Starting phenix.real_space_refine on Tue Nov 19 01:26:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cxg_27055/11_2024/8cxg_27055.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cxg_27055/11_2024/8cxg_27055.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cxg_27055/11_2024/8cxg_27055.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cxg_27055/11_2024/8cxg_27055.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cxg_27055/11_2024/8cxg_27055.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cxg_27055/11_2024/8cxg_27055.cif" } resolution = 3.2 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= 1.000 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: 4 Type Number sf(0) Gaussians S 115 5.16 5 C 11636 2.51 5 N 3149 2.21 5 O 3481 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 18381 Number of models: 1 Model: "" Number of chains: 12 Chain: "H" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 933 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "L" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 852 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 8, 'TRANS': 100} Chain: "A" Number of atoms: 3721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3721 Classifications: {'peptide': 492} Link IDs: {'PTRANS': 16, 'TRANS': 475} Chain breaks: 1 Chain: "D" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 600 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "h" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 933 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "l" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 852 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 8, 'TRANS': 100} Chain: "B" Number of atoms: 3721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3721 Classifications: {'peptide': 492} Link IDs: {'PTRANS': 16, 'TRANS': 475} Chain breaks: 1 Chain: "E" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 600 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "C" Number of atoms: 3790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3790 Classifications: {'peptide': 501} Link IDs: {'PTRANS': 16, 'TRANS': 484} Chain: "F" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 600 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "1" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 933 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "2" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 846 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 8, 'TRANS': 99} Time building chain proxies: 10.13, per 1000 atoms: 0.55 Number of scatterers: 18381 At special positions: 0 Unit cell: (107.06, 207.76, 115.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 115 16.00 O 3481 8.00 N 3149 7.00 C 11636 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=22, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 3 " - pdb=" SG CYS A 30 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 121 " distance=2.08 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 116 " distance=2.03 Simple disulfide: pdb=" SG CYS A 190 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 308 " - pdb=" SG CYS A 339 " distance=1.72 Simple disulfide: pdb=" SG CYS h 22 " - pdb=" SG CYS h 96 " distance=2.03 Simple disulfide: pdb=" SG CYS l 23 " - pdb=" SG CYS l 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 3 " - pdb=" SG CYS B 30 " distance=2.51 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 121 " distance=1.75 Simple disulfide: pdb=" SG CYS B 74 " - pdb=" SG CYS B 105 " distance=2.08 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 116 " distance=2.03 Simple disulfide: pdb=" SG CYS B 190 " - pdb=" SG CYS B 291 " distance=2.02 Simple disulfide: pdb=" SG CYS C 3 " - pdb=" SG CYS C 30 " distance=1.38 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 121 " distance=1.18 Simple disulfide: pdb=" SG CYS C 74 " - pdb=" SG CYS C 105 " distance=2.79 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 116 " distance=2.03 Simple disulfide: pdb=" SG CYS C 190 " - pdb=" SG CYS C 291 " distance=2.02 Simple disulfide: pdb=" SG CYS C 308 " - pdb=" SG CYS C 339 " distance=1.24 Simple disulfide: pdb=" SG CYS 1 22 " - pdb=" SG CYS 1 96 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 23 " - pdb=" SG CYS 2 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.20 Conformation dependent library (CDL) restraints added in 2.5 seconds 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4328 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 31 sheets defined 20.9% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.22 Creating SS restraints... Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.576A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 87 removed outlier: 3.634A pdb=" N SER A 86 " --> pdb=" O ASP A 83 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASP A 87 " --> pdb=" O LYS A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 269 removed outlier: 3.696A pdb=" N HIS A 266 " --> pdb=" O GLU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 425 Processing helix chain 'A' and resid 426 through 431 Processing helix chain 'A' and resid 437 through 457 Processing helix chain 'A' and resid 461 through 479 Processing helix chain 'A' and resid 483 through 499 removed outlier: 3.504A pdb=" N LEU A 498 " --> pdb=" O VAL A 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 11 removed outlier: 4.018A pdb=" N THR D 9 " --> pdb=" O SER D 6 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 39 Processing helix chain 'D' and resid 40 through 53 removed outlier: 3.968A pdb=" N LEU D 44 " --> pdb=" O PRO D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 71 Processing helix chain 'h' and resid 28 through 30 No H-bonds generated for 'chain 'h' and resid 28 through 30' Processing helix chain 'h' and resid 87 through 91 Processing helix chain 'l' and resid 79 through 83 removed outlier: 3.621A pdb=" N PHE l 83 " --> pdb=" O PRO l 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 87 removed outlier: 3.811A pdb=" N SER B 86 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASP B 87 " --> pdb=" O LYS B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 196 removed outlier: 