Starting phenix.real_space_refine on Sat Aug 3 02:24:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q97_18270/08_2024/8q97_18270.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q97_18270/08_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_18270/08_2024/8q97_18270.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q97_18270/08_2024/8q97_18270.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q97_18270/08_2024/8q97_18270.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q97_18270/08_2024/8q97_18270.cif" } 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-5409/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: 7.31, per 1000 atoms: 1.10 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: 5.22 Conformation dependent library (CDL) restraints added in 1.4 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: 0.73 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: 2.05 Time building geometry restraints manager: 5.52 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 Time spend for trying shortcut: 0.00 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: 3.560 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: 0.180 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 30.040 Find NCS groups from input model: 0.240 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:12.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.490 ------------------------------------------------------------------------------- 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 : 0.561 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: 2.8569 time to fit residues: 265.9272 Evaluate side-chains 64 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.579 ------------------------------------------------------------------------------- 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: 6.9990 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 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: 0.7864 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3300 Z= 0.280 Angle : 0.882 12.286 4416 Z= 0.484 Chirality : 0.050 0.130 498 Planarity : 0.003 0.021 558 Dihedral : 6.183 18.106 432 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.81 % Allowed : 15.32 % Favored : 83.87 % 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: -2.03 (0.33), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.54 (0.25), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS F 374 PHE 0.013 0.002 PHE F 346 TYR 0.016 0.004 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 67 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 64 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 ASP cc_start: 0.8272 (m-30) cc_final: 0.8059 (t0) REVERT: A 347 LYS cc_start: 0.8828 (mttp) cc_final: 0.8586 (mtpm) REVERT: A 353 LYS cc_start: 0.8522 (tttt) cc_final: 0.8308 (tttp) REVERT: C 370 LYS cc_start: 0.7035 (tttt) cc_final: 0.6420 (mttt) REVERT: B 345 ASP cc_start: 0.8390 (m-30) cc_final: 0.8158 (OUTLIER) REVERT: F 370 LYS cc_start: 0.7335 (tttt) cc_final: 0.6542 (mttt) outliers start: 3 outliers final: 3 residues processed: 64 average time/residue: 2.5727 time to fit residues: 169.1170 Evaluate side-chains 62 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 60 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain F residue 345 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 chunk 10 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN D 327 ASN ** B 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3592 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= 0.246 Angle : 0.809 11.910 4416 Z= 0.447 Chirality : 0.049 0.126 498 Planarity : 0.003 0.015 558 Dihedral : 5.972 16.792 432 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.61 % Allowed : 16.13 % Favored : 82.26 % 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 (0.35), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.34 (0.26), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 374 PHE 0.013 0.002 PHE F 346 TYR 0.013 0.003 TYR A 310 ARG 0.001 0.000 ARG E 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 66 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 60 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 LYS cc_start: 0.8596 (tttt) cc_final: 0.8362 (tttp) REVERT: C 349 ARG cc_start: 0.7967 (mtp180) cc_final: 0.6446 (mmp-170) REVERT: C 370 LYS cc_start: 0.7066 (tttt) cc_final: 0.6435 (mttt) REVERT: E 349 ARG cc_start: 0.8062 (mtp180) cc_final: 0.6968 (pmt-80) REVERT: F 370 LYS cc_start: 0.7142 (tttt) cc_final: 0.6481 (mttt) outliers start: 6 outliers final: 0 residues processed: 61 average time/residue: 2.7004 time to fit residues: 168.3763 Evaluate side-chains 57 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.560 ------------------------------------------------------------------------------- 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: 0.6980 chunk 18 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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: 0.7920 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3300 Z= 0.247 Angle : 0.760 12.012 4416 Z= 0.433 Chirality : 0.049 0.123 498 Planarity : 0.003 0.020 558 Dihedral : 5.636 15.654 432 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.34 % Allowed : 17.20 % Favored : 81.45 % 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: -1.57 (0.37), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.19 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 329 PHE 0.011 0.002 PHE A 346 TYR 0.011 0.002 TYR A 310 ARG 0.001 0.000 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: 5 poor density : 58 time to evaluate : 0.556 Fit side-chains 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: 0.6468 (mmp-170) REVERT: C 370 LYS cc_start: 0.7130 (tttt) cc_final: 0.6474 (mttt) REVERT: B 349 ARG cc_start: 0.7968 (ttm-80) cc_final: 0.7705 (ttm170) REVERT: E 317 LYS cc_start: 0.8463 (mttm) cc_final: 