Starting phenix.real_space_refine on Sun Mar 17 02:30:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vd9_31911/03_2024/7vd9_31911_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vd9_31911/03_2024/7vd9_31911.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vd9_31911/03_2024/7vd9_31911.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vd9_31911/03_2024/7vd9_31911.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vd9_31911/03_2024/7vd9_31911_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vd9_31911/03_2024/7vd9_31911_updated.pdb" } resolution = 2.29 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 4 7.16 5 P 12 5.49 5 S 52 5.16 5 C 10421 2.51 5 N 2895 2.21 5 O 3042 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 17": "OE1" <-> "OE2" Residue "D GLU 119": "OE1" <-> "OE2" Residue "D ASP 202": "OD1" <-> "OD2" Residue "D GLU 344": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16426 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4017 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 498, 4007 Classifications: {'peptide': 498} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 461} Conformer: "B" Number of residues, atoms: 498, 4007 Classifications: {'peptide': 498} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 461} bond proxies already assigned to first conformer: 4115 Chain: "B" Number of atoms: 4017 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 498, 4007 Classifications: {'peptide': 498} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 461} Conformer: "B" Number of residues, atoms: 498, 4007 Classifications: {'peptide': 498} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 461} bond proxies already assigned to first conformer: 4115 Chain: "C" Number of atoms: 4017 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 498, 4007 Classifications: {'peptide': 498} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 461} Conformer: "B" Number of residues, atoms: 498, 4007 Classifications: {'peptide': 498} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 461} bond proxies already assigned to first conformer: 4115 Chain: "D" Number of atoms: 4011 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 497, 4001 Classifications: {'peptide': 497} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 460} Conformer: "B" Number of residues, atoms: 497, 4001 Classifications: {'peptide': 497} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 460} bond proxies already assigned to first conformer: 4109 Chain: "A" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'HEM': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'HEM': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'HEM': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'HEM': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N ASER A 120 " occ=0.63 ... (10 atoms not shown) pdb=" OG BSER A 120 " occ=0.37 residue: pdb=" N AGLY A 121 " occ=0.63 ... (6 atoms not shown) pdb=" O BGLY A 121 " occ=0.37 residue: pdb=" N ASER B 120 " occ=0.82 ... (10 atoms not shown) pdb=" OG BSER B 120 " occ=0.18 residue: pdb=" N AGLY B 121 " occ=0.82 ... (6 atoms not shown) pdb=" O BGLY B 121 " occ=0.18 residue: pdb=" N ASER C 120 " occ=0.64 ... (10 atoms not shown) pdb=" OG BSER C 120 " occ=0.36 residue: pdb=" N AGLY C 121 " occ=0.64 ... (6 atoms not shown) pdb=" O BGLY C 121 " occ=0.36 residue: pdb=" N ASER D 120 " occ=0.89 ... (10 atoms not shown) pdb=" OG BSER D 120 " occ=0.11 residue: pdb=" N AGLY D 121 " occ=0.89 ... (6 atoms not shown) pdb=" O BGLY D 121 " occ=0.11 Time building chain proxies: 15.72, per 1000 atoms: 0.96 Number of scatterers: 16426 At special positions: 0 Unit cell: (113.1, 109.2, 83.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 4 26.01 S 52 16.00 P 12 15.00 O 3042 8.00 N 2895 7.00 C 10421 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.53 Conformation dependent library (CDL) restraints added in 5.8 seconds 3998 Ramachandran restraints generated. 1999 Oldfield, 0 Emsley, 1999 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3726 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 77 helices and 4 sheets defined 34.2% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.01 Creating SS restraints... Processing helix chain 'A' and resid 7 through 19 removed outlier: 6.744A pdb=" N MET A 12 " --> pdb=" O ALA A 8 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N GLN A 13 " --> pdb=" O SER A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 66 Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 158 through 168 Proline residue: A 162 - end of helix Processing helix chain 'A' and resid 179 through 188 Processing helix chain 'A' and resid 190 through 200 removed outlier: 4.168A pdb=" N HIS A 194 " --> pdb=" O GLU A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 209 through 211 No H-bonds generated for 'chain 'A' and resid 209 through 211' Processing helix chain 'A' and resid 247 through 256 Processing helix chain 'A' and resid 260 through 270 Processing helix chain 'A' and resid 286 through 290 Processing helix chain 'A' and resid 325 through 328 No H-bonds generated for 'chain 'A' and resid 325 through 328' Processing helix chain 'A' and resid 349 through 366 removed outlier: 3.728A pdb=" N PHE A 356 " --> pdb=" O GLN A 352 " (cutoff:3.500A) Proline residue: A 359 - end of helix Processing helix chain 'A' and resid 370 through 372 No H-bonds generated for 'chain 'A' and resid 370 through 372' Processing helix chain 'A' and resid 416 through 418 No H-bonds generated for 'chain 'A' and resid 416 through 418' Processing helix chain 'A' and resid 441 through 449 Processing helix chain 'A' and resid 453 through 469 removed outlier: 5.047A pdb=" N ASP A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 485 Processing helix chain 'A' and resid 487 through 500 Processing helix chain 'B' and resid 11 through 18 Processing