4.601A pdb=" N LEU B 196 " --> pdb=" O PRO B 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 192 through 196' Processing helix chain 'B' and resid 263 through 269 Processing helix chain 'B' and resid 405 through 425 Processing helix chain 'B' and resid 425 through 430 Processing helix chain 'B' and resid 437 through 457 Processing helix chain 'B' and resid 463 through 479 Processing helix chain 'B' and resid 482 through 500 Processing helix chain 'E' and resid 6 through 11 removed outlier: 3.847A pdb=" N THR E 9 " --> pdb=" O SER E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 39 Processing helix chain 'E' and resid 40 through 53 removed outlier: 3.956A pdb=" N LEU E 44 " --> pdb=" O PRO E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 74 Proline residue: E 72 - end of helix Processing helix chain 'C' and resid 82 through 87 removed outlier: 3.594A pdb=" N SER C 86 " --> pdb=" O ASP C 83 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP C 87 " --> pdb=" O LYS C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 269 Processing helix chain 'C' and resid 405 through 425 Processing helix chain 'C' and resid 426 through 431 Processing helix chain 'C' and resid 437 through 457 Processing helix chain 'C' and resid 463 through 479 Processing helix chain 'C' and resid 483 through 500 removed outlier: 3.695A pdb=" N GLY C 493 " --> pdb=" O LEU C 489 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 11 removed outlier: 3.889A pdb=" N THR F 9 " --> pdb=" O SER F 6 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 39 removed outlier: 3.919A pdb=" N HIS F 28 " --> pdb=" O GLU F 24 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU F 29 " --> pdb=" O TYR F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 53 Processing helix chain 'F' and resid 56 through 74 Proline residue: F 72 - end of helix Processing helix chain '1' and resid 28 through 30 No H-bonds generated for 'chain '1' and resid 28 through 30' Processing helix chain '1' and resid 87 through 91 Processing helix chain '2' and resid 79 through 83 removed outlier: 3.517A pdb=" N PHE 2 83 " --> pdb=" O PRO 2 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 11 through 12 current: chain 'H' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 58 through 60 current: chain 'H' and resid 110 through 112 Processing sheet with id=AA3, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AA4, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.608A pdb=" N LEU L 11 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 10 through 13 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 41 through 50 current: chain 'A' and resid 126 through 129 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 126 through 129 current: chain 'A' and resid 164 through 169 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 164 through 169 current: chain 'A' and resid 210 through 214 removed outlier: 4.021A pdb=" N HIS A 210 " --> pdb=" O ALA A 275 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 21 through 26 removed outlier: 4.561A pdb=" N LYS A 290 " --> pdb=" O GLU A 191 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 63 through 65 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 63 through 65 current: chain 'A' and resid 113 through 121 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 243 through 248 removed outlier: 3.751A pdb=" N ARG A 252 " --> pdb=" O ALA A 248 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 312 through 320 removed outlier: 6.724A pdb=" N THR A 315 " --> pdb=" O GLN A 331 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N GLN A 331 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ILE A 317 " --> pdb=" O GLU A 329 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLU A 329 " --> pdb=" O ILE A 317 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 339 through 340 Processing sheet with id=AB2, first strand: chain 'A' and resid 353 through 355 removed outlier: 4.843A pdb=" N THR A 353 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N VAL A 347 " --> pdb=" O THR A 353 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N MET A 345 " --> pdb=" O VAL A 355 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'h' and resid 3 through 7 Processing sheet with id=AB4, first strand: chain 'h' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'h' and resid 11 through 12 current: chain 'h' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'h' and resid 58 through 60 current: chain 'h' and resid 110 through 112 Processing sheet with id=AB5, first strand: chain 'l' and resid 4 through 6 Processing sheet with id=AB6, first strand: chain 'l' and resid 10 through 13 removed outlier: 6.660A pdb=" N LEU l 33 " --> pdb=" O TYR l 49 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N TYR l 49 " --> pdb=" O LEU l 33 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N TRP l 35 " --> pdb=" O LEU l 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 10 through 11 removed outlier: 6.587A pdb=" N ASP B 10 " --> pdb=" O THR B 32 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 41 through 51 current: chain 'B' and resid 110 through 129 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 110 through 129 current: chain 'B' and resid 164 through 169 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 164 through 169 current: chain 'B' and resid 210 through 214 removed outlier: 4.515A pdb=" N HIS B 210 " --> pdb=" O ALA B 275 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 21 through 26 removed outlier: 4.638A pdb=" N LYS B 290 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ASP B 296 " --> pdb=" O SER B 185 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N SER B 185 " --> pdb=" O ASP B 296 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 243 through 247 Processing sheet with id=AC1, first strand: chain 'B' and resid 312 through 314 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 312 through 314 current: chain 'B' and resid 326 through 332 Processing sheet with id=AC2, first strand: chain 'B' and resid 339 through 340 Processing sheet with id=AC3, first strand: chain 'B' and resid 343 through 346 Processing