0.8145 (mttm) REVERT: E 349 ARG cc_start: 0.8111 (mtp180) cc_final: 0.7024 (pmt-80) REVERT: F 317 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.8101 (mttm) REVERT: F 349 ARG cc_start: 0.7900 (mtp180) cc_final: 0.6241 (mmp-170) REVERT: F 370 LYS cc_start: 0.7162 (tttt) cc_final: 0.6495 (mttt) outliers start: 5 outliers final: 2 residues processed: 61 average time/residue: 3.0447 time to fit residues: 190.0121 Evaluate side-chains 57 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 54 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain E residue 351 GLN Chi-restraints excluded: chain F residue 317 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 36 optimal weight: 8.9990 chunk 10 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 374 HIS ** 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: 0.7983 moved from start: 0.4494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 3300 Z= 0.388 Angle : 0.800 11.980 4416 Z= 0.456 Chirality : 0.049 0.131 498 Planarity : 0.003 0.019 558 Dihedral : 6.006 16.291 432 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % 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: -1.59 (0.37), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.20 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 329 PHE 0.014 0.002 PHE F 346 TYR 0.014 0.003 TYR A 310 ARG 0.001 0.000 ARG F 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 65 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 62 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 349 ARG cc_start: 0.8023 (mtp180) cc_final: 0.6490 (mmp-170) REVERT: C 370 LYS cc_start: 0.7186 (tttt) cc_final: 0.6568 (mttt) REVERT: E 349 ARG cc_start: 0.8106 (mtp180) cc_final: 0.7309 (ptp90) REVERT: F 317 LYS cc_start: 0.8469 (mtpp) cc_final: 0.8156 (mttm) REVERT: F 370 LYS cc_start: 0.7290 (tttt) cc_final: 0.6627 (mttt) outliers start: 3 outliers final: 2 residues processed: 64 average time/residue: 2.7993 time to fit residues: 183.7243 Evaluate side-chains 57 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 55 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain B 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: 3.9990 chunk 33 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 29 optimal weight: 0.4980 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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: 0.7940 moved from start: 0.4605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3300 Z= 0.197 Angle : 0.767 12.051 4416 Z= 0.435 Chirality : 0.049 0.127 498 Planarity : 0.002 0.021 558 Dihedral : 5.665 15.838 432 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.08 % Allowed : 20.16 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.37), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.20 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 374 PHE 0.016 0.002 PHE A 346 TYR 0.009 0.002 TYR A 310 ARG 0.001 0.000 ARG F 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: 4 poor density : 55 time to evaluate : 0.552 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: 0.8003 (mtp180) cc_final: 0.6473 (mmp-170) REVERT: C 370 LYS cc_start: 0.7179 (tttt) cc_final: 0.6499 (pttt) REVERT: F 317 LYS cc_start: 0.8439 (mtpp) cc_final: 0.8134 (mttm) REVERT: F 349 ARG cc_start: 0.7945 (mtp180) cc_final: 0.6271 (mmp-170) REVERT: F 370 LYS cc_start: 0.7239 (tttt) cc_final: 0.6569 (mttt) outliers start: 4 outliers final: 1 residues processed: 58 average time/residue: 2.9447 time to fit residues: 174.9534 Evaluate side-chains 55 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 54 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 321 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 7 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 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: 0.7957 moved from start: 0.4766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3300 Z= 0.247 Angle : 0.740 12.054 4416 Z= 0.428 Chirality : 0.048 0.125 498 Planarity : 0.003 0.022 558 Dihedral : 5.508 15.778 432 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.54 % Allowed : 21.24 % Favored : 78.23 % 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: -1.57 (0.38), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.19 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 374 PHE 0.008 0.001 PHE F 346 TYR 0.011 0.002 TYR A 310 ARG 0.001 0.000 ARG B 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 : 0.549 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: C 349 ARG cc_start: 0.8029 (mtp180) cc_final: 0.6414 (mmp-170) REVERT: C 370 LYS cc_start: 0.7154 (tttt) cc_final: 0.6479 (pttt) REVERT: F 317 LYS cc_start: 0.8450 (mtpp) cc_final: 0.8181 (mttm) REVERT: F 349 ARG cc_start: 0.7963 (mtp180) cc_final: 0.6296 (mmp-170) REVERT: F 370 LYS cc_start: 0.7268 (tttt) cc_final: 0.6618 (mttt) outliers start: 2 outliers final: 2 residues processed: 55 average time/residue: 2.7910 time to fit residues: 157.5090 Evaluate side-chains 54 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 52 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain E residue 351 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 37 optimal weight: 0.0040 chunk 22 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 overall best weight: 1.5398 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.4801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3300 Z= 0.188 Angle : 0.724 12.074 4416 Z= 0.421 Chirality : 0.048 0.124 498 Planarity : 0.002 0.021 558 Dihedral : 5.370 15.599 432 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.27 % Allowed : 21.51 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.38), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.21 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 374 PHE 0.014 0.001 PHE A 346 TYR 0.009 0.002 TYR A 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 52 