Starting phenix.real_space_refine on Mon Mar 11 02:25:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q97_18270/03_2024/8q97_18270.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q97_18270/03_2024/8q97_18270.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q97_18270/03_2024/8q97_18270.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q97_18270/03_2024/8q97_18270.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q97_18270/03_2024/8q97_18270.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q97_18270/03_2024/8q97_18270.pdb" } resolution = 2.99 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= 0.002 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: 5 Type Number sf(0) Gaussians S 6 5.16 5 C 2046 2.51 5 N 588 2.21 5 O 606 1.98 5 H 3396 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 338": "OE1" <-> "OE2" Residue "A ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 338": "OE1" <-> "OE2" Residue "D ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 338": "OE1" <-> "OE2" Residue "B TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 338": "OE1" <-> "OE2" Residue "B ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 338": "OE1" <-> "OE2" Residue "E ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 338": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6642 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1107 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 71, 1104 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Conformer: "B" Number of residues, atoms: 71, 1104 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} bond proxies already assigned to first conformer: 1110 Chain: "D" Number of atoms: 1107 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 71, 1104 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Conformer: "B" Number of residues, atoms: 71, 1104 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} bond proxies already assigned to first conformer: 1110 Chain: "C" Number of atoms: 1107 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 71, 1104 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Conformer: "B" Number of residues, atoms: 71, 1104 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} bond proxies already assigned to first conformer: 1110 Chain: "B" Number of atoms: 1107 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 71, 1104 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Conformer: "B" Number of residues, atoms: 71, 1104 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} bond proxies already assigned to first conformer: 1110 Chain: "E" Number of atoms: 1107 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 71, 1104 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Conformer: "B" Number of residues, atoms: 71, 1104 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} bond proxies already assigned to first conformer: 1110 Chain: "F" Number of atoms: 1107 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 71, 1104 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Conformer: "B" Number of residues, atoms: 71, 1104 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} bond proxies already assigned to first conformer: 1110 Time building chain proxies: 6.15, per 1000 atoms: 0.93 Number of scatterers: 6642 At special positions: 0 Unit cell: (99.704, 139.256, 39.552, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 6 16.00 O 606 8.00 N 588 7.00 C 2046 6.00 H 3396 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.91 Conformation dependent library (CDL) restraints added in 1.2 seconds 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 744 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 46.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 309 through 310 removed outlier: 6.520A pdb=" N VAL A 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.750A pdb=" N VAL A 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 317 through 325 Processing sheet with id=AA4, first strand: chain 'D' and resid 337 through 342 removed outlier: 6.621A pdb=" N GLU A 338 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N SER D 341 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LYS A 340 " --> pdb=" O SER D 341 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 345 through 346 removed outlier: 6.629A pdb=" N ASP A 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 350 through 354 removed outlier: 6.657A pdb=" N GLN A 351 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N ILE D 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LYS A 353 " --> pdb=" O ILE D 354 