sheet with id=AC4, first strand: chain 'C' and resid 10 through 13 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 41 through 50 current: chain 'C' and resid 112 through 129 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 112 through 129 current: chain 'C' and resid 164 through 169 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 164 through 169 current: chain 'C' and resid 210 through 214 removed outlier: 3.951A pdb=" N HIS C 210 " --> pdb=" O ALA C 275 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 20 through 26 removed outlier: 4.605A pdb=" N LYS C 290 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ASP C 296 " --> pdb=" O SER C 185 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N SER C 185 " --> pdb=" O ASP C 296 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 243 through 246 Processing sheet with id=AC7, first strand: chain 'C' and resid 312 through 314 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 312 through 314 current: chain 'C' and resid 326 through 332 Processing sheet with id=AC8, first strand: chain 'C' and resid 339 through 340 Processing sheet with id=AC9, first strand: chain 'C' and resid 343 through 346 removed outlier: 3.774A pdb=" N ILE C 389 " --> pdb=" O ILE C 396 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE C 396 " --> pdb=" O ILE C 389 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain '1' and resid 3 through 7 removed outlier: 3.577A pdb=" N LEU 1 20 " --> pdb=" O PHE 1 81 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain '1' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain '1' and resid 11 through 12 current: chain '1' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain '1' and resid 58 through 60 current: chain '1' and resid 110 through 112 Processing sheet with id=AD3, first strand: chain '2' and resid 4 through 6 Processing sheet with id=AD4, first strand: chain '2' and resid 10 through 13 removed outlier: 6.502A pdb=" N LEU 2 33 " --> pdb=" O TYR 2 49 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N TYR 2 49 " --> pdb=" O LEU 2 33 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N TRP 2 35 " --> pdb=" O LEU 2 47 " (cutoff:3.500A) 630 hydrogen bonds defined for protein. 1650 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: 5.88 Time building geometry restraints manager: 5.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 2975 1.29 - 1.43: 5117 1.43 - 1.57: 10529 1.57 - 1.72: 0 1.72 - 1.86: 179 Bond restraints: 18800 Sorted by residual: bond pdb=" CA CYS A 121 " pdb=" C CYS A 121 " ideal model delta sigma weight residual 1.522 1.408 0.114 1.20e-02 6.94e+03 9.05e+01 bond pdb=" C VAL A 243 " pdb=" O VAL A 243 " ideal model delta sigma weight residual 1.236 1.145 0.091 1.04e-02 9.25e+03 7.60e+01 bond pdb=" CA VAL A 243 " pdb=" CB VAL A 243 " ideal model delta sigma weight residual 1.541 1.459 0.082 1.28e-02 6.10e+03 4.15e+01 bond pdb=" CA PHE B 198 " pdb=" C PHE B 198 " ideal model delta sigma weight residual 1.524 1.444 0.080 1.29e-02 6.01e+03 3.87e+01 bond pdb=" CA THR C 126 " pdb=" C THR C 126 " ideal model delta sigma weight residual 1.521 1.444 0.077 1.24e-02 6.50e+03 3.82e+01 ... (remaining 18795 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.05: 25046 3.05 - 6.10: 365 6.10 - 9.15: 62 9.15 - 12.20: 14 12.20 - 15.25: 4 Bond angle restraints: 25491 Sorted by residual: angle pdb=" N LEU C 242 " pdb=" CA LEU C 242 " pdb=" C LEU C 242 " ideal model delta sigma weight residual 113.17 100.84 12.33 1.26e+00 6.30e-01 9.58e+01 angle pdb=" N ASN B 237 " pdb=" CA ASN B 237 " pdb=" C ASN B 237 " ideal model delta sigma weight residual 111.36 121.20 -9.84 1.09e+00 8.42e-01 8.15e+01 angle pdb=" N PRO l 95 " pdb=" CA PRO l 95 " pdb=" C PRO l 95 " ideal model delta sigma weight residual 110.70 121.59 -10.89 1.22e+00 6.72e-01 7.97e+01 angle pdb=" N SER B 433 " pdb=" CA SER B 433 " pdb=" C SER B 433 " ideal model delta sigma weight residual 110.70 124.32 -13.62 1.55e+00 4.16e-01 7.72e+01 angle pdb=" CA GLY B 195 " pdb=" C GLY B 195 " pdb=" N LEU B 196 " ideal model delta sigma weight residual 117.04 125.73 -8.69 9.90e-01 1.02e+00 7.70e+01 ... (remaining 25486 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 10279 17.75 - 35.50: 620 35.50 - 53.25: 136 53.25 - 71.00: 38 71.00 - 88.75: 8 Dihedral angle restraints: 11081 sinusoidal: 4278 harmonic: 6803 Sorted by residual: dihedral pdb=" CB CYS A 308 " pdb=" SG CYS A 308 " pdb=" SG CYS A 339 " pdb=" CB CYS A 339 " ideal model delta sinusoidal sigma weight residual -86.00 -174.75 88.75 1 1.00e+01 1.00e-02 9.39e+01 dihedral pdb=" CB CYS C 3 " pdb=" SG CYS C 3 " pdb=" SG CYS C 30 " pdb=" CB CYS C 30 " ideal model delta sinusoidal sigma weight residual -86.00 -156.44 70.44 1 1.00e+01 1.00e-02 6.39e+01 dihedral pdb=" CB CYS A 3 " pdb=" SG CYS A 3 " pdb=" SG CYS A 30 " pdb=" CB CYS A 30 " ideal model delta sinusoidal sigma weight residual -86.00 -149.85 63.85 1 1.00e+01 1.00e-02 5.37e+01 ... (remaining 11078 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 2748 0.123 - 0.246: 80 0.246 - 0.369: 10 0.369 - 0.492: 6 0.492 - 0.615: 4 Chirality restraints: 2848 Sorted by residual: chirality pdb=" CA LYS B 123 " pdb=" N LYS B 123 " pdb=" C LYS B 123 " pdb=" CB LYS B 123 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.62 2.00e-01 2.50e+01 9.46e+00 chirality pdb=" CA MET C 349 " pdb=" N MET C 349 " pdb=" C MET C 349 " pdb=" CB MET C 349 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.59 2.00e-01 2.50e+01 8.76e+00 chirality pdb=" CA LYS A 123 " pdb=" N LYS A 123 " pdb=" C LYS A 123 " pdb=" CB LYS A 123 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.58e+00 ... (remaining 2845 not shown) Planarity restraints: 3232 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 238 " -0.028 2.00e-02 2.50e+03 5.76e-02 3.32e+01 pdb=" C ASN A 238 " 0.100 2.00e-02 2.50e+03 pdb=" O ASN A 238 " -0.038 2.00e-02 2.50e+03 pdb=" N LYS A 239 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 121 " 0.022 2.00e-02 2.50e+03 4.52e-02 2.04e+01 pdb=" C CYS B 121 " -0.078 2.00e-02 2.50e+03 pdb=" O CYS B 121 " 0.029 2.00e-02 2.50e+03 pdb=" N SER B 122 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 359 " 