helix chain 'B' and resid 55 through 66 Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 158 through 168 Proline residue: B 162 - end of helix Processing helix chain 'B' and resid 179 through 188 Processing helix chain 'B' and resid 190 through 200 removed outlier: 4.138A pdb=" N HIS B 194 " --> pdb=" O GLU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 204 No H-bonds generated for 'chain 'B' and resid 202 through 204' Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'B' and resid 247 through 256 Processing helix chain 'B' and resid 260 through 270 Processing helix chain 'B' and resid 286 through 291 Processing helix chain 'B' and resid 325 through 328 No H-bonds generated for 'chain 'B' and resid 325 through 328' Processing helix chain 'B' and resid 349 through 366 removed outlier: 3.755A pdb=" N PHE B 356 " --> pdb=" O GLN B 352 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR B 358 " --> pdb=" O ARG B 354 " (cutoff:3.500A) Proline residue: B 359 - end of helix Processing helix chain 'B' and resid 370 through 372 No H-bonds generated for 'chain 'B' and resid 370 through 372' Processing helix chain 'B' and resid 416 through 418 No H-bonds generated for 'chain 'B' and resid 416 through 418' Processing helix chain 'B' and resid 441 through 448 Processing helix chain 'B' and resid 453 through 469 removed outlier: 4.989A pdb=" N ASP B 469 " --> pdb=" O GLY B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 485 Processing helix chain 'B' and resid 487 through 500 Processing helix chain 'C' and resid 11 through 18 Processing helix chain 'C' and resid 55 through 66 Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 158 through 168 Proline residue: C 162 - end of helix Processing helix chain 'C' and resid 179 through 188 Processing helix chain 'C' and resid 190 through 200 removed outlier: 4.179A pdb=" N HIS C 194 " --> pdb=" O GLU C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 204 No H-bonds generated for 'chain 'C' and resid 202 through 204' Processing helix chain 'C' and resid 209 through 211 No H-bonds generated for 'chain 'C' and resid 209 through 211' Processing helix chain 'C' and resid 247 through 256 Processing helix chain 'C' and resid 260 through 270 Processing helix chain 'C' and resid 286 through 290 Processing helix chain 'C' and resid 325 through 328 No H-bonds generated for 'chain 'C' and resid 325 through 328' Processing helix chain 'C' and resid 349 through 365 removed outlier: 3.709A pdb=" N PHE C 356 " --> pdb=" O GLN C 352 " (cutoff:3.500A) Proline residue: C 359 - end of helix Processing helix chain 'C' and resid 370 through 372 No H-bonds generated for 'chain 'C' and resid 370 through 372' Processing helix chain 'C' and resid 374 through 376 No H-bonds generated for 'chain 'C' and resid 374 through 376' Processing helix chain 'C' and resid 416 through 418 No H-bonds generated for 'chain 'C' and resid 416 through 418' Processing helix chain 'C' and resid 441 through 449 Processing helix chain 'C' and resid 453 through 469 removed outlier: 5.006A pdb=" N ASP C 469 " --> pdb=" O GLY C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 485 Processing helix chain 'C' and resid 487 through 500 Processing helix chain 'D' and resid 11 through 19 removed outlier: 3.620A pdb=" N ARG D 19 " --> pdb=" O TRP D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 66 Processing helix chain 'D' and resid 98 through 100 No H-bonds generated for 'chain 'D' and resid 98 through 100' Processing helix chain 'D' and resid 158 through 168 Proline residue: D 162 - end of helix Processing helix chain 'D' and resid 179 through 188 Processing helix chain 'D' and resid 190 through 199 removed outlier: 4.059A pdb=" N HIS D 194 " --> pdb=" O GLU D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 204 No H-bonds generated for 'chain 'D' and resid 202 through 204' Processing helix chain 'D' and resid 209 through 211 No H-bonds generated for 'chain 'D' and resid 209 through 211' Processing helix chain 'D' and resid 247 through 256 Processing helix chain 'D' and resid 260 through 270 Processing helix chain 'D' and resid 286 through 291 Processing helix chain 'D' and resid 325 through 328 No H-bonds generated for 'chain 'D' and resid 325 through 328' Processing helix chain 'D' and resid 349 through 365 removed outlier: 3.717A pdb=" N PHE D 356 " --> pdb=" O GLN D 352 " (cutoff:3.500A) Proline residue: D 359 - end of helix Processing helix chain 'D' and resid 370 through 372 No H-bonds generated for 'chain 'D' and resid 370 through 372' Processing helix chain 'D' and resid 416 through 418 No H-bonds generated for 'chain 'D' and resid 416 through 418' Processing helix chain 'D' and resid 441 through 448 Processing helix chain 'D' and resid 453 through 467 Processing helix chain 'D' and resid 472 through 485 Processing helix chain 'D' and resid 487 through 500 Processing sheet with id= A, first strand: chain 'A' and resid 141 through 148 removed outlier: 7.108A pdb=" N TYR A 84 " --> pdb=" O LEU A 318 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N LEU A 318 " --> pdb=" O TYR A 84 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N GLU A 86 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N LEU A 316 " --> pdb=" O GLU A 86 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N PHE A 279 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LYS A 315 " --> pdb=" O TRP A 277 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N TRP A 277 " --> pdb=" O LYS A 315 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 141 through 148 removed outlier: 7.117A pdb=" N TYR B 84 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N LEU B 318 " --> pdb=" O TYR B 84 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N GLU B 86 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N LEU B 316 " --> pdb=" O GLU B 86 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N