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 357 through 361 removed outlier: 6.162A pdb=" N ASP A 358 " --> pdb=" O ASN D 359 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N THR D 361 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE A 360 " --> pdb=" O THR D 361 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 368 through 377 removed outlier: 6.612A pdb=" N LYS A 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N GLU D 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ILE A 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N HIS D 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N THR A 373 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N LEU D 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LYS A 375 " --> pdb=" O LEU D 376 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 309 through 310 removed outlier: 6.463A pdb=" N VAL B 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 313 through 314 removed outlier: 6.770A pdb=" N VAL B 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 317 through 325 removed outlier: 6.335A pdb=" N LYS B 317 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N SER E 320 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N THR B 319 " --> pdb=" O SER E 320 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N CYS E 322 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LYS B 321 " --> pdb=" O CYS E 322 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N SER E 324 " --> pdb=" O LYS B 321 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N GLY B 323 " --> pdb=" O SER E 324 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 337 through 342 Processing sheet with id=AB4, first strand: chain 'E' and resid 345 through 346 removed outlier: 6.683A pdb=" N ASP B 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 350 through 354 removed outlier: 6.602A pdb=" N GLN B 351 " --> pdb=" O SER E 352 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N ILE E 354 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LYS B 353 " --> pdb=" O ILE E 354 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 357 through 361 removed outlier: 6.192A pdb=" N ASP B 358 " --> pdb=" O ASN E 359 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N THR E 361 " --> pdb=" O ASP B 358 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE B 360 " --> pdb=" O THR E 361 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 368 through 377 removed outlier: 6.656A pdb=" N LYS B 369 " --> pdb=" O LYS E 370 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N GLU E 372 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ILE B 371 " --> pdb=" O GLU E 372 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N HIS E 374 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N THR B 373 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N LEU E 376 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LYS B 375 " --> pdb=" O LEU E 376 " (cutoff:3.500A) 79 hydrogen bonds defined for protein. 237 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: 2.08 Time building geometry restraints manager: 5.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.90 - 1.33: 4134 1.33 - 1.76: 2546 1.76 - 2.18: 10 2.18 - 2.61: 0 2.61 - 3.04: 6 Bond restraints: 6696 Sorted by residual: bond pdb=" N LYS A 343 " pdb=" H BLYS A 343 " ideal model delta sigma weight residual 0.860 3.040 -2.180 2.00e-02 2.50e+03 1.19e+04 bond pdb=" N LYS B 343 " pdb=" H BLYS B 343 " ideal model delta sigma weight residual 0.860 3.013 -2.153 2.00e-02 2.50e+03 1.16e+04 bond pdb=" N LYS E 343 " pdb=" H BLYS E 343 " ideal model delta sigma weight residual 0.860 2.872 -2.012 2.00e-02 2.50e+03 1.01e+04 bond pdb=" N LYS D 343 " pdb=" H BLYS D 343 " ideal model delta sigma weight residual 0.860 2.852 -1.992 2.00e-02 2.50e+03 9.92e+03 bond pdb=" N LYS F 343 " pdb=" H BLYS F 343 " ideal model delta sigma weight residual 0.860 2.840 -1.980 2.00e-02 2.50e+03 9.80e+03 ... (remaining 6691 not shown) Histogram of bond angle deviations from ideal: 12.14 - 35.46: 11 35.46 - 58.78: 1 58.78 - 82.10: 6 82.10 - 105.42: 151 105.42 - 128.74: 12053 Bond angle restraints: 12222 Sorted by residual: angle pdb=" C LYS E 340 " pdb=" N SER E 341 " pdb=" H BSER E 341 " ideal model delta sigma weight residual 123.78 12.14 111.64 3.00e+00 1.11e-01 1.38e+03 angle pdb=" C LYS B 340 " pdb=" N SER B 341 " pdb=" H BSER B 341 " ideal model delta sigma weight residual 123.78 12.97 110.81 3.00e+00 1.11e-01 1.36e+03 angle pdb=" C LYS D 340 " pdb=" N SER D 341 " pdb=" H BSER D 341 " ideal model delta sigma weight residual 123.78 14.67 109.11 3.00e+00 1.11e-01 