0.024 2.00e-02 2.50e+03 4.37e-02 1.91e+01 pdb=" C ILE B 359 " -0.076 2.00e-02 2.50e+03 pdb=" O ILE B 359 " 0.026 2.00e-02 2.50e+03 pdb=" N THR B 360 " 0.026 2.00e-02 2.50e+03 ... (remaining 3229 not shown) Histogram of nonbonded interaction distances: 1.08 - 1.84: 25 1.84 - 2.61: 390 2.61 - 3.37: 23228 3.37 - 4.14: 44280 4.14 - 4.90: 79722 Nonbonded interactions: 147645 Sorted by model distance: nonbonded pdb=" NH2 ARG C 2 " pdb=" OE1 GLU C 44 " model vdw 1.081 3.120 nonbonded pdb=" CG2 ILE 2 29 " pdb=" NE2 GLN 2 90 " model vdw 1.189 3.540 nonbonded pdb=" CZ ARG C 2 " pdb=" OE1 GLU C 44 " model vdw 1.192 3.270 nonbonded pdb=" CG PRO C 224 " pdb=" CD1 LEU C 242 " model vdw 1.266 3.860 nonbonded pdb=" O GLY B 104 " pdb=" CE2 PHE 2 32 " model vdw 1.284 3.340 ... (remaining 147640 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '1' selection = chain 'H' selection = chain 'h' } ncs_group { reference = chain '2' selection = (chain 'L' and resid 1 through 108) selection = (chain 'l' and resid 1 through 108) } ncs_group { reference = chain 'A' selection = chain 'B' selection = (chain 'C' and (resid 1 through 150 or resid 160 through 501)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.690 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 41.610 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.120 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: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 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 : 0.008 0.121 18800 Z= 0.546 Angle : 0.961 15.253 25491 Z= 0.595 Chirality : 0.061 0.615 2848 Planarity : 0.006 0.088 3232 Dihedral : 12.574 85.278 6687 Min Nonbonded Distance : 1.081 Molprobity Statistics. All-atom Clashscore : 28.53 Ramachandran Plot: Outliers : 0.42 % Allowed : 8.77 % Favored : 90.81 % Rotamer: Outliers : 2.73 % Allowed : 8.04 % Favored : 89.23 % Cbeta Deviations : 0.42 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.16), residues: 2371 helix: -0.76 (0.23), residues: 421 sheet: -0.34 (0.18), residues: 767 loop : -2.50 (0.15), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 101 HIS 0.005 0.001 HIS C 288 PHE 0.015 0.002 PHE F 42 TYR 0.024 0.002 TYR E 25 ARG 0.006 0.001 ARG C 193 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 410 time to evaluate : 2.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 34 MET cc_start: 0.9321 (mmm) cc_final: 0.8978 (mmm) REVERT: H 57 SER cc_start: 0.7649 (t) cc_final: 0.7390 (p) REVERT: H 97 VAL cc_start: 0.9267 (OUTLIER) cc_final: 0.8749 (m) REVERT: B 466 ILE cc_start: 0.7980 (OUTLIER) cc_final: 0.7697 (tt) REVERT: C 349 MET cc_start: 0.6014 (mmm) cc_final: 0.4935 (ptp) REVERT: C 460 MET cc_start: 0.7468 (ptp) cc_final: 0.7185 (ptp) REVERT: 1 109 MET cc_start: 0.0576 (mtp) cc_final: -0.2075 (mtm) outliers start: 54 outliers final: 19 residues processed: 456 average time/residue: 0.2929 time to fit residues: 208.3083 Evaluate side-chains 332 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 311 time to evaluate : 2.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 193 ARG Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain 2 residue 94 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 198 optimal weight: 20.0000 chunk 178 optimal weight: 0.9990 chunk 98 optimal weight: 20.0000 chunk 60 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 95 optimal weight: 50.0000 chunk 184 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 112 optimal weight: 6.9990 chunk 137 optimal weight: 6.9990 chunk 213 optimal weight: 220.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN L 42 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 103 ASN A 148 HIS A 163 ASN A 344 GLN ** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 HIS A 478 ASN ** D 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 GLN D 17 GLN h 39 GLN l 42 GLN l 90 GLN B 85 GLN B 103 ASN B 148 HIS ** B 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 7 HIS C 103 ASN C 134 ASN C 163 ASN C 350 GLN C 362 ASN C 447 GLN C 478 ASN ** F 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 39 GLN 2 42 GLN ** 2 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 18800 Z= 0.288 Angle : 0.734 19.565 25491 Z= 0.380 Chirality : 0.046 0.265 2848 Planarity : 0.006 0.128 3232 Dihedral : 6.492 58.840 2616 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.69 % Favored : 91.27 % Rotamer: Outliers : 3.94 % Allowed : 13.70 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.17), residues: 2371 helix: -0.03 (0.24), residues: 436 sheet: -0.05 (0.18), residues: 825 loop : -2.15 (0.17), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP L 94 HIS 0.007 0.001 HIS B 288 PHE 0.021 0.002 PHE 2 32 TYR 0.014 0.001 TYR A 61 ARG 0.008 0.001 ARG B 73 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 336 time to evaluate : 2.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 34 MET cc_start: 0.9357 (mmm) cc_final: 0.9095 (mmm) REVERT: H 97 VAL cc_start: 0.9195 (OUTLIER) cc_final: 0.8769 (m) REVERT: H 116 THR cc_start: 0.9072 (OUTLIER) cc_final: 0.8743 (p) REVERT: D 25 TYR cc_start: 0.6955 (OUTLIER) cc_final: 0.5008 (p90) REVERT: 1 109 MET cc_start: 0.0333 (mtp) cc_final: -0.1998 (mtm) outliers start: 78 outliers final: 37 residues processed: 385 average time/residue: 0.2689 time to fit residues: 165.1854 Evaluate side-chains 339 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 299 time to evaluate : 2.