm-30) cc_final: 0.8819 (mm-30) REVERT: A 329 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8299 (tttm) REVERT: A 360 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7612 (tttm) REVERT: B 73 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7353 (mp0) REVERT: B 229 LYS cc_start: 0.7624 (mtpm) cc_final: 0.7320 (mttp) REVERT: B 293 ASP cc_start: 0.8252 (m-30) cc_final: 0.7999 (m-30) REVERT: B 335 GLU cc_start: 0.8499 (pm20) cc_final: 0.8211 (pm20) REVERT: B 354 GLN cc_start: 0.8616 (mm-40) cc_final: 0.8319 (mm-40) REVERT: B 362 GLU cc_start: 0.8477 (mt-10) cc_final: 0.7970 (mt-10) REVERT: C 41 ASN cc_start: 0.8204 (m110) cc_final: 0.8001 (m110) REVERT: C 84 GLU cc_start: 0.8438 (tt0) cc_final: 0.8201 (tt0) REVERT: C 96 ARG cc_start: 0.7918 (mtp85) cc_final: 0.7708 (mtt-85) REVERT: C 122 GLN cc_start: 0.8731 (tt0) cc_final: 0.8512 (tt0) REVERT: C 223 ASP cc_start: 0.8358 (t0) cc_final: 0.7993 (t0) REVERT: C 325 THR cc_start: 0.8660 (m) cc_final: 0.8393 (p) REVERT: C 355 GLN cc_start: 0.8249 (mm110) cc_final: 0.7966 (mp-120) outliers start: 27 outliers final: 15 residues processed: 200 average time/residue: 1.6081 time to fit residues: 337.8738 Evaluate side-chains 204 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 185 time to evaluate : 0.994 ------------------------------------------------------------------------------- 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 180 ASP 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 A residue 366 SER 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 222 LEU Chi-restraints excluded: chain B residue 237 ILE 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 352 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 0.9990 chunk 52 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 101 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 89 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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: 0.8982 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8973 Z= 0.264 Angle : 0.598 7.335 12162 Z= 0.293 Chirality : 0.047 0.135 1344 Planarity : 0.005 0.038 1557 Dihedral : 11.499 166.624 1239 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.58 % Allowed : 15.35 % Favored : 81.07 % 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: 1.38 (0.25), residues: 1107 helix: 0.75 (0.25), residues: 456 sheet: 0.74 (0.36), residues: 201 loop : 1.49 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP A 341 HIS 0.004 0.001 HIS B 162 PHE 0.011 0.001 PHE B 256 TYR 0.010 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 215 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 181 time to evaluate : 1.020 Fit side-chains REVERT: A 65 ILE cc_start: 0.9380 (OUTLIER) cc_final: 0.8835 (pp) REVERT: A 73 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7439 (mp0) REVERT: A 96 ARG cc_start: 0.8031 (mtp85) cc_final: 0.7777 (mtm-85) REVERT: A 329 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8315 (tttm) REVERT: B 73 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7403 (mp0) REVERT: B 229 LYS cc_start: 0.7662 (mtpm) cc_final: 0.7353 (mttt) REVERT: B 335 GLU cc_start: 0.8542 (pm20) cc_final: 0.8270 (pm20) REVERT: B 354 GLN cc_start: 0.8681 (mm-40) cc_final: 0.8433 (mm-40) REVERT: C 84 GLU cc_start: 0.8461 (tt0) cc_final: 0.8239 (tt0) REVERT: C 122 GLN cc_start: 0.8766 (tt0) cc_final: 0.8536 (tt0) REVERT: C 223 ASP cc_start: 0.8393 (t0) cc_final: 0.8027 (t0) REVERT: C 325 THR cc_start: 0.8650 (m) cc_final: 0.8431 (p) outliers start: 34 outliers final: 17 residues processed: 197 average time/residue: 1.6335 time to fit residues: 337.7241 Evaluate side-chains 210 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 189 time to evaluate : 0.962 ------------------------------------------------------------------------------- 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 180 ASP 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 366 SER 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 222 LEU Chi-restraints excluded: chain B residue 237 ILE 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 292 LYS Chi-restraints excluded: chain C residue 352 THR 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: 3.9990 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: 