1.32e+03 angle pdb=" C LYS F 340 " pdb=" N SER F 341 " pdb=" H BSER F 341 " ideal model delta sigma weight residual 123.78 15.25 108.53 3.00e+00 1.11e-01 1.31e+03 angle pdb=" C LYS A 340 " pdb=" N SER A 341 " pdb=" H BSER A 341 " ideal model delta sigma weight residual 123.65 15.28 108.37 3.00e+00 1.11e-01 1.30e+03 ... (remaining 12217 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.98: 2728 14.98 - 29.96: 164 29.96 - 44.93: 92 44.93 - 59.91: 56 59.91 - 74.89: 56 Dihedral angle restraints: 3096 sinusoidal: 1770 harmonic: 1326 Sorted by residual: dihedral pdb=" CA GLY A 355 " pdb=" C GLY A 355 " pdb=" N SER A 356 " pdb=" CA SER A 356 " ideal model delta harmonic sigma weight residual 180.00 155.60 24.40 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA VAL A 318 " pdb=" C VAL A 318 " pdb=" N THR A 319 " pdb=" CA THR A 319 " ideal model delta harmonic sigma weight residual -180.00 -157.85 -22.15 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA VAL A 350 " pdb=" C VAL A 350 " pdb=" N GLN A 351 " pdb=" CA GLN A 351 " ideal model delta harmonic sigma weight residual 180.00 158.59 21.41 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 3093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 283 0.072 - 0.144: 157 0.144 - 0.216: 37 0.216 - 0.287: 13 0.287 - 0.359: 8 Chirality restraints: 498 Sorted by residual: chirality pdb=" CA HIS C 329 " pdb=" N HIS C 329 " pdb=" C HIS C 329 " pdb=" CB HIS C 329 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" CA HIS D 329 " pdb=" N HIS D 329 " pdb=" C HIS D 329 " pdb=" CB HIS D 329 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" CA HIS F 329 " pdb=" N HIS F 329 " pdb=" C HIS F 329 " pdb=" CB HIS F 329 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.76e+00 ... (remaining 495 not shown) Planarity restraints: 978 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 338 " 0.198 2.00e-02 2.50e+03 2.62e-01 6.87e+02 pdb=" N VAL A 339 " -0.443 2.00e-02 2.50e+03 pdb=" CA VAL A 339 " 0.189 2.00e-02 2.50e+03 pdb=" H BVAL A 339 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU F 338 " 0.199 2.00e-02 2.50e+03 2.61e-01 6.83e+02 pdb=" N VAL F 339 " -0.442 2.00e-02 2.50e+03 pdb=" CA VAL F 339 " 0.189 2.00e-02 2.50e+03 pdb=" H BVAL F 339 " 0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU C 338 " 0.199 2.00e-02 2.50e+03 2.61e-01 6.80e+02 pdb=" N VAL C 339 " -0.441 2.00e-02 2.50e+03 pdb=" CA VAL C 339 " 0.188 2.00e-02 2.50e+03 pdb=" H BVAL C 339 " 0.053 2.00e-02 2.50e+03 ... (remaining 975 not shown) Histogram of nonbonded interaction distances: 0.53 - 1.34: 8 1.34 - 2.16: 448 2.16 - 2.97: 16746 2.97 - 3.79: 26158 3.79 - 4.60: 42109 Warning: very small nonbonded interaction distances. Nonbonded interactions: 85469 Sorted by model distance: nonbonded pdb=" O LYS C 340 " pdb=" H BSER C 341 " model vdw 0.527 1.960 nonbonded pdb=" O LYS A 340 " pdb=" H BSER A 341 " model vdw 0.551 1.960 nonbonded pdb=" O LYS F 340 " pdb=" H BSER F 341 " model vdw 0.589 1.960 nonbonded pdb=" O LYS B 340 " pdb=" H BSER B 341 " model vdw 0.604 1.960 nonbonded pdb=" O LYS D 340 " pdb=" H BSER D 341 " model vdw 0.748 1.960 ... (remaining 85464 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 308 through 338 or resid 340 or resid 342 or resid 344 thr \ ough 378)) selection = (chain 'B' and (resid 308 through 338 or resid 340 or resid 342 or resid 344 thr \ ough 378)) selection = (chain 'C' and (resid 308 through 338 or resid 340 or resid 342 or resid 344 thr \ ough 378)) selection = (chain 'D' and (resid 308 through 338 or resid 340 or resid 342 or resid 344 thr \ ough 378)) selection = (chain 'E' and (resid 308 through 338 or resid 340 or resid 342 or resid 344 thr \ ough 378)) selection = (chain 'F' and (resid 308 through 338 or resid 340 or resid 342 or resid 344 thr \ ough 378)) } 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=0.50 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: 2.590 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: 0.170 Extract box with map and model: 11.310 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 28.500 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 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 : 0.011 0.033 3300 Z= 0.749 Angle : 2.017 9.222 4416 Z= 1.331 Chirality : 0.099 0.359 498 Planarity : 0.012 0.107 558 Dihedral : 12.244 74.889 1260 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.32), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.86 (0.24), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.017 0.005 HIS B 374 PHE 0.044 0.015 PHE B 346 TYR 0.192 0.059 TYR B 310 ARG 0.003 0.001 