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 288 HIS Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain h residue 75 SER Chi-restraints excluded: chain h residue 101 SER Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 90 GLN Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 85 GLN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain C residue 15 MET Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 288 HIS Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain F residue 34 ASN Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 55 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 118 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 chunk 177 optimal weight: 9.9990 chunk 145 optimal weight: 9.9990 chunk 58 optimal weight: 10.0000 chunk 213 optimal weight: 320.0000 chunk 230 optimal weight: 50.0000 chunk 190 optimal weight: 8.9990 chunk 212 optimal weight: 9.9990 chunk 72 optimal weight: 10.0000 chunk 171 optimal weight: 30.0000 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 ASN ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 HIS B 288 HIS ** B 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 HIS ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 HIS C 235 HIS C 478 ASN ** 2 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 18800 Z= 0.434 Angle : 0.753 17.951 25491 Z= 0.393 Chirality : 0.047 0.255 2848 Planarity : 0.006 0.115 3232 Dihedral : 6.015 56.841 2593 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.36 % Favored : 90.59 % Rotamer: Outliers : 5.61 % Allowed : 15.22 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.17), residues: 2371 helix: 0.25 (0.25), residues: 435 sheet: 0.17 (0.19), residues: 816 loop : -2.00 (0.17), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 400 HIS 0.007 0.001 HIS C 288 PHE 0.018 0.002 PHE A 431 TYR 0.017 0.001 TYR H 105 ARG 0.007 0.001 ARG E 31 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 307 time to evaluate : 2.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 95 TYR cc_start: 0.8988 (m-80) cc_final: 0.8713 (m-80) REVERT: H 107 TYR cc_start: 0.9521 (p90) cc_final: 0.9171 (p90) REVERT: H 116 THR cc_start: 0.9077 (OUTLIER) cc_final: 0.8743 (p) REVERT: C 197 ASP cc_start: 0.6518 (t0) cc_final: 0.6276 (t0) REVERT: C 379 ASP cc_start: 0.6387 (t0) cc_final: 0.6142 (t0) REVERT: 1 109 MET cc_start: 0.0575 (mtp) cc_final: -0.2055 (mtm) outliers start: 111 outliers final: 68 residues processed: 380 average time/residue: 0.2724 time to fit residues: 166.0069 Evaluate side-chains 358 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 289 time to evaluate : 2.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 288 HIS Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 454 LYS Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain h residue 6 GLU Chi-restraints excluded: chain h residue 21 SER Chi-restraints excluded: chain h residue 63 SER Chi-restraints excluded: chain h residue 75 SER Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 31 THR Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 67 SER Chi-restraints excluded: chain l residue 94 TRP Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 288 HIS Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain C residue 15 MET Chi-restraints excluded: chain C residue 27 HIS Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 288 HIS Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 460 MET Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 34 ASN Chi-restraints excluded: chain 1 residue 35 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 211 optimal weight: 10.0000 chunk 160 optimal weight: 9.9990 chunk 110 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 102 optimal weight: 9.9990 chunk 143 optimal weight: 2.9990 chunk 214 optimal weight: 7.9990 chunk 227 optimal weight: 50.0000 chunk 112 optimal weight: 8.9990 chunk 203 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 90 GLN B 85 GLN ** B 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 18800 Z= 0.325 Angle : 0.686 12.601 25491 Z= 0.359 Chirality : 0.045 0.259 2848 Planarity : 0.005 0.095 3232 Dihedral : 5.826 59.235 2591 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.70 % Favored : 90.26 % Rotamer: Outliers : 5.06 % Allowed : 16.94 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.17), residues: 2371 helix: 0.42 (0.26), residues: 433 sheet: 0.33 (0.19), residues: 807 loop : -1.86 (0.17), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 400 HIS 0.007 0.001 HIS C 288 PHE 0.015 0.001 PHE A 431 TYR 0.025 0.001 TYR H 105 ARG 0.005 0.000 ARG E 31 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 306 time to evaluate : 1.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 95 TYR cc_start: 0.8958 (m-80) cc_final: 0.8703 (m-80) REVERT: L 94 TRP cc_start: 0.7702 (OUTLIER) cc_final: 0.5756 (t60) REVERT: D 25 TYR cc_start: 0.6982 (OUTLIER) cc_final: 0.4993 (p90) REVERT: F 13 GLN cc_start: 0.7837 (tp-100) cc_final: 0.7620 (mm-40) REVERT: 1 109 MET cc_start: 0.0556 (mtp) cc_final: -0.2350 (mtm) outliers start: 100 outliers final: 62 residues processed: 377 average time/residue: 0.2832 time to fit residues: 172.1027 Evaluate side-chains 359 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 295 time to evaluate : 2.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 94 TRP Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 288 HIS Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain h residue 6 GLU Chi-restraints excluded: chain h residue 63 SER Chi-restraints excluded: chain h residue 75 SER Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 31 THR Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 63 SER Chi-restraints excluded: chain l residue 67 SER Chi-restraints excluded: chain l residue 90 GLN Chi-restraints excluded: chain l residue 94 TRP Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain C residue 27 HIS Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 288 HIS Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 460 MET Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain 1 residue 35 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 189 optimal weight: 30.0000 chunk 128 optimal weight: 20.0000 chunk 3 optimal weight: 40.0000 chunk 169 optimal weight: 8.9990 chunk 93 optimal weight: 40.0000 chunk 193 optimal weight: 20.0000 chunk 157 optimal weight: 20.0000 chunk 0 optimal weight: 60.0000 chunk 115 optimal weight: 20.0000 chunk 203 optimal weight: 8.9990 chunk 57 optimal weight: 6.9990 overall best weight: 12.