4.9990 chunk 96 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 21 optimal weight: 0.0070 overall best weight: 1.5804 ------------------------------------------------------------------------------- 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: 0.8991 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8973 Z= 0.309 Angle : 0.621 7.502 12162 Z= 0.306 Chirality : 0.048 0.138 1344 Planarity : 0.005 0.038 1557 Dihedral : 11.641 167.884 1239 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.15 % Allowed : 15.88 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.25), residues: 1107 helix: 0.69 (0.25), residues: 453 sheet: 0.72 (0.36), residues: 201 loop : 1.45 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP A 341 HIS 0.005 0.001 HIS C 174 PHE 0.011 0.002 PHE B 256 TYR 0.010 0.001 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 213 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 183 time to evaluate : 1.077 Fit side-chains REVERT: A 65 ILE cc_start: 0.9382 (OUTLIER) cc_final: 0.8838 (pp) REVERT: A 73 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7464 (mp0) REVERT: A 96 ARG cc_start: 0.8034 (mtp85) cc_final: 0.7771 (mtm-85) REVERT: A 328 ILE cc_start: 0.9395 (OUTLIER) cc_final: 0.9018 (mm) REVERT: A 329 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8288 (tttm) REVERT: B 73 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7435 (mp0) REVERT: B 229 LYS cc_start: 0.7640 (mtpm) cc_final: 0.7330 (mttt) REVERT: B 293 ASP cc_start: 0.8315 (m-30) cc_final: 0.8003 (m-30) REVERT: B 335 GLU cc_start: 0.8526 (pm20) cc_final: 0.8286 (pm20) REVERT: B 354 GLN cc_start: 0.8717 (mm-40) cc_final: 0.8459 (mm-40) REVERT: B 362 GLU cc_start: 0.8435 (mt-10) cc_final: 0.7852 (mt-10) REVERT: C 84 GLU cc_start: 0.8472 (tt0) cc_final: 0.8271 (tt0) REVERT: C 122 GLN cc_start: 0.8784 (tt0) cc_final: 0.8552 (tt0) REVERT: C 223 ASP cc_start: 0.8424 (t0) cc_final: 0.8051 (t0) REVERT: C 355 GLN cc_start: 0.8269 (mm110) cc_final: 0.7956 (mp-120) outliers start: 30 outliers final: 16 residues processed: 196 average time/residue: 1.6478 time to fit residues: 339.0219 Evaluate side-chains 203 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 182 time to evaluate : 1.068 ------------------------------------------------------------------------------- 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 180 ASP Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 328 ILE 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 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 324 SER Chi-restraints excluded: chain C residue 352 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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: 0.8966 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8973 Z= 0.194 Angle : 0.568 7.534 12162 Z= 0.274 Chirality : 0.045 0.136 1344 Planarity : 0.004 0.035 1557 Dihedral : 11.429 175.976 1239 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.15 % Allowed : 15.98 % 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: 1.49 (0.25), residues: 1107 helix: 0.84 (0.25), residues: 453 sheet: 0.76 (0.36), residues: 201 loop : 1.58 (0.29), residues: 453 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 0.011 0.001 PHE B 256 TYR 0.008 0.001 TYR B 295 ARG 0.007 0.000 ARG A 373 *********************** 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 223 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 193 time to evaluate : 1.051 Fit side-chains REVERT: A 65 ILE cc_start: 0.9376 (OUTLIER) cc_final: 0.8811 (pp) REVERT: A 73 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7429 (mp0) REVERT: A 96 ARG cc_start: 0.8036 (mtp85) cc_final: 0.7778 (mtm-85) REVERT: A 328 ILE cc_start: 0.9372 (OUTLIER) cc_final: 0.8992 (mm) REVERT: A 329 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8323 (tttm) REVERT: B 73 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7437 (mp0) REVERT: B 229 LYS cc_start: 0.7657 (mtpm) cc_final: 0.7356 (mttt) REVERT: B 335 GLU cc_start: 0.8532 (pm20) cc_final: 0.8290 (pm20) REVERT: B 354 GLN cc_start: 0.8653 (mm-40) cc_final: 0.8347 (mm-40) REVERT: B 362 GLU cc_start: 0.8427 (mt-10) cc_final: 0.7839 (mt-10) REVERT: C 122 GLN cc_start: 0.8759 (tt0) cc_final: 0.8528 (tt0) REVERT: C 223 ASP cc_start: 0.8390 (t0) cc_final: 