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 ASP cc_start: 0.8224 (m-30) cc_final: 0.7960 (t0) REVERT: D 345 ASP cc_start: 0.8509 (m-30) cc_final: 0.8220 (t0) REVERT: D 349 ARG cc_start: 0.8006 (mtp180) cc_final: 0.6879 (ppt90) REVERT: C 370 LYS cc_start: 0.6995 (tttt) cc_final: 0.6400 (mttt) REVERT: B 345 ASP cc_start: 0.8449 (m-30) cc_final: 0.8052 (OUTLIER) REVERT: E 349 ARG cc_start: 0.8049 (mtp180) cc_final: 0.6872 (pmt-80) REVERT: F 345 ASP cc_start: 0.8292 (m-30) cc_final: 0.7904 (t0) REVERT: F 370 LYS cc_start: 0.7061 (tttt) cc_final: 0.6629 (mttt) outliers start: 0 outliers final: 1 residues processed: 91 average time/residue: 2.8644 time to fit residues: 266.6582 Evaluate side-chains 64 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 336 GLN F 368 ASN ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3300 Z= 0.272 Angle : 0.872 12.260 4416 Z= 0.474 Chirality : 0.048 0.126 498 Planarity : 0.003 0.020 558 Dihedral : 6.304 18.274 432 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 0.81 % Allowed : 13.98 % Favored : 85.22 % 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 (0.33), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.53 (0.25), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS F 374 PHE 0.011 0.002 PHE F 346 TYR 0.015 0.003 TYR A 310 ARG 0.002 0.001 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 59 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 370 LYS cc_start: 0.7028 (tttt) cc_final: 0.6464 (mttt) REVERT: B 345 ASP cc_start: 0.8394 (m-30) cc_final: 0.8143 (t0) REVERT: F 370 LYS cc_start: 0.7250 (tttt) cc_final: 0.6590 (mttt) outliers start: 3 outliers final: 0 residues processed: 59 average time/residue: 2.6688 time to fit residues: 161.6142 Evaluate side-chains 54 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 8.9990 chunk 10 optimal weight: 7.9990 chunk 38 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 ASN ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3300 Z= 0.235 Angle : 0.769 11.931 4416 Z= 0.433 Chirality : 0.049 0.125 498 Planarity : 0.002 0.013 558 Dihedral : 5.740 15.433 432 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.81 % Allowed : 14.78 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.35), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.30 (0.26), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 329 PHE 0.009 0.001 PHE A 346 TYR 0.013 0.002 TYR A 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 62 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 349 ARG cc_start: 0.8000 (mtp180) cc_final: 0.6463 (mmp-170) REVERT: C 370 LYS cc_start: 0.7170 (tttt) cc_final: 0.6520 (mttt) REVERT: E 349 ARG cc_start: 0.8076 (mtp180) cc_final: 0.6945 (pmt-80) REVERT: F 370 LYS cc_start: 0.7182 (tttt) cc_final: 0.6483 (pttt) outliers start: 3 outliers final: 0 residues processed: 63 average time/residue: 2.8485 time to fit residues: 183.9549 Evaluate side-chains 56 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 7.9990 chunk 18 optimal weight: 9.9990 chunk 25 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 0.0270 chunk 23 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 overall best weight: 3.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.4322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3300 Z= 0.306 Angle : 0.786 11.972 4416 Z= 0.445 Chirality : 0.048 0.124 498 Planarity : 0.003 0.016 558 Dihedral : 5.819 15.546 432 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.08 % Allowed : 16.13 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.36), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.10 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 374 PHE 0.011 0.002 PHE F 346 TYR 0.012 0.003 TYR A 310 ARG 0.004 0.001 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 59 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 349 ARG cc_start: 0.8022 (mtp180) cc_final: 0.6480 (mmp-170) REVERT: C 370 LYS cc_start: 0.7216 (tttt) cc_final: 0.6559 (mttt) REVERT: E 349 ARG cc_start: 0.8064 (mtp180) cc_final: 0.6926 (pmt-80) REVERT: F 370 LYS cc_start: 0.7242 (tttt) cc_final: 0.6574 (mttt) outliers start: 4 outliers final: 2 residues processed: 61 average time/residue: 2.3940 time to fit residues: 150.3567 Evaluate side-chains 56 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 54 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain E residue 351 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.4561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 3300 Z= 0.359 Angle : 0.767 11.937 4416 Z= 0.444 Chirality : 0.048 0.131 498 Planarity : 0.003 0.017 558 Dihedral : 5.901 15.407 432 