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 35 HIS ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 90 GLN B 85 GLN B 163 ASN ** B 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 ASN ** 2 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.095 18800 Z= 0.608 Angle : 0.815 15.986 25491 Z= 0.427 Chirality : 0.049 0.289 2848 Planarity : 0.006 0.089 3232 Dihedral : 6.207 53.309 2591 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.84 % Favored : 89.12 % Rotamer: Outliers : 5.92 % Allowed : 17.34 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.17), residues: 2371 helix: 0.45 (0.26), residues: 422 sheet: 0.40 (0.19), residues: 811 loop : -1.90 (0.18), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP B 101 HIS 0.008 0.001 HIS C 288 PHE 0.022 0.002 PHE A 431 TYR 0.028 0.002 TYR H 105 ARG 0.008 0.001 ARG E 31 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 284 time to evaluate : 2.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 107 TYR cc_start: 0.9551 (p90) cc_final: 0.9246 (p90) REVERT: H 116 THR cc_start: 0.9044 (OUTLIER) cc_final: 0.8689 (p) REVERT: D 74 TYR cc_start: 0.4847 (OUTLIER) cc_final: 0.3157 (m-80) REVERT: h 32 TYR cc_start: 0.8489 (m-80) cc_final: 0.8260 (m-80) REVERT: l 91 ARG cc_start: 0.9076 (mmt90) cc_final: 0.8760 (mtt180) REVERT: B 140 MET cc_start: 0.7350 (mmm) cc_final: 0.7058 (mmm) REVERT: B 433 SER cc_start: 0.7917 (OUTLIER) cc_final: 0.7612 (p) REVERT: 1 109 MET cc_start: 0.0927 (mtp) cc_final: -0.2826 (mpp) outliers start: 117 outliers final: 83 residues processed: 365 average time/residue: 0.2913 time to fit residues: 167.7838 Evaluate side-chains 363 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 277 time to evaluate : 2.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 288 HIS Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain h residue 6 GLU Chi-restraints excluded: chain h residue 63 SER Chi-restraints excluded: chain h residue 75 SER Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 22 SER Chi-restraints excluded: chain l residue 26 SER Chi-restraints excluded: chain l residue 31 THR Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 63 SER Chi-restraints excluded: chain l residue 67 SER Chi-restraints excluded: chain l residue 90 GLN Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 85 GLN Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 288 HIS Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain C residue 15 MET Chi-restraints excluded: chain C residue 27 HIS Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 288 HIS Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 460 MET Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 34 ASN Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain 1 residue 35 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 76 optimal weight: 2.9990 chunk 204 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 133 optimal weight: 0.0970 chunk 56 optimal weight: 2.9990 chunk 227 optimal weight: 30.0000 chunk 188 optimal weight: 8.9990 chunk 105 optimal weight: 6.9990 chunk 18 optimal weight: 0.3980 chunk 75 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 90 GLN B 85 GLN ** B 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 18800 Z= 0.203 Angle : 0.653 12.774 25491 Z= 0.339 Chirality : 0.044 0.219 2848 Planarity : 0.005 0.092 3232 Dihedral : 5.680 59.098 2591 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.24 % Favored : 90.72 % Rotamer: Outliers : 3.69 % Allowed : 19.97 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.17), residues: 2371 helix: 0.59 (0.26), residues: 427 sheet: 0.45 (0.19), residues: 794 loop : -1.78 (0.17), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 101 HIS 0.006 0.001 HIS A 288 PHE 0.016 0.001 PHE F 42 TYR 0.016 0.001 TYR A 61 ARG 0.004 0.000 ARG F 31 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 315 time to evaluate : 2.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 116 THR cc_start: 0.9073 (OUTLIER) cc_final: 0.8649 (p) REVERT: L 94 TRP cc_start: 0.7565 (OUTLIER) cc_final: 0.5473 (t60) REVERT: D 25 TYR cc_start: 0.6696 (OUTLIER) cc_final: 0.4773 (p90) REVERT: D 74 TYR cc_start: 0.4759 (OUTLIER) cc_final: 0.3523 (m-80) REVERT: l 91 ARG cc_start: 0.9025 (mmt90) cc_final: 0.8772 (mtt180) REVERT: B 477 LEU cc_start: 0.7367 (OUTLIER) cc_final: 0.7043 (mp) REVERT: 1 109 MET cc_start: 0.0791 (mtp) cc_final: -0.1980 (mtt) outliers start: 73 outliers final: 56 residues processed: 362 average time/residue: 0.2791 time to fit residues: 160.2153 Evaluate side-chains 368 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 307 time to evaluate : 2.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 94 TRP Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 288 HIS Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain h residue 6 GLU Chi-restraints excluded: chain h residue 75 SER Chi-restraints excluded: chain l residue 31 THR Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 67 SER Chi-restraints excluded: chain l residue 90 GLN Chi-restraints excluded: chain l residue 94 TRP Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 288 HIS Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain C residue 15 MET Chi-restraints excluded: chain C residue 27 HIS Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 288 HIS Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 460 MET Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain 1 residue 35 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 219 optimal weight: 2.9990 chunk 25 optimal weight: 0.2980 chunk 129 optimal weight: 10.0000 chunk 166 optimal weight: 8.9990 chunk 128 optimal weight: 7.9990 chunk 191 optimal weight: 7.9990 chunk 126 optimal weight: 8.9990 chunk 226 optimal weight: 7.9990 chunk 141 optimal weight: 10.0000 chunk 138 optimal weight: 0.2980 chunk 104 optimal weight: 10.0000 overall best weight: 3.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 90 GLN B 85 GLN ** B 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 ASN F 17 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 18800 Z= 0.242 Angle : 0.651 10.786 25491 Z= 0.339 Chirality : 0.044 0.264 2848 Planarity : 0.005 0.093 3232 Dihedral : 5.493 57.132 2589 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.66 % Favored : 90.30 % Rotamer: Outliers : 4.55 % Allowed : 20.22 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.18), residues: 2371 helix: 0.75 (0.27), residues: 416 sheet: 0.54 (0.19), residues: 794 loop : -1.65 (0.18), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP B 101 HIS 0.006 0.001 HIS C 288 PHE 0.017 0.001 PHE A 314 TYR 0.019 0.001 TYR h 32 ARG 0.005 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 304 time to evaluate : 2.