PHE B 279 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LYS B 315 " --> pdb=" O TRP B 277 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N TRP B 277 " --> pdb=" O LYS B 315 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 141 through 148 removed outlier: 7.123A pdb=" N TYR C 84 " --> pdb=" O LEU C 318 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU C 318 " --> pdb=" O TYR C 84 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N GLU C 86 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LEU C 316 " --> pdb=" O GLU C 86 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N PHE C 279 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LYS C 315 " --> pdb=" O TRP C 277 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N TRP C 277 " --> pdb=" O LYS C 315 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 141 through 148 removed outlier: 7.095A pdb=" N TYR D 84 " --> pdb=" O LEU D 318 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N LEU D 318 " --> pdb=" O TYR D 84 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N GLU D 86 " --> pdb=" O LEU D 316 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N LEU D 316 " --> pdb=" O GLU D 86 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N PHE D 279 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LYS D 315 " --> pdb=" O TRP D 277 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N TRP D 277 " --> pdb=" O LYS D 315 " (cutoff:3.500A) 524 hydrogen bonds defined for protein. 1389 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.81 Time building geometry restraints manager: 7.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.39: 7276 1.39 - 1.56: 9542 1.56 - 1.73: 20 1.73 - 1.89: 96 1.89 - 2.06: 16 Bond restraints: 16950 Sorted by residual: bond pdb=" CG PRO D 406 " pdb=" CD PRO D 406 " ideal model delta sigma weight residual 1.512 1.487 0.025 2.70e-02 1.37e+03 8.91e-01 bond pdb=" CG PRO C 406 " pdb=" CD PRO C 406 " ideal model delta sigma weight residual 1.512 1.487 0.025 2.70e-02 1.37e+03 8.84e-01 bond pdb=" CG PRO B 406 " pdb=" CD PRO B 406 " ideal model delta sigma weight residual 1.512 1.487 0.025 2.70e-02 1.37e+03 8.69e-01 bond pdb=" CB GLU D 290 " pdb=" CG GLU D 290 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.57e-01 bond pdb=" CB GLN B 195 " pdb=" CG GLN B 195 " ideal model delta sigma weight residual 1.520 1.543 -0.023 3.00e-02 1.11e+03 6.06e-01 ... (remaining 16945 not shown) Histogram of bond angle deviations from ideal: 89.04 - 107.10: 817 107.10 - 125.15: 21806 125.15 - 143.21: 497 143.21 - 161.26: 0 161.26 - 179.31: 8 Bond angle restraints: 23128 Sorted by residual: angle pdb=" C ARG D 388 " pdb=" N ASP D 389 " pdb=" CA ASP D 389 " ideal model delta sigma weight residual 121.31 126.88 -5.57 1.49e+00 4.50e-01 1.40e+01 angle pdb=" C ARG B 388 " pdb=" N ASP B 389 " pdb=" CA ASP B 389 " ideal model delta sigma weight residual 121.31 126.77 -5.46 1.49e+00 4.50e-01 1.34e+01 angle pdb=" CB MET D 394 " pdb=" CG MET D 394 " pdb=" SD MET D 394 " ideal model delta sigma weight residual 112.70 123.10 -10.40 3.00e+00 1.11e-01 1.20e+01 angle pdb=" C ARG A 388 " pdb=" N ASP A 389 " pdb=" CA ASP A 389 " ideal model delta sigma weight residual 121.54 127.19 -5.65 1.91e+00 2.74e-01 8.74e+00 angle pdb=" N ASP D 389 " pdb=" CA ASP D 389 " pdb=" C ASP D 389 " ideal model delta sigma weight residual 110.35 114.40 -4.05 1.40e+00 5.10e-01 8.39e+00 ... (remaining 23123 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 8631 17.69 - 35.38: 876 35.38 - 53.07: 273 53.07 - 70.76: 80 70.76 - 88.45: 36 Dihedral angle restraints: 9896 sinusoidal: 4087 harmonic: 5809 Sorted by residual: dihedral pdb=" CA CYS D 393 " pdb=" C CYS D 393 " pdb=" N MET D 394 " pdb=" CA MET D 394 " ideal model delta harmonic sigma weight residual -180.00 -154.75 -25.25 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA ASP D 180 " pdb=" CB ASP D 180 " pdb=" CG ASP D 180 " pdb=" OD1 ASP D 180 " ideal model delta sinusoidal sigma weight residual -30.00 -88.06 58.06 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" CA ASP A 180 " pdb=" CB ASP A 180 " pdb=" CG ASP A 180 " pdb=" OD1 ASP A 180 " ideal model delta sinusoidal sigma weight residual -30.00 -87.20 57.20 1 2.00e+01 2.50e-03 1.10e+01 ... (remaining 9893 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1331 0.029 - 0.059: 650 0.059 - 0.088: 208 0.088 - 0.118: 127 0.118 - 0.147: 19 Chirality restraints: 2335 Sorted by residual: chirality pdb=" CA ILE B 373 " pdb=" N ILE B 373 " pdb=" C ILE B 373 " pdb=" CB ILE B 373 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.43e-01 chirality pdb=" CA ILE C 373 " pdb=" N ILE C 373 " pdb=" C ILE C 373 " pdb=" CB ILE C 373 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.33e-01 chirality pdb=" CA TYR C 358 " pdb=" N TYR C 358 " pdb=" C TYR C 358 " pdb=" CB TYR C 358 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.15e-01 ... (remaining 2332 not shown) Planarity restraints: 3067 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 6 " -0.041 5.00e-02 4.00e+02 6.31e-02 6.37e+00 pdb=" N PRO C 7 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO C 7 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 7 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 346 " 0.032 5.00e-02 4.00e+02 4.82e-02 3.71e+00 pdb=" N PRO C 347 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO C 347 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 347 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 346 " -0.031 5.00e-02 4.00e+02 4.70e-02 3.53e+00 pdb=" N PRO D 347 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO D 347 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 347 " -0.026 5.00e-02 4.00e+02 ... (remaining 3064 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 1009 2.74 - 3.28: 16266 3.28 - 3.82: 29828 3.82 - 4.36: 36824 4.36 - 4.90: 60764 Nonbonded