0.8023 (t0) REVERT: C 229 LYS cc_start: 0.8012 (mtpp) cc_final: 0.7739 (mttp) REVERT: C 355 GLN cc_start: 0.8264 (mm110) cc_final: 0.7940 (mp-120) outliers start: 30 outliers final: 16 residues processed: 207 average time/residue: 1.5942 time to fit residues: 347.5689 Evaluate side-chains 210 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 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 73 GLU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 328 ILE 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 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 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 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: 5.9990 chunk 60 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 106 optimal weight: 0.0570 chunk 66 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 63 optimal weight: 0.0070 chunk 32 optimal weight: 0.0570 overall best weight: 0.6238 ------------------------------------------------------------------------------- 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: 0.8946 moved from start: 0.1632 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= 0.159 Angle : 0.549 7.556 12162 Z= 0.262 Chirality : 0.044 0.138 1344 Planarity : 0.004 0.044 1557 Dihedral : 11.015 172.692 1239 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.26 % Allowed : 16.30 % Favored : 80.44 % 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: 1.62 (0.26), residues: 1107 helix: 0.93 (0.25), residues: 453 sheet: 0.80 (0.36), residues: 201 loop : 1.68 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 80 HIS 0.003 0.001 HIS A 162 PHE 0.010 0.001 PHE B 256 TYR 0.008 0.001 TYR B 295 ARG 0.015 0.000 ARG A 373 *********************** 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 225 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 194 time to evaluate : 1.069 Fit side-chains REVERT: A 65 ILE cc_start: 0.9382 (OUTLIER) cc_final: 0.8805 (pp) REVERT: A 73 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7420 (mp0) REVERT: A 96 ARG cc_start: 0.8039 (mtp85) cc_final: 0.7772 (mtm-85) REVERT: A 328 ILE cc_start: 0.9363 (OUTLIER) cc_final: 0.9011 (mm) REVERT: A 329 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8314 (tttm) REVERT: B 73 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7420 (mp0) REVERT: B 226 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7297 (mm-30) REVERT: B 229 LYS cc_start: 0.7593 (mtpm) cc_final: 0.7283 (mttt) REVERT: B 293 ASP cc_start: 0.8265 (m-30) cc_final: 0.7984 (m-30) REVERT: B 362 GLU cc_start: 0.8414 (mt-10) cc_final: 0.7822 (mt-10) REVERT: C 122 GLN cc_start: 0.8729 (tt0) cc_final: 0.8516 (tt0) REVERT: C 223 ASP cc_start: 0.8356 (t0) cc_final: 0.7985 (t0) REVERT: C 355 GLN cc_start: 0.8244 (mm110) cc_final: 0.7925 (mp-120) outliers start: 31 outliers final: 20 residues processed: 207 average time/residue: 1.5292 time to fit residues: 332.9468 Evaluate side-chains 216 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 191 time to evaluate : 1.080 ------------------------------------------------------------------------------- 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 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 328 ILE 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 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 84 GLU Chi-restraints excluded: chain C residue 160 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 9 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 97 optimal weight: 0.0020 chunk 102 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- 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: 0.8950 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8973 Z= 0.171 Angle : 0.560 7.876 12162 Z= 0.266 Chirality : 0.045 0.143 1344 Planarity : 0.004 0.047 1557 Dihedral : 10.898 168.531 1239 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.26 % Allowed : 16.61 % Favored : 80.13 % 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 (0.26), residues: 1107 helix: 0.95 (0.25), residues: 453 sheet: 0.78 (0.36), residues: 201 loop : 1.71 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 80 HIS 0.003 0.001 HIS A 162 PHE 0.010 0.001 PHE B 256 TYR 0.008 0.001 TYR B 295 ARG 0.014 0.000 ARG A 373 *********************** 