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 107 TYR cc_start: 0.9458 (p90) cc_final: 0.9240 (p90) REVERT: H 116 THR cc_start: 0.9070 (OUTLIER) cc_final: 0.8646 (p) REVERT: L 94 TRP cc_start: 0.7443 (OUTLIER) cc_final: 0.5210 (t60) REVERT: D 25 TYR cc_start: 0.6643 (OUTLIER) cc_final: 0.4918 (p90) REVERT: D 74 TYR cc_start: 0.4738 (OUTLIER) cc_final: 0.3194 (m-80) REVERT: B 477 LEU cc_start: 0.7290 (OUTLIER) cc_final: 0.6924 (mp) REVERT: 1 109 MET cc_start: 0.0710 (mtp) cc_final: -0.2894 (mpp) outliers start: 90 outliers final: 67 residues processed: 364 average time/residue: 0.2701 time to fit residues: 158.2793 Evaluate side-chains 371 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 299 time to evaluate : 1.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 94 TRP Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 288 HIS Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain h residue 6 GLU Chi-restraints excluded: chain h residue 64 VAL Chi-restraints excluded: chain h residue 75 SER Chi-restraints excluded: chain l residue 26 SER Chi-restraints excluded: chain l residue 31 THR Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 67 SER Chi-restraints excluded: chain l residue 90 GLN Chi-restraints excluded: chain l residue 94 TRP Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 288 HIS Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain C residue 15 MET Chi-restraints excluded: chain C residue 27 HIS Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 288 HIS Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 460 MET Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain 1 residue 35 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 140 optimal weight: 20.0000 chunk 90 optimal weight: 50.0000 chunk 135 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 44 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 chunk 144 optimal weight: 20.0000 chunk 154 optimal weight: 30.0000 chunk 111 optimal weight: 10.0000 chunk 21 optimal weight: 0.6980 chunk 178 optimal weight: 10.0000 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 35 HIS l 90 GLN B 85 GLN ** B 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 18800 Z= 0.262 Angle : 0.664 12.605 25491 Z= 0.344 Chirality : 0.044 0.209 2848 Planarity : 0.005 0.093 3232 Dihedral : 5.470 56.069 2589 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.78 % Favored : 90.17 % Rotamer: Outliers : 4.50 % Allowed : 20.58 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.18), residues: 2371 helix: 0.80 (0.27), residues: 413 sheet: 0.52 (0.19), residues: 812 loop : -1.64 (0.18), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP B 101 HIS 0.006 0.001 HIS C 288 PHE 0.014 0.001 PHE F 42 TYR 0.017 0.001 TYR H 107 ARG 0.005 0.000 ARG l 91 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 293 time to evaluate : 2.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 116 THR cc_start: 0.9079 (OUTLIER) cc_final: 0.8646 (p) REVERT: L 94 TRP cc_start: 0.7513 (OUTLIER) cc_final: 0.5183 (t60) REVERT: D 25 TYR cc_start: 0.6591 (OUTLIER) cc_final: 0.4868 (p90) REVERT: D 74 TYR cc_start: 0.4827 (OUTLIER) cc_final: 0.3278 (m-80) REVERT: B 140 MET cc_start: 0.7152 (mmm) cc_final: 0.6840 (mmm) REVERT: B 477 LEU cc_start: 0.7384 (OUTLIER) cc_final: 0.7016 (mp) REVERT: C 151 MET cc_start: 0.5387 (mmm) cc_final: 0.4989 (mmt) REVERT: 1 109 MET cc_start: 0.0780 (mtp) cc_final: -0.2925 (mpp) outliers start: 89 outliers final: 76 residues processed: 349 average time/residue: 0.2725 time to fit residues: 151.8786 Evaluate side-chains 369 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 288 time to evaluate : 2.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 94 TRP Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 288 HIS Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain h residue 6 GLU Chi-restraints excluded: chain h residue 64 VAL Chi-restraints excluded: chain h residue 75 SER Chi-restraints excluded: chain l residue 26 SER Chi-restraints excluded: chain l residue 31 THR Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 63 SER Chi-restraints excluded: chain l residue 67 SER Chi-restraints excluded: chain l residue 90 GLN Chi-restraints excluded: chain l residue 94 TRP Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 288 HIS Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain C residue 15 MET Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 288 HIS Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 460 MET Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain 1 residue 35 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 206 optimal weight: 8.9990 chunk 216 optimal weight: 20.0000 chunk 197 optimal weight: 20.0000 chunk 211 optimal weight: 20.0000 chunk 127 optimal weight: 20.0000 chunk 91 optimal weight: 50.0000 chunk 165 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 190 optimal weight: 4.9990 chunk 199 optimal weight: 3.9990 chunk 210 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 90 GLN B 85 GLN ** B 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 18800 Z= 0.316 Angle : 0.688 14.526 25491 Z= 0.355 Chirality : 0.045 0.193 2848 Planarity : 0.005 0.093 3232 Dihedral : 5.521 56.938 2589 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.87 % Favored : 90.09 % Rotamer: Outliers : 4.55 % Allowed : 21.23 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.18), residues: 2371 helix: 0.65 (0.26), residues: 422 sheet: 0.53 (0.19), residues: 811 loop : -1.63 (0.18), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 101 HIS 0.007 0.001 HIS C 288 PHE 0.014 0.001 PHE A 431 TYR 0.017 0.001 TYR H 107 ARG 0.013 0.000 ARG l 91 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 284 time to evaluate : 1.