interactions: 144691 Sorted by model distance: nonbonded pdb=" NE2 GLN A 415 " pdb=" OG SER A 417 " model vdw 2.194 2.520 nonbonded pdb=" OE1 GLN D 415 " pdb=" OG SER D 417 " model vdw 2.224 2.440 nonbonded pdb=" NZ LYS B 301 " pdb=" O ASP B 438 " model vdw 2.226 2.520 nonbonded pdb=" OD2 ASP A 360 " pdb=" NH1 ARG C 66 " model vdw 2.231 2.520 nonbonded pdb=" NZ LYS D 301 " pdb=" O ASP D 438 " model vdw 2.232 2.520 ... (remaining 144686 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 5 through 119 or resid 122 through 501 or resid 601 throug \ h 602)) selection = (chain 'B' and (resid 5 through 119 or resid 122 through 501 or resid 1201 throu \ gh 1202)) selection = (chain 'C' and (resid 5 through 119 or resid 122 through 501 or resid 601 throug \ h 602)) selection = (chain 'D' and (resid 5 through 119 or resid 122 through 501 or resid 601 throug \ h 602)) } 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=0.11 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: 1.280 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: 0.010 Extract box with map and model: 8.210 Check model and map are aligned: 0.260 Set scattering table: 0.160 Process input model: 56.370 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.130 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:13.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 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 : 0.002 0.044 16950 Z= 0.158 Angle : 0.543 10.399 23128 Z= 0.272 Chirality : 0.042 0.147 2335 Planarity : 0.005 0.063 3067 Dihedral : 17.252 88.450 6170 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.33 % Allowed : 18.62 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.41 (0.19), residues: 1999 helix: 1.21 (0.20), residues: 698 sheet: 0.61 (0.33), residues: 283 loop : -0.45 (0.20), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 183 HIS 0.006 0.001 HIS A 102 PHE 0.015 0.001 PHE D 409 TYR 0.012 0.001 TYR D 236 ARG 0.002 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3998 Ramachandran restraints generated. 1999 Oldfield, 0 Emsley, 1999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3998 Ramachandran restraints generated. 1999 Oldfield, 0 Emsley, 1999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 195 time to evaluate : 1.909 Fit side-chains REVERT: A 56 VAL cc_start: 0.5998 (m) cc_final: 0.5692 (p) REVERT: A 88 THR cc_start: 0.6685 (p) cc_final: 0.6219 (t) REVERT: A 93 LYS cc_start: 0.6270 (OUTLIER) cc_final: 0.6060 (mtmm) REVERT: B 88 THR cc_start: 0.6459 (p) cc_final: 0.5977 (t) REVERT: B 396 ASP cc_start: 0.4877 (p0) cc_final: 0.4614 (p0) REVERT: B 455 GLN cc_start: 0.6161 (mt0) cc_final: 0.5922 (mt0) REVERT: C 43 THR cc_start: 0.6639 (p) cc_final: 0.6249 (t) REVERT: C 178 ASP cc_start: 0.5934 (t0) cc_final: 0.5711 (m-30) REVERT: C 306 LYS cc_start: 0.5656 (mppt) cc_final: 0.5157 (mmtt) REVERT: C 488 ASP cc_start: 0.5925 (m-30) cc_final: 0.5691 (t0) REVERT: D 88 THR cc_start: 0.6537 (p) cc_final: 0.6064 (t) outliers start: 38 outliers final: 35 residues processed: 231 average time/residue: 1.1867 time to fit residues: 307.9579 Evaluate side-chains 216 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 180 time to evaluate : 1.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain C residue 5 ARG Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 422 SER Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 361 THR Chi-restraints excluded: chain D residue 413 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 2.9990 chunk 148 optimal weight: 5.9990 chunk 82 optimal weight: 8.9990 chunk 50 optimal weight: 8.9990 chunk 100 optimal weight: 9.9990 chunk 79 optimal weight: 7.9990 chunk 153 optimal weight: 6.9990 chunk 59 optimal weight: 9.9990 chunk 93 optimal weight: 20.0000 chunk 114 optimal weight: 6.9990 chunk 177 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 HIS ** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 HIS ** C 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 492 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 16950 Z= 0.420 Angle : 0.828 9.256 23128 Z= 0.435 Chirality : 0.053 0.159 2335 Planarity : 0.008 0.065 3067 Dihedral : 10.276 94.387 2322 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.64 % Favored : 95.31 % Rotamer: Outliers : 5.06 % Allowed : 16.81 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.68 (0.18), residues: 1999 helix: -0.23 (0.19), residues: 699 sheet: 0.35 (0.31), residues: 294 loop : -0.78 (0.19), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 183 HIS 0.012 0.002 HIS A 102 PHE 0.027 0.003 PHE D 200 TYR 0.022 0.003 TYR C 280 ARG 0.011 0.001 ARG D 382 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3998 Ramachandran restraints generated. 1999 Oldfield, 0 Emsley, 1999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3998 Ramachandran restraints generated. 1999 Oldfield, 0 Emsley, 1999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 179 time to evaluate : 1.968 Fit side-chains REVERT: A 10 ASP cc_start: 0.6206 (m-30) cc_final: 0.5702 (m-30) REVERT: A 12 MET cc_start: 0.7358 (OUTLIER) cc_final: 0.6723 (mtm) REVERT: B 88 THR cc_start: 0.6349 (p) cc_final: 0.5828 (t) REVERT: B 349 LYS cc_start: 0.7358 (OUTLIER) cc_final: 0.7025 (mttp) REVERT: C 56 VAL cc_start: 0.6287 (OUTLIER) cc_final: 0.6020 (p) REVERT: C 306 LYS cc_start: 0.5652 (OUTLIER) cc_final: 0.5401 (mppt) REVERT: D 51 LEU cc_start: 0.7005 (OUTLIER) cc_final: 0.6787 (mm) REVERT: D 88 THR cc_start: 0.6534 (p) cc_final: 0.6062 (t) outliers start: 85 outliers final: 48 residues processed: 250 average time/residue: 1.1650 time to fit residues: 327.3323 Evaluate side-chains 235 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 182 time to evaluate : 1.