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.54 % Allowed : 18.55 % Favored : 80.91 % 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: -1.52 (0.37), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.15 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 374 PHE 0.011 0.002 PHE C 346 TYR 0.014 0.003 TYR A 310 ARG 0.002 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 49 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 370 LYS cc_start: 0.7243 (tttt) cc_final: 0.6591 (mttt) REVERT: F 317 LYS cc_start: 0.8508 (mtpp) cc_final: 0.8167 (mttm) REVERT: F 370 LYS cc_start: 0.7260 (tttt) cc_final: 0.6628 (mttt) outliers start: 2 outliers final: 2 residues processed: 50 average time/residue: 2.3624 time to fit residues: 121.8464 Evaluate side-chains 49 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 47 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain E residue 351 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 ASN ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.4644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3300 Z= 0.196 Angle : 0.717 11.985 4416 Z= 0.419 Chirality : 0.048 0.123 498 Planarity : 0.002 0.017 558 Dihedral : 5.562 15.678 432 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.81 % Allowed : 19.62 % Favored : 79.57 % 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: -1.50 (0.36), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.13 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 374 PHE 0.011 0.001 PHE A 378 TYR 0.010 0.002 TYR A 310 ARG 0.000 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 56 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 349 ARG cc_start: 0.8032 (mtp180) cc_final: 0.6491 (mmp-170) REVERT: C 370 LYS cc_start: 0.7213 (tttt) cc_final: 0.6540 (pttt) REVERT: E 349 ARG cc_start: 0.8043 (mtp180) cc_final: 0.6931 (pmt-80) REVERT: F 317 LYS cc_start: 0.8467 (mtpp) cc_final: 0.8163 (mttm) REVERT: F 370 LYS cc_start: 0.7213 (tttt) cc_final: 0.6535 (pttt) outliers start: 3 outliers final: 1 residues processed: 57 average time/residue: 2.6421 time to fit residues: 154.6432 Evaluate side-chains 55 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 54 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 351 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 18 optimal weight: 0.4980 chunk 16 optimal weight: 5.9990 chunk 12 optimal weight: 0.0870 chunk 7 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 overall best weight: 1.0962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.4726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3300 Z= 0.153 Angle : 0.687 12.026 4416 Z= 0.404 Chirality : 0.048 0.122 498 Planarity : 0.002 0.012 558 Dihedral : 5.051 14.687 432 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.54 % Allowed : 19.62 % Favored : 79.84 % 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: -1.48 (0.36), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.12 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 330 PHE 0.006 0.001 PHE A 378 TYR 0.009 0.002 TYR F 310 ARG 0.000 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 55 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 315 LEU cc_start: 0.8198 (pp) cc_final: 0.7989 (pt) REVERT: C 349 ARG cc_start: 0.8032 (mtp180) cc_final: 0.6443 (mmm160) REVERT: C 370 LYS cc_start: 0.7217 (tttt) cc_final: 0.6526 (pttt) REVERT: E 349 ARG cc_start: 0.8011 (mtp180) cc_final: 0.6920 (pmt-80) REVERT: F 317 LYS cc_start: 0.8445 (mtpp) cc_final: 0.8159 (mttm) REVERT: F 349 ARG cc_start: 0.7946 (mtp180) cc_final: 0.6291 (mmp-170) REVERT: F 370 LYS cc_start: 0.7207 (tttt) cc_final: 0.6524 (pttt) outliers start: 2 outliers final: 0 residues processed: 55 average time/residue: 2.8801 time to fit residues: 162.4583 Evaluate side-chains 52 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 35 optimal weight: 0.2980 chunk 37 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 327 ASN ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.4834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3300 Z= 0.143 Angle : 0.684 12.073 4416 Z= 0.403 Chirality : 0.048 0.120 498 Planarity : 0.002 0.011 558 Dihedral : 4.922 14.407 432 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.00 % Allowed : 20.43 % Favored : 79.57 % 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: -1.44 (0.36), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.09 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 330 PHE 0.005 0.001 PHE A 378 TYR 0.009 0.002 TYR F 310 ARG 0.000 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 349 ARG cc_start: 0.7979 (mtp180) cc_final: 