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 116 THR cc_start: 0.9073 (OUTLIER) cc_final: 0.8619 (p) REVERT: L 94 TRP cc_start: 0.7484 (OUTLIER) cc_final: 0.5212 (t60) REVERT: A 317 ILE cc_start: 0.7274 (OUTLIER) cc_final: 0.6843 (pt) REVERT: D 25 TYR cc_start: 0.6608 (OUTLIER) cc_final: 0.4708 (p90) REVERT: D 74 TYR cc_start: 0.4851 (OUTLIER) cc_final: 0.3244 (m-80) REVERT: B 140 MET cc_start: 0.7162 (mmm) cc_final: 0.6841 (mmm) REVERT: B 477 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.7052 (mp) REVERT: C 151 MET cc_start: 0.5419 (mmm) cc_final: 0.5119 (mmt) REVERT: 1 109 MET cc_start: 0.0800 (mtp) cc_final: -0.2972 (mpp) outliers start: 90 outliers final: 79 residues processed: 338 average time/residue: 0.2774 time to fit residues: 149.8656 Evaluate side-chains 364 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 279 time to evaluate : 2.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 94 TRP Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 288 HIS Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain h residue 6 GLU Chi-restraints excluded: chain h residue 64 VAL Chi-restraints excluded: chain h residue 75 SER Chi-restraints excluded: chain l residue 22 SER Chi-restraints excluded: chain l residue 26 SER Chi-restraints excluded: chain l residue 31 THR Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 63 SER Chi-restraints excluded: chain l residue 67 SER Chi-restraints excluded: chain l residue 90 GLN Chi-restraints excluded: chain l residue 94 TRP Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 288 HIS Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain C residue 15 MET Chi-restraints excluded: chain C residue 27 HIS Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 288 HIS Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 460 MET Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain 1 residue 35 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 138 optimal weight: 8.9990 chunk 223 optimal weight: 50.0000 chunk 136 optimal weight: 9.9990 chunk 105 optimal weight: 20.0000 chunk 155 optimal weight: 5.9990 chunk 234 optimal weight: 40.0000 chunk 215 optimal weight: 50.0000 chunk 186 optimal weight: 20.0000 chunk 19 optimal weight: 30.0000 chunk 144 optimal weight: 20.0000 chunk 114 optimal weight: 7.9990 overall best weight: 10.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 90 GLN B 85 GLN ** B 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.078 18800 Z= 0.505 Angle : 0.778 13.852 25491 Z= 0.404 Chirality : 0.048 0.203 2848 Planarity : 0.005 0.093 3232 Dihedral : 5.882 56.412 2589 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.59 % Favored : 89.37 % Rotamer: Outliers : 4.40 % Allowed : 21.39 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.18), residues: 2371 helix: 0.48 (0.26), residues: 424 sheet: 0.44 (0.19), residues: 806 loop : -1.62 (0.18), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP B 101 HIS 0.008 0.001 HIS C 288 PHE 0.018 0.002 PHE A 431 TYR 0.024 0.002 TYR F 25 ARG 0.016 0.001 ARG l 91 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 264 time to evaluate : 2.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 116 THR cc_start: 0.9051 (OUTLIER) cc_final: 0.8582 (p) REVERT: A 317 ILE cc_start: 0.7572 (OUTLIER) cc_final: 0.7145 (pt) REVERT: D 74 TYR cc_start: 0.4889 (OUTLIER) cc_final: 0.3123 (m-80) REVERT: B 140 MET cc_start: 0.7243 (mmm) cc_final: 0.6931 (mmm) REVERT: B 349 MET cc_start: 0.7445 (mmt) cc_final: 0.7056 (mmt) REVERT: C 151 MET cc_start: 0.5433 (mmm) cc_final: 0.5144 (mmt) REVERT: 1 109 MET cc_start: 0.0816 (mtp) cc_final: -0.3046 (mpp) outliers start: 87 outliers final: 75 residues processed: 321 average time/residue: 0.2793 time to fit residues: 143.3367 Evaluate side-chains 349 residues out of total 1978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 271 time to evaluate : 2.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 94 TRP Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 288 HIS Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain h residue 6 GLU Chi-restraints excluded: chain h residue 64 VAL Chi-restraints excluded: chain h residue 75 SER Chi-restraints excluded: chain l residue 22 SER Chi-restraints excluded: chain l residue 26 SER Chi-restraints excluded: chain l residue 31 THR Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 63 SER Chi-restraints excluded: chain l residue 67 SER Chi-restraints excluded: chain l residue 90 GLN Chi-restraints excluded: chain l residue 94 TRP Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 85 GLN Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 288 HIS Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain C residue 15 MET Chi-restraints excluded: chain C residue 27 HIS Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 288 HIS Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain 1 residue 35 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 148 optimal weight: 5.9990 chunk 198 optimal weight: 9.9990 chunk 57 optimal weight: 5.9990 chunk 171 optimal weight: 0.2980 chunk 27 optimal weight: 7.9990 chunk 51 optimal weight: 7.9990 chunk 186 optimal weight: 10.0000 chunk 78 optimal weight: 80.0000 chunk 191 optimal weight: 8.9990 chunk 23 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 overall best weight: 4.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 90 GLN B 85 GLN ** B 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 ASN ** 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 = 0.3852 r_free = 0.3852 target = 0.158243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.115605 restraints weight = 36344.561| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 3.07 r_work: 0.3006 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 18800 Z= 0.273 Angle : 0.683 12.021 25491 Z= 0.353 Chirality : 0.045 0.229 2848 Planarity : 0.005 0.094 3232 Dihedral : 5.656 59.568 2589 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.87 % Favored : 90.09 % Rotamer: Outliers : 3.99 % Allowed : 21.49 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.18), residues: 2371 helix: 0.57 (0.26), residues: 424 sheet: 0.42 (0.19), residues: 822 loop : -1.58 (0.18), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP B 101 HIS 0.007 0.001 HIS C 288 PHE 0.017 0.001 PHE E 42 TYR 0.020 0.001 TYR A 61 ARG 0.010 0.000 ARG l 91 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4239.29 seconds wall clock time: 79 minutes 8.24 seconds (4748.24 seconds total)