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain C residue 5 ARG Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 306 LYS Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 422 SER Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 148 ASN Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 306 LYS Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 413 GLU Chi-restraints excluded: chain D residue 479 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 148 optimal weight: 6.9990 chunk 121 optimal weight: 9.9990 chunk 49 optimal weight: 20.0000 chunk 178 optimal weight: 6.9990 chunk 192 optimal weight: 2.9990 chunk 158 optimal weight: 10.0000 chunk 176 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 143 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 HIS C 40 ASN ** C 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 492 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 16950 Z= 0.309 Angle : 0.716 7.389 23128 Z= 0.374 Chirality : 0.049 0.147 2335 Planarity : 0.006 0.063 3067 Dihedral : 9.676 89.714 2316 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 4.36 % Allowed : 17.34 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.71 (0.18), residues: 1999 helix: -0.33 (0.18), residues: 699 sheet: 0.42 (0.31), residues: 294 loop : -0.76 (0.19), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 183 HIS 0.009 0.001 HIS A 102 PHE 0.020 0.003 PHE D 200 TYR 0.019 0.002 TYR C 280 ARG 0.008 0.001 ARG D 382 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3998 Ramachandran restraints generated. 1999 Oldfield, 0 Emsley, 1999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3998 Ramachandran restraints generated. 1999 Oldfield, 0 Emsley, 1999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 181 time to evaluate : 2.111 Fit side-chains REVERT: A 10 ASP cc_start: 0.6186 (m-30) cc_final: 0.5705 (m-30) REVERT: A 12 MET cc_start: 0.7342 (OUTLIER) cc_final: 0.6735 (mtm) REVERT: A 88 THR cc_start: 0.6564 (p) cc_final: 0.6199 (t) REVERT: A 221 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7776 (tttm) REVERT: B 88 THR cc_start: 0.6297 (p) cc_final: 0.5779 (t) REVERT: C 56 VAL cc_start: 0.6232 (OUTLIER) cc_final: 0.5946 (p) REVERT: C 294 PHE cc_start: 0.5887 (OUTLIER) cc_final: 0.5576 (m-80) REVERT: D 88 THR cc_start: 0.6538 (p) cc_final: 0.6047 (t) REVERT: D 468 LYS cc_start: 0.6484 (OUTLIER) cc_final: 0.6253 (ttpp) outliers start: 73 outliers final: 46 residues processed: 244 average time/residue: 1.2011 time to fit residues: 328.7070 Evaluate side-chains 226 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 175 time to evaluate : 1.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 221 LYS Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain C residue 5 ARG Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 294 PHE Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 422 SER Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 148 ASN Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 413 GLU Chi-restraints excluded: chain D residue 468 LYS Chi-restraints excluded: chain D residue 479 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 9.9990 chunk 134 optimal weight: 10.0000 chunk 92 optimal weight: 9.9990 chunk 19 optimal weight: 0.9990 chunk 85 optimal weight: 10.0000 chunk 119 optimal weight: 20.0000 chunk 178 optimal weight: 0.9990 chunk 189 optimal weight: 7.9990 chunk 93 optimal weight: 9.9990 chunk 169 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 ASN B 466 HIS C 40 ASN C 148 ASN ** C 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 433 ASN ** D 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 492 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 16950 Z= 0.329 Angle : 0.739 8.032 23128 Z= 0.386 Chirality : 0.050 0.148 2335 Planarity : 0.007 0.063 3067 Dihedral : 9.745 88.687 2313 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.19 % Favored : 94.76 % Rotamer: Outliers : 4.60 % Allowed : 17.16 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.88 (0.18), residues: 1999 helix: -0.48 (0.18), residues: 699 sheet: 0.32 (0.31), residues: 298 loop : -0.86 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 183 HIS 0.009 0.002 HIS A 102 PHE 0.022 0.003 PHE D 200 TYR 0.021 0.003 TYR C 280 ARG 0.008 0.001 ARG D 382 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3998 Ramachandran restraints generated. 1999 Oldfield, 0 Emsley, 1999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3998 Ramachandran restraints generated. 1999 Oldfield, 0 Emsley, 1999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 178 time to evaluate : 1.966 Fit side-chains REVERT: A 10 ASP cc_start: 0.6206 (m-30) cc_final: 0.5721 (m-30) REVERT: A 12 MET cc_start: 0.7336 (OUTLIER) cc_final: 0.6723 (mtm) REVERT: A 88 THR cc_start: 0.6489 (p) cc_final: 0.6141 (t) REVERT: A 221 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7804 (tttm) REVERT: B 88 THR cc_start: 0.6217 (p) cc_final: 0.5715 (t) REVERT: C 294 PHE cc_start: 0.5907 (OUTLIER) cc_final: 0.5549 (m-80) REVERT: D 88 THR cc_start: 0.6508 (p) cc_final: 0.6058 (t) outliers start: 77 outliers final: 50 residues processed: 244 average time/residue: 1.0959 time to fit residues: 302.4448 Evaluate side-chains 222 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 169 time to evaluate : 1.