0.6470 (mmm160) REVERT: C 370 LYS cc_start: 0.7236 (tttt) cc_final: 0.6528 (pttt) REVERT: E 349 ARG cc_start: 0.7996 (mtp180) cc_final: 0.6903 (pmt-80) REVERT: F 317 LYS cc_start: 0.8459 (mtpp) cc_final: 0.8179 (mttm) REVERT: F 349 ARG cc_start: 0.7953 (mtp180) cc_final: 0.6330 (mmp-170) REVERT: F 370 LYS cc_start: 0.7205 (tttt) cc_final: 0.6504 (pttt) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 2.7143 time to fit residues: 147.9120 Evaluate side-chains 53 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.3980 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 18 optimal weight: 0.4980 chunk 27 optimal weight: 7.9990 chunk 41 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.4911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3300 Z= 0.139 Angle : 0.676 12.067 4416 Z= 0.399 Chirality : 0.048 0.119 498 Planarity : 0.002 0.010 558 Dihedral : 4.772 13.923 432 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.00 % Allowed : 20.43 % Favored : 79.57 % 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: -1.36 (0.36), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.03 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 330 PHE 0.005 0.001 PHE A 346 TYR 0.009 0.002 TYR F 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 349 ARG cc_start: 0.7970 (mtp180) cc_final: 0.6294 (mmp-170) REVERT: C 370 LYS cc_start: 0.7269 (tttt) cc_final: 0.6534 (pttt) REVERT: E 349 ARG cc_start: 0.7988 (mtp180) cc_final: 0.6897 (pmt-80) REVERT: F 317 LYS cc_start: 0.8478 (mtpp) cc_final: 0.8190 (mttm) REVERT: F 349 ARG cc_start: 0.7952 (mtp180) cc_final: 0.6338 (mmp-170) REVERT: F 370 LYS cc_start: 0.7230 (tttt) cc_final: 0.6504 (pttt) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 2.6041 time to fit residues: 147.2502 Evaluate side-chains 51 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 34 optimal weight: 0.0270 chunk 6 optimal weight: 0.9980 overall best weight: 1.6042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.4974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3300 Z= 0.180 Angle : 0.688 12.048 4416 Z= 0.404 Chirality : 0.048 0.129 498 Planarity : 0.002 0.010 558 Dihedral : 4.873 14.068 432 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.00 % Allowed : 20.97 % Favored : 79.03 % 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: -1.30 (0.37), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.98 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 374 PHE 0.005 0.001 PHE A 346 TYR 0.008 0.002 TYR A 310 ARG 0.001 0.000 ARG A 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 368 ASN cc_start: 0.7882 (m110) cc_final: 0.7593 (m-40) REVERT: C 349 ARG cc_start: 0.7999 (mtp180) cc_final: 0.6455 (mmm160) REVERT: C 370 LYS cc_start: 0.7261 (tttt) cc_final: 0.6546 (pttt) REVERT: F 317 LYS cc_start: 0.8495 (mtpp) cc_final: 0.8208 (mttm) REVERT: F 349 ARG cc_start: 0.7972 (mtp180) cc_final: 0.6348 (mmp-170) REVERT: F 370 LYS cc_start: 0.7241 (tttt) cc_final: 0.6528 (pttt) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 2.5096 time to fit residues: 129.2354 Evaluate side-chains 49 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 0.8980 chunk 1 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.192319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.164489 restraints weight = 21328.480| |-----------------------------------------------------------------------------| r_work (start): 0.4367 rms_B_bonded: 2.39 r_work: 0.4263 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.4164 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.4164 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4180 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4180 r_free = 0.4180 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4180 r_free = 0.4180 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.4180 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.5027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3300 Z= 0.148 Angle : 0.681 12.051 4416 Z= 0.400 Chirality : 0.048 0.120 498 Planarity : 0.002 0.010 558 Dihedral : 4.754 14.060 432 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 1.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.27 % Allowed : 20.70 % Favored : 79.03 % 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: -1.28 (0.37), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.97 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 374 PHE 0.004 0.001 PHE A 346 TYR 0.009 0.002 TYR F 310 ARG 0.001 0.000 ARG A 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4186.36 seconds wall clock time: 73 minutes 49.90 seconds (4429.90 seconds total)