Starting phenix.real_space_refine on Tue Aug 6 12:32:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wzk_37955/08_2024/8wzk_37955.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wzk_37955/08_2024/8wzk_37955.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wzk_37955/08_2024/8wzk_37955.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wzk_37955/08_2024/8wzk_37955.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wzk_37955/08_2024/8wzk_37955.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wzk_37955/08_2024/8wzk_37955.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 4 7.16 5 P 12 5.49 5 S 52 5.16 5 C 10392 2.51 5 N 2884 2.21 5 O 3024 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 54": "OD1" <-> "OD2" Residue "B GLU 101": "OE1" <-> "OE2" Residue "B ASP 128": "OD1" <-> "OD2" Residue "B ASP 207": "OD1" <-> "OD2" Residue "B TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 290": "OE1" <-> "OE2" Residue "B TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 396": "OD1" <-> "OD2" Residue "B GLU 454": "OE1" <-> "OE2" Residue "B GLU 461": "OE1" <-> "OE2" Residue "A ASP 54": "OD1" <-> "OD2" Residue "A GLU 101": "OE1" <-> "OE2" Residue "A ASP 128": "OD1" <-> "OD2" Residue "A ASP 207": "OD1" <-> "OD2" Residue "A TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 290": "OE1" <-> "OE2" Residue "A TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 396": "OD1" <-> "OD2" Residue "A GLU 454": "OE1" <-> "OE2" Residue "A GLU 461": "OE1" <-> "OE2" Residue "C ASP 54": "OD1" <-> "OD2" Residue "C GLU 101": "OE1" <-> "OE2" Residue "C ASP 128": "OD1" <-> "OD2" Residue "C ASP 207": "OD1" <-> "OD2" Residue "C TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 290": "OE1" <-> "OE2" Residue "C TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 396": "OD1" <-> "OD2" Residue "C GLU 454": "OE1" <-> "OE2" Residue "C GLU 461": "OE1" <-> "OE2" Residue "D ASP 54": "OD1" <-> "OD2" Residue "D GLU 101": "OE1" <-> "OE2" Residue "D ASP 128": "OD1" <-> "OD2" Residue "D ASP 207": "OD1" <-> "OD2" Residue "D TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 290": "OE1" <-> "OE2" Residue "D TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 396": "OD1" <-> "OD2" Residue "D GLU 454": "OE1" <-> "OE2" Residue "D GLU 461": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 16368 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 4001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 4001 Classifications: {'peptide': 497} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 460} Chain: "A" Number of atoms: 4001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 4001 Classifications: {'peptide': 497} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 460} Chain: "C" Number of atoms: 4001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 4001 Classifications: {'peptide': 497} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 460} Chain: "D" Number of atoms: 4001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 4001 Classifications: {'peptide': 497} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 460} Chain: "B" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'HEM': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'HEM': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'HEM': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'HEM': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.19, per 1000 atoms: 0.50 Number of scatterers: 16368 At special positions: 0 Unit cell: (108.07, 114.49, 84.53, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 4 26.01 S 52 16.00 P 12 15.00 O 3024 8.00 N 2884 7.00 C 10392 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.04 Conformation dependent library (CDL) restraints added in 2.7 seconds 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3712 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 8 sheets defined 39.0% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.71 Creating SS restraints... Processing helix chain 'B' and resid 10 through 19 Processing helix chain 'B' and resid 54 through 65 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 157 through 159 No H-bonds generated for 'chain 'B' and resid 157 through 159' Processing helix chain 'B' and resid 160 through 169 Processing helix chain 'B' and resid 178 through 189 Processing helix chain 'B' and resid 192 through 201 Processing helix chain 'B' and resid 202 through 205 removed outlier: 3.625A pdb=" N ILE B 205 " --> pdb=" O ASP B 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 202 through 205' Processing helix chain 'B' and resid 246 through 257 removed outlier: 3.895A pdb=" N GLN B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 272 Processing helix chain 'B' and resid 285 through 291 Processing helix chain 'B' and resid 324 through 329 Processing helix chain 'B' and resid 348 through 366 removed outlier: 3.912A pdb=" N PHE B 356 " --> pdb=" O GLN B 352 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR B 358 " --> pdb=" O ARG B 354 " (cutoff:3.500A) Proline residue: B 359 - end of helix Processing helix chain 'B' and resid 369 through 373 Processing helix chain 'B' and resid 415 through 419 removed outlier: 3.642A pdb=" N LEU B 419 " --> pdb=" O PRO B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 450 Processing helix chain 'B' and resid 452 through 468 Processing helix chain 'B' and resid 471 through 486 Processing helix chain 'B' and resid 486 through 501 Processing helix chain 'A' and resid 10 through 19 Processing helix chain 'A' and resid 54 through 65 Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 157 through 159 No H-bonds generated for 'chain 'A' and resid 157 through 159' Processing helix chain 'A' and resid 160 through 169 Processing helix chain 'A' and resid 178 through 189 Processing helix chain 'A' and resid 192 through 201 Processing helix chain 'A' and resid 202 through 205 removed outlier: 3.625A pdb=" N ILE A 205 " --> pdb=" O ASP A 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 202 through 205' Processing helix chain 'A' and resid 246 through 257 removed outlier: 3.895A pdb=" N GLN A 255 " --> pdb=" O ALA A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 272 Processing helix chain 'A' and resid 285 through 291 Processing helix chain 'A' and resid 324 through 329 Processing helix chain 'A' and resid 348 through 366 removed outlier: 3.912A pdb=" N PHE A 356 " --> pdb=" O GLN A 352 