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 221 LYS Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain C residue 5 ARG Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 294 PHE Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 148 ASN Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 413 GLU Chi-restraints excluded: chain D residue 479 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 5.9990 chunk 107 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 141 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 chunk 161 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 96 optimal weight: 0.9980 chunk 170 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 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 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 HIS B 494 GLN C 148 ASN ** C 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 433 ASN ** D 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 481 ASN D 492 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16950 Z= 0.172 Angle : 0.558 5.772 23128 Z= 0.286 Chirality : 0.044 0.147 2335 Planarity : 0.005 0.060 3067 Dihedral : 7.869 67.818 2312 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.68 % Allowed : 18.15 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.30 (0.18), residues: 1999 helix: 0.13 (0.19), residues: 699 sheet: 0.52 (0.31), residues: 296 loop : -0.58 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 183 HIS 0.006 0.001 HIS A 102 PHE 0.012 0.001 PHE A 136 TYR 0.019 0.001 TYR B 236 ARG 0.004 0.000 ARG B 170 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3998 Ramachandran restraints generated. 1999 Oldfield, 0 Emsley, 1999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3998 Ramachandran restraints generated. 1999 Oldfield, 0 Emsley, 1999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 203 time to evaluate : 1.884 Fit side-chains REVERT: A 12 MET cc_start: 0.7284 (OUTLIER) cc_final: 0.6608 (mtm) REVERT: A 88 THR cc_start: 0.6476 (p) cc_final: 0.6073 (t) REVERT: A 199 LEU cc_start: 0.8019 (tp) cc_final: 0.7777 (tp) REVERT: B 88 THR cc_start: 0.6360 (p) cc_final: 0.5794 (t) REVERT: B 199 LEU cc_start: 0.7983 (tp) cc_final: 0.7683 (tp) REVERT: B 221 LYS cc_start: 0.7868 (ttpt) cc_final: 0.7649 (ttpt) REVERT: B 396 ASP cc_start: 0.5048 (p0) cc_final: 0.4721 (p0) REVERT: B 455 GLN cc_start: 0.6365 (mt0) cc_final: 0.6056 (mt0) REVERT: C 88 THR cc_start: 0.6369 (p) cc_final: 0.6000 (t) REVERT: C 199 LEU cc_start: 0.7988 (tp) cc_final: 0.7716 (tp) REVERT: C 294 PHE cc_start: 0.5818 (OUTLIER) cc_final: 0.5581 (m-80) REVERT: C 306 LYS cc_start: 0.5653 (mppt) cc_final: 0.5099 (mmtt) REVERT: D 22 GLN cc_start: 0.3126 (OUTLIER) cc_final: 0.2896 (pt0) REVERT: D 88 THR cc_start: 0.6604 (p) cc_final: 0.6099 (t) REVERT: D 493 ILE cc_start: 0.7257 (mm) cc_final: 0.7047 (mt) outliers start: 44 outliers final: 22 residues processed: 241 average time/residue: 1.1402 time to fit residues: 309.5087 Evaluate side-chains 208 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 183 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 294 PHE Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain D residue 22 GLN Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 323 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 0.9990 chunk 170 optimal weight: 9.9990 chunk 37 optimal weight: 0.7980 chunk 111 optimal weight: 8.9990 chunk 46 optimal weight: 6.9990 chunk 189 optimal weight: 9.9990 chunk 157 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 HIS B 466 HIS ** C 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 HIS ** D 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 466 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16950 Z= 0.184 Angle : 0.566 5.896 23128 Z= 0.290 Chirality : 0.044 0.146 2335 Planarity : 0.005 0.058 3067 Dihedral : 7.729 66.694 2291 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.56 % Allowed : 18.21 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.19 (0.19), residues: 1999 helix: 0.23 (0.19), residues: 699 sheet: 0.59 (0.31), residues: 296 loop : -0.52 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 183 HIS 0.006 0.001 HIS A 102 PHE 0.012 0.002 PHE B 136 TYR 0.019 0.002 TYR B 236 ARG 0.004 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3998 Ramachandran restraints generated. 1999 Oldfield, 0 Emsley, 1999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3998 Ramachandran restraints generated. 1999 Oldfield, 0 Emsley, 1999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 191 time to evaluate : 1.850 Fit side-chains REVERT: A 10 ASP cc_start: 0.6109 (m-30) cc_final: 0.5656 (m-30) REVERT: A 12 MET cc_start: 0.7345 (OUTLIER) cc_final: 0.6672 (mtm) REVERT: A 88 THR cc_start: 0.6440 (p) cc_final: 0.6042 (t) REVERT: A 199 LEU cc_start: 0.8077 (tp) cc_final: 0.7863 (tp) REVERT: B 88 THR cc_start: 0.6316 (p) cc_final: 0.5754 (t) REVERT: B 199 LEU cc_start: 0.7984 (tp) cc_final: 0.7727 (tp) REVERT: B 396 ASP cc_start: 0.5088 (p0) cc_final: 0.4690 (p0) REVERT: B 455 GLN cc_start: 0.6355 (mt0) cc_final: 0.6051 (mt0) REVERT: C 199 LEU cc_start: 0.8001 (tp) cc_final: 0.7756 (tp) REVERT: C 294 PHE cc_start: 0.5824 (OUTLIER) cc_final: 0.5594 (m-80) REVERT: D 22 GLN cc_start: 0.3135 (OUTLIER) cc_final: 0.2899 (pt0) REVERT: D 88 THR cc_start: 0.6630 (p) cc_final: 0.6137 (t) REVERT: D 199 LEU cc_start: 0.8006 (tp) cc_final: 0.7749 (tp) REVERT: D 396 ASP cc_start: 0.5662 (OUTLIER) cc_final: 0.5455 (t0) outliers start: 42 outliers final: 24 residues processed: 226 average time/residue: 1.2405 time to fit residues: 313.3981 Evaluate side-chains 210 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 182 time to evaluate : 1.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 294 PHE Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain D residue 22 GLN Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 396 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 5.9990 chunk 21 optimal weight: 20.0000 chunk 108 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 159 optimal weight: 20.0000 chunk 105 optimal weight: 6.9990 chunk 188 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 115 optimal weight: 9.9990 chunk 87 optimal weight: 0.6980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 HIS B 494 GLN ** C 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 HIS ** D 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 466 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16950 Z= 0.198 Angle : 0.583 5.851 23128 Z= 0.300 Chirality : 0.045 0.146 2335 Planarity : 0.005 0.057 3067 Dihedral : 7.890 67.945 2290 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.50 % Allowed : 18.50 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.19 (0.19), residues: 1999 helix: 0.23 (0.19), residues: 699 sheet: 0.53 (0.31), residues: 296 loop : -0.51 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 183 HIS 0.006 0.001 HIS A 102 PHE 0.013 0.002 PHE B 279 TYR 0.019 0.002 TYR B 236 ARG 0.004 0.000 ARG D 382 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3998 Ramachandran restraints generated. 