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 51 time to evaluate : 0.521 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: 0.8005 (mtp180) cc_final: 0.6425 (mmp-170) REVERT: C 370 LYS cc_start: 0.7131 (tttt) cc_final: 0.6471 (pttt) REVERT: E 349 ARG cc_start: 0.8122 (mtp180) cc_final: 0.7003 (pmt-80) REVERT: F 317 LYS cc_start: 0.8428 (mtpp) cc_final: 0.8174 (mttm) REVERT: F 349 ARG cc_start: 0.7955 (mtp180) cc_final: 0.6293 (mmp-170) REVERT: F 370 LYS cc_start: 0.7258 (tttt) cc_final: 0.6553 (pttt) outliers start: 1 outliers final: 1 residues processed: 52 average time/residue: 2.9185 time to fit residues: 155.5016 Evaluate side-chains 51 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 50 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 321 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 24 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 41 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 368 ASN ** 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: 0.7952 moved from start: 0.4919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3300 Z= 0.222 Angle : 0.725 12.109 4416 Z= 0.423 Chirality : 0.048 0.123 498 Planarity : 0.002 0.022 558 Dihedral : 5.348 15.547 432 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.54 % Allowed : 21.51 % Favored : 77.96 % 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: -1.58 (0.38), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.20 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 374 PHE 0.007 0.001 PHE F 346 TYR 0.010 0.002 TYR A 310 ARG 0.001 0.000 ARG D 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 56 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 54 time to evaluate : 0.557 Fit side-chains 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: 0.7604 (m-40) REVERT: C 349 ARG cc_start: 0.8057 (mtp180) cc_final: 0.6518 (mmm160) REVERT: C 370 LYS cc_start: 0.7201 (tttt) cc_final: 0.6527 (pttt) REVERT: E 349 ARG cc_start: 0.8090 (mtp180) cc_final: 0.7040 (pmt-80) REVERT: F 317 LYS cc_start: 0.8497 (mtpp) cc_final: 0.8277 (mttm) REVERT: F 349 ARG cc_start: 0.8020 (mtp180) cc_final: 0.6362 (mmp-170) REVERT: F 370 LYS cc_start: 0.7294 (tttt) cc_final: 0.6568 (pttt) outliers start: 2 outliers final: 2 residues processed: 55 average time/residue: 2.8553 time to fit residues: 161.3128 Evaluate side-chains 54 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 52 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain F residue 321 LYS 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: 0.9980 chunk 35 optimal weight: 0.0970 chunk 10 optimal weight: 8.9990 chunk 30 optimal weight: 0.0040 chunk 4 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.9792 ------------------------------------------------------------------------------- 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 368 ASN ** 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: 0.7926 moved from start: 0.4995 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= 0.154 Angle : 0.717 12.110 4416 Z= 0.418 Chirality : 0.049 0.122 498 Planarity : 0.002 0.021 558 Dihedral : 5.210 15.536 432 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.54 % Allowed : 21.51 % Favored : 77.96 % 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: -1.60 (0.38), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.21 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 374 PHE 0.013 0.001 PHE A 346 TYR 0.008 0.002 TYR A 310 ARG 0.000 0.000 ARG F 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 53 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 51 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 368 ASN cc_start: 0.7869 (m110) cc_final: 0.7593 (m-40) REVERT: C 349 ARG cc_start: 0.8044 (mtp180) cc_final: 0.6508 (mmm160) REVERT: C 370 LYS cc_start: 0.7177 (tttt) cc_final: 0.6488 (pttt) REVERT: F 317 LYS cc_start: 0.8478 (mtpp) cc_final: 0.8258 (mttm) REVERT: F 349 ARG cc_start: 0.7994 (mtp180) cc_final: 0.6353 (mmp-170) REVERT: F 370 LYS cc_start: 0.7288 (tttt) cc_final: 0.6558 (pttt) outliers start: 2 outliers final: 2 residues processed: 52 average time/residue: 2.8710 time to fit residues: 153.4685 Evaluate side-chains 52 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 50 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 351 GLN Chi-restraints excluded: chain F residue 321 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 41 optimal weight: 5.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 368 ASN ** 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 = 0.4508 r_free = 0.4508 target = 0.191172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.163593 restraints weight = 21536.982| |-----------------------------------------------------------------------------| r_work (start): 0.4325 rms_B_bonded: 2.24 r_work: 0.4258 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.4176 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.4176 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4049 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4049 r_free = 0.4049 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4048 r_free = 0.4048 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.4048 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.5178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3300 Z= 0.169 Angle : 0.710 12.081 4416 Z= 0.414 Chirality : 0.048 0.132 498 Planarity : 0.002 0.021 558 Dihedral : 5.076 15.243 432 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.54 % Allowed : 22.04 % Favored : 77.42 % 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 (0.38), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.20 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 330 PHE 0.009 0.001 PHE A 378 TYR 0.008 0.002 TYR F 310 ARG 0.003 0.000 ARG E 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4260.11 seconds wall clock time: 76 minutes 34.90 seconds (4594.90 seconds total)