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 222 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 191 time to evaluate : 1.018 Fit side-chains REVERT: A 65 ILE cc_start: 0.9381 (OUTLIER) cc_final: 0.8779 (pp) REVERT: A 73 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7411 (mp0) REVERT: A 96 ARG cc_start: 0.8036 (mtp85) cc_final: 0.7780 (mtm-85) REVERT: A 212 ASP cc_start: 0.8930 (t70) cc_final: 0.8659 (t70) REVERT: A 328 ILE cc_start: 0.9369 (OUTLIER) cc_final: 0.9019 (mm) REVERT: A 329 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8315 (tttm) REVERT: A 360 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7582 (tttm) REVERT: B 226 GLU cc_start: 0.7534 (mt-10) cc_final: 0.7298 (mm-30) REVERT: B 229 LYS cc_start: 0.7588 (mtpm) cc_final: 0.7282 (mttt) REVERT: B 335 GLU cc_start: 0.8538 (pm20) cc_final: 0.8332 (pm20) REVERT: B 362 GLU cc_start: 0.8407 (mt-10) cc_final: 0.7810 (mt-10) REVERT: C 122 GLN cc_start: 0.8729 (tt0) cc_final: 0.8515 (tt0) REVERT: C 223 ASP cc_start: 0.8365 (t0) cc_final: 0.7984 (t0) REVERT: C 229 LYS cc_start: 0.7977 (mtpp) cc_final: 0.7706 (mttp) REVERT: C 355 GLN cc_start: 0.8253 (mm110) cc_final: 0.7921 (mp-120) outliers start: 31 outliers final: 22 residues processed: 201 average time/residue: 1.5701 time to fit residues: 331.6586 Evaluate side-chains 215 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 188 time to evaluate : 1.102 ------------------------------------------------------------------------------- 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 180 ASP Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 328 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 1.9990 chunk 60 optimal weight: 0.0010 chunk 43 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 chunk 99 optimal weight: 0.2980 chunk 65 optimal weight: 0.9990 chunk 105 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 overall best weight: 0.5586 ------------------------------------------------------------------------------- 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: 0.8936 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8973 Z= 0.151 Angle : 0.549 8.288 12162 Z= 0.259 Chirality : 0.044 0.144 1344 Planarity : 0.004 0.050 1557 Dihedral : 10.525 159.316 1239 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.47 % Allowed : 16.61 % Favored : 79.92 % 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 (0.26), residues: 1107 helix: 0.97 (0.25), residues: 456 sheet: 0.80 (0.36), residues: 201 loop : 1.78 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 80 HIS 0.003 0.001 HIS A 162 PHE 0.010 0.001 PHE B 256 TYR 0.008 0.001 TYR B 295 ARG 0.015 0.000 ARG A 373 *********************** 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 224 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 191 time to evaluate : 1.080 Fit side-chains REVERT: A 65 ILE cc_start: 0.9378 (OUTLIER) cc_final: 0.8803 (pp) REVERT: A 73 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7400 (mp0) REVERT: A 96 ARG cc_start: 0.8026 (mtp85) cc_final: 0.7766 (mtm-85) REVERT: A 212 ASP cc_start: 0.8898 (t70) cc_final: 0.8606 (t70) REVERT: A 328 ILE cc_start: 0.9360 (OUTLIER) cc_final: 0.9009 (mm) REVERT: A 329 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8297 (tttm) REVERT: A 360 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7561 (tttm) REVERT: B 226 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7334 (mm-30) REVERT: B 229 LYS cc_start: 0.7541 (mtpm) cc_final: 0.7228 (mttt) REVERT: B 362 GLU cc_start: 0.8389 (mt-10) cc_final: 0.7807 (mt-10) REVERT: C 69 LYS cc_start: 0.8958 (mptm) cc_final: 0.8741 (mptp) REVERT: C 122 GLN cc_start: 0.8709 (tt0) cc_final: 0.8501 (tt0) REVERT: C 223 ASP cc_start: 0.8333 (t0) cc_final: 0.7960 (t0) REVERT: C 229 LYS cc_start: 0.7990 (mtpp) cc_final: 0.7713 (mttp) REVERT: C 329 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8491 (tmtm) REVERT: C 355 GLN cc_start: 0.8259 (mm110) cc_final: 0.7934 (mp-120) outliers start: 33 outliers final: 22 residues processed: 203 average time/residue: 1.5760 time to fit residues: 335.9668 Evaluate side-chains 217 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 189 time to evaluate : 0.977 ------------------------------------------------------------------------------- 