1999 Oldfield, 0 Emsley, 1999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3998 Ramachandran restraints generated. 1999 Oldfield, 0 Emsley, 1999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 187 time to evaluate : 1.961 Fit side-chains REVERT: A 10 ASP cc_start: 0.6063 (m-30) cc_final: 0.5606 (m-30) REVERT: A 12 MET cc_start: 0.7349 (OUTLIER) cc_final: 0.6706 (mtm) REVERT: A 88 THR cc_start: 0.6490 (p) cc_final: 0.6086 (t) REVERT: A 221 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7679 (tttm) REVERT: B 88 THR cc_start: 0.6285 (p) cc_final: 0.5736 (t) REVERT: B 396 ASP cc_start: 0.5085 (p0) cc_final: 0.4703 (p0) REVERT: B 455 GLN cc_start: 0.6354 (mt0) cc_final: 0.6082 (mt0) REVERT: C 199 LEU cc_start: 0.8025 (tp) cc_final: 0.7779 (tp) REVERT: C 294 PHE cc_start: 0.5844 (OUTLIER) cc_final: 0.5594 (m-80) REVERT: C 306 LYS cc_start: 0.5629 (mppt) cc_final: 0.5109 (mmtt) REVERT: D 22 GLN cc_start: 0.3116 (OUTLIER) cc_final: 0.2889 (pt0) REVERT: D 88 THR cc_start: 0.6559 (p) cc_final: 0.6104 (t) outliers start: 41 outliers final: 26 residues processed: 223 average time/residue: 1.2395 time to fit residues: 309.7412 Evaluate side-chains 211 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 181 time to evaluate : 1.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 221 LYS Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 294 PHE Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain D residue 22 GLN Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 236 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 1.9990 chunk 75 optimal weight: 0.0170 chunk 112 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 37 optimal weight: 0.0470 chunk 36 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 93 optimal weight: 20.0000 chunk 17 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 overall best weight: 1.2122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 HIS ** C 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 HIS ** D 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 466 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16950 Z= 0.170 Angle : 0.550 5.936 23128 Z= 0.279 Chirality : 0.044 0.147 2335 Planarity : 0.005 0.056 3067 Dihedral : 7.368 63.673 2290 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.09 % Allowed : 18.91 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.07 (0.19), residues: 1999 helix: 0.36 (0.19), residues: 699 sheet: 0.58 (0.31), residues: 296 loop : -0.45 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 183 HIS 0.006 0.001 HIS A 102 PHE 0.012 0.001 PHE C 409 TYR 0.019 0.001 TYR D 236 ARG 0.003 0.000 ARG B 170 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3998 Ramachandran restraints generated. 1999 Oldfield, 0 Emsley, 1999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3998 Ramachandran restraints generated. 1999 Oldfield, 0 Emsley, 1999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 191 time to evaluate : 1.930 Fit side-chains REVERT: A 10 ASP cc_start: 0.6074 (m-30) cc_final: 0.5621 (m-30) REVERT: A 12 MET cc_start: 0.7338 (OUTLIER) cc_final: 0.6691 (mtm) REVERT: A 88 THR cc_start: 0.6490 (p) cc_final: 0.6077 (t) REVERT: A 199 LEU cc_start: 0.7936 (tp) cc_final: 0.7627 (tp) REVERT: B 88 THR cc_start: 0.6313 (p) cc_final: 0.5759 (t) REVERT: B 396 ASP cc_start: 0.5053 (p0) cc_final: 0.4670 (p0) REVERT: B 455 GLN cc_start: 0.6336 (mt0) cc_final: 0.6036 (mt0) REVERT: C 294 PHE cc_start: 0.5794 (OUTLIER) cc_final: 0.5564 (m-80) REVERT: C 306 LYS cc_start: 0.5606 (mppt) cc_final: 0.5094 (mmtt) REVERT: D 22 GLN cc_start: 0.3143 (OUTLIER) cc_final: 0.2927 (pt0) REVERT: D 88 THR cc_start: 0.6616 (p) cc_final: 0.6124 (t) REVERT: D 199 LEU cc_start: 0.8014 (tp) cc_final: 0.7725 (tp) outliers start: 34 outliers final: 23 residues processed: 220 average time/residue: 1.2260 time to fit residues: 301.5908 Evaluate side-chains 206 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 180 time to evaluate : 1.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 294 PHE Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain D residue 22 GLN Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 255 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 10.0000 chunk 180 optimal weight: 6.9990 chunk 165 optimal weight: 0.8980 chunk 176 optimal weight: 5.9990 chunk 105 optimal weight: 8.9990 chunk 76 optimal weight: 3.9990 chunk 138 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 159 optimal weight: 10.0000 chunk 166 optimal weight: 5.9990 chunk 175 optimal weight: 1.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 HIS ** B 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 466 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16950 Z= 0.243 Angle : 0.635 6.405 23128 Z= 0.328 Chirality : 0.046 0.142 2335 Planarity : 0.005 0.057 3067 Dihedral : 8.439 76.158 2290 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.39 % Allowed : 18.91 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.30 (0.18), residues: 1999 helix: 0.16 (0.19), residues: 698 sheet: 0.42 (0.31), residues: 299 loop : -0.57 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 183 HIS 0.006 0.001 HIS A 102 PHE 0.017 0.002 PHE B 200 TYR 0.019 0.002 TYR C 236 ARG 0.006 0.001 ARG D 382 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3998 Ramachandran restraints generated. 1999 Oldfield, 0 Emsley, 1999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3998 Ramachandran restraints generated. 1999 Oldfield, 0 Emsley, 1999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 176 time to evaluate : 1.805 Fit side-chains REVERT: A 10 ASP cc_start: 0.6124 (m-30) cc_final: 0.5656 (m-30) REVERT: A 12 MET cc_start: 0.7362 (OUTLIER) cc_final: 0.6731 (mtm) REVERT: A 56 VAL cc_start: 0.6338 (m) cc_final: 0.6040 (p) REVERT: A 88 THR cc_start: 0.6388 (p) cc_final: 0.6005 (t) REVERT: A 221 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7728 (tttm) REVERT: B 88 THR cc_start: 0.6265 (p) cc_final: 0.5761 (t) REVERT: B 455 GLN cc_start: 0.6361 (mt0) cc_final: 0.6071 (mt0) REVERT: C 12 MET cc_start: 0.7317 (OUTLIER) cc_final: 0.6689 (mtm) REVERT: C 56 VAL cc_start: 0.6053 (m) cc_final: 0.5786 (p) REVERT: C 294 PHE cc_start: 0.5876 (OUTLIER) cc_final: 0.5618 (m-80) REVERT: D 22 GLN cc_start: 0.3093 (OUTLIER) cc_final: 0.2855 (pt0) REVERT: D 88 THR cc_start: 0.6489 (p) cc_final: 0.6055 (t) outliers start: 39 outliers final: 26 residues processed: 208 average time/residue: 1.2557 time to fit residues: 292.4505 Evaluate side-chains 203 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 172 time to evaluate : 1.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 221 LYS Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain C residue 12 MET Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 294 PHE Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain D residue 22 GLN Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 236 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 0.0980 chunk 186 optimal weight: 9.9990 chunk 113 optimal weight: 5.9990 chunk 88 optimal weight: 0.0870 chunk 129 optimal weight: 10.0000 chunk 195 optimal weight: 10.0000 chunk 179 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 120 optimal weight: 10.0000 chunk 95 optimal weight: 0.3980 overall best weight: 1.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 494 GLN ** C 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16950 Z= 0.194 Angle : 0.583 6.195 23128 Z= 0.299 Chirality : 0.045 0.146 2335 Planarity : 0.005 0.057 3067 Dihedral : 7.856 69.752 2290 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.98 % Allowed : 19.02 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.18 (0.19), residues: 1999 helix: 0.27 (0.19), residues: 698 sheet: 0.52 (0.31), residues: 294 loop : -0.51 (0.19), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 183 HIS 0.006 0.001 HIS A 102 PHE 0.014 0.002 PHE C 409 TYR 0.019 0.002 TYR D 236 ARG 0.003 0.000 ARG B 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3998 Ramachandran restraints generated. 1999 Oldfield, 0 Emsley, 1999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3998 Ramachandran restraints generated. 1999 Oldfield, 0 Emsley, 1999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 176 time to evaluate : 2.039 Fit side-chains REVERT: A 10 ASP cc_start: 0.6070 (m-30) cc_final: 0.5610 (m-30) REVERT: A 12 MET cc_start: 0.7335 (OUTLIER) cc_final: 0.6696 (mtm) REVERT: A 88 THR cc_start: 0.6420 (p) cc_final: 0.6018 (t) REVERT: A 221 LYS cc_start: 0.8112 (OUTLIER) cc_final: 0.7690 (tttm) REVERT: B 88 THR cc_start: 0.6296 (p) cc_final: 0.5752 (t) REVERT: B 221 LYS cc_start: 0.7967 (ttpt) cc_final: 0.7657 (ttpt) REVERT: B 396 ASP cc_start: 0.5079 (p0) cc_final: 0.4706 (p0) REVERT: B 455 GLN cc_start: 0.6386 (mt0) cc_final: 0.6107 (mt0) REVERT: C 56 VAL cc_start: 0.5906 (m) cc_final: 0.5617 (p) REVERT: C 294 PHE cc_start: 0.5834 (OUTLIER) cc_final: 0.5585 (m-80) REVERT: D 22 GLN cc_start: 0.3106 (OUTLIER) cc_final: 0.2888 (pt0) REVERT: D 88 THR cc_start: 0.6533 (p) cc_final: 0.6083 (t) outliers start: 32 outliers final: 25 residues processed: 205 average time/residue: 1.2462 time to fit residues: 285.4575 Evaluate side-chains 203 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 174 time to evaluate : 1.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 221 LYS Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain C residue 18 GLN Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 294 PHE Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain D residue 22 GLN Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 236 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 1.9990 chunk 165 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 chunk 143 optimal weight: 8.9990 chunk 22 optimal weight: 0.5980 chunk 43 optimal weight: 5.9990 chunk 155 optimal weight: 0.9990 chunk 65 optimal weight: 0.2980 chunk 159 optimal weight: 9.9990 chunk 19 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 ASN ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 494 GLN ** C 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.169405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.143112 restraints weight = 25801.033| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 1.53 r_work: 0.3538 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3409 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3409 r_free = 0.3409 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3409 r_free = 0.3409 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3409 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16950 Z= 0.156 Angle : 0.532 7.014 23128 Z= 0.267 Chirality : 0.043 0.148 2335 Planarity : 0.005 0.056 3067 Dihedral : 6.933 59.604 2290 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.92 % Allowed : 19.20 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.03 (0.19), residues: 1999 helix: 0.51 (0.20), residues: 699 sheet: 0.55 (0.31), residues: 296 loop : -0.41 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 183 HIS 0.006 0.001 HIS A 102 PHE 0.012 0.001 PHE C 409 TYR 0.018 0.001 TYR B 236 ARG 0.003 0.000 ARG B 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5767.77 seconds wall clock time: 102 minutes 30.49 seconds (6150.49 seconds total)