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 180 ASP Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 328 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 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 148 ARG Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 277 ARG 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 84 GLU 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 50 optimal weight: 0.7980 chunk 73 optimal weight: 0.0980 chunk 110 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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: 0.8961 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8973 Z= 0.209 Angle : 0.584 8.567 12162 Z= 0.279 Chirality : 0.046 0.147 1344 Planarity : 0.005 0.049 1557 Dihedral : 10.826 165.327 1239 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.26 % Allowed : 17.03 % 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: 1.59 (0.26), residues: 1107 helix: 0.91 (0.25), residues: 453 sheet: 0.76 (0.36), residues: 201 loop : 1.68 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 341 HIS 0.003 0.001 HIS A 102 PHE 0.010 0.001 PHE B 256 TYR 0.008 0.001 TYR B 295 ARG 0.016 0.001 ARG A 373 ********************** 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: 31 poor density : 186 time to evaluate : 1.236 Fit side-chains REVERT: A 65 ILE cc_start: 0.9383 (OUTLIER) cc_final: 0.8786 (pp) REVERT: A 73 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.7380 (mp0) REVERT: A 96 ARG cc_start: 0.8036 (mtp85) cc_final: 0.7779 (mtm-85) REVERT: A 328 ILE cc_start: 0.9378 (OUTLIER) cc_final: 0.9028 (mm) REVERT: A 329 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8311 (tttm) REVERT: A 360 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7595 (tttm) REVERT: B 226 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7346 (mm-30) REVERT: B 229 LYS cc_start: 0.7575 (mtpm) cc_final: 0.7255 (mttt) REVERT: B 362 GLU cc_start: 0.8498 (mt-10) cc_final: 0.7883 (mt-10) REVERT: C 122 GLN cc_start: 0.8735 (tt0) cc_final: 0.8511 (tt0) REVERT: C 223 ASP cc_start: 0.8379 (t0) cc_final: 0.8006 (t0) REVERT: C 229 LYS cc_start: 0.8024 (mtpp) cc_final: 0.7741 (mttp) REVERT: C 329 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8535 (tmtm) REVERT: C 355 GLN cc_start: 0.8269 (mm110) cc_final: 0.7934 (mp-120) outliers start: 31 outliers final: 21 residues processed: 198 average time/residue: 1.6163 time to fit residues: 336.1350 Evaluate side-chains 213 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 186 time to evaluate : 1.065 ------------------------------------------------------------------------------- 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 180 ASP Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 328 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 A residue 366 SER Chi-restraints excluded: chain B residue 7 GLN 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 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 84 GLU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 180 ASP 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: 0.5980 chunk 13 optimal weight: 0.6980 chunk 24 optimal weight: 0.4980 chunk 88 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 77 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 63 optimal weight: 0.0000 overall best weight: 0.4584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.112347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.099035 restraints weight = 10245.914| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 1.29 r_work: 0.2922 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8973 Z= 0.142 Angle : 0.548 8.667 12162 Z= 0.258 Chirality : 0.044 0.143 1344 Planarity : 0.004 0.050 1557 Dihedral : 10.289 157.905 1239 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.63 % Allowed : 17.67 % 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: 1.78 (0.26), residues: 1107 helix: 1.02 (0.25), residues: 456 sheet: 0.93 (0.36), residues: 198 loop : 1.79 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 80 HIS 0.003 0.001 HIS A 162 PHE 0.010 0.001 PHE B 256 TYR 0.008 0.001 TYR B 295 ARG 0.016 0.000 ARG A 373 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5066.58 seconds wall clock time: 90 minutes 41.77 seconds (5441.77 seconds total)