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR A 358 " --> pdb=" O ARG A 354 " (cutoff:3.500A) Proline residue: A 359 - end of helix Processing helix chain 'A' and resid 369 through 373 Processing helix chain 'A' and resid 415 through 419 removed outlier: 3.642A pdb=" N LEU A 419 " --> pdb=" O PRO A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 450 Processing helix chain 'A' and resid 452 through 468 Processing helix chain 'A' and resid 471 through 486 Processing helix chain 'A' and resid 486 through 501 Processing helix chain 'C' and resid 10 through 19 Processing helix chain 'C' and resid 54 through 65 Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 157 through 159 No H-bonds generated for 'chain 'C' and resid 157 through 159' Processing helix chain 'C' and resid 160 through 169 Processing helix chain 'C' and resid 178 through 189 Processing helix chain 'C' and resid 192 through 201 Processing helix chain 'C' and resid 202 through 205 removed outlier: 3.625A pdb=" N ILE C 205 " --> pdb=" O ASP C 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 202 through 205' Processing helix chain 'C' and resid 246 through 257 removed outlier: 3.895A pdb=" N GLN C 255 " --> pdb=" O ALA C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 272 Processing helix chain 'C' and resid 285 through 291 Processing helix chain 'C' and resid 324 through 329 Processing helix chain 'C' and resid 348 through 366 removed outlier: 3.912A pdb=" N PHE C 356 " --> pdb=" O GLN C 352 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR C 358 " --> pdb=" O ARG C 354 " (cutoff:3.500A) Proline residue: C 359 - end of helix Processing helix chain 'C' and resid 369 through 373 Processing helix chain 'C' and resid 415 through 419 removed outlier: 3.641A pdb=" N LEU C 419 " --> pdb=" O PRO C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 450 Processing helix chain 'C' and resid 452 through 468 Processing helix chain 'C' and resid 471 through 486 Processing helix chain 'C' and resid 486 through 501 Processing helix chain 'D' and resid 10 through 19 Processing helix chain 'D' and resid 54 through 65 Processing helix chain 'D' and resid 97 through 101 Processing helix chain 'D' and resid 157 through 159 No H-bonds generated for 'chain 'D' and resid 157 through 159' Processing helix chain 'D' and resid 160 through 169 Processing helix chain 'D' and resid 178 through 189 Processing helix chain 'D' and resid 192 through 201 Processing helix chain 'D' and resid 202 through 205 removed outlier: 3.625A pdb=" N ILE D 205 " --> pdb=" O ASP D 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 202 through 205' Processing helix chain 'D' and resid 246 through 257 removed outlier: 3.895A pdb=" N GLN D 255 " --> pdb=" O ALA D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 272 Processing helix chain 'D' and resid 285 through 291 Processing helix chain 'D' and resid 324 through 329 Processing helix chain 'D' and resid 348 through 366 removed outlier: 3.912A pdb=" N PHE D 356 " --> pdb=" O GLN D 352 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR D 358 " --> pdb=" O ARG D 354 " (cutoff:3.500A) Proline residue: D 359 - end of helix Processing helix chain 'D' and resid 369 through 373 Processing helix chain 'D' and resid 415 through 419 removed outlier: 3.642A pdb=" N LEU D 419 " --> pdb=" O PRO D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 450 Processing helix chain 'D' and resid 452 through 468 Processing helix chain 'D' and resid 471 through 486 Processing helix chain 'D' and resid 486 through 501 Processing sheet with id=AA1, first strand: chain 'B' and resid 42 through 44 removed outlier: 3.979A pdb=" N ILE A 423 " --> pdb=" O VAL D 429 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 343 through 345 removed outlier: 5.955A pdb=" N ILE B 281 " --> pdb=" O PRO B 312 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N LEU B 316 " --> pdb=" O GLU B 86 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N GLU B 86 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N LEU B 318 " --> pdb=" O TYR B 84 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N TYR B 84 " --> pdb=" O LEU B 318 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 423 through 424 removed outlier: 3.979A pdb=" N ILE B 423 " --> pdb=" O VAL C 429 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 423 through 424 removed outlier: 3.979A pdb=" N ILE C 423 " --> pdb=" O VAL B 429 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 343 through 345 removed outlier: 5.954A pdb=" N ILE A 281 " --> pdb=" O PRO A 312 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N LEU A 316 " --> pdb=" O GLU A 86 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N GLU A 86 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N LEU A 318 " --> pdb=" O TYR A 84 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N TYR A 84 " --> pdb=" O LEU A 318 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 42 through 44 removed outlier: 3.977A pdb=" N ILE D 423 " --> pdb=" O VAL A 429 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 343 through 345 removed outlier: 5.955A pdb=" N ILE C 281 " --> pdb=" O PRO C 312 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N LEU C 316 " --> pdb=" O GLU C 86 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N GLU C 86 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N LEU C 318 " --> pdb=" O TYR C 84 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N TYR C 84 " --> pdb=" O LEU C 318 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 343 through 345 removed outlier: 5.954A pdb=" N ILE D 281 " --> pdb=" O PRO D 312 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N LEU D 316 " --> pdb=" O GLU D 86 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N GLU D 86 " --> pdb=" O LEU D 316 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N LEU D 318 " --> pdb=" O TYR D 84 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N TYR D 84 " --> pdb=" O LEU D 318 " (cutoff:3.500A) 660 hydrogen bonds defined for protein. 1884 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.77 Time building geometry restraints manager: 6.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.37: 5884 1.37 - 1.56: 10880 1.56 - 1.76: 20 1.76 - 1.95: 92 1.95 - 2.14: 12 Bond restraints: 16888 Sorted by residual: bond pdb=" O2B NDP D3002 " pdb=" P2B NDP D3002 " ideal model delta sigma weight residual 1.833 1.620 0.213 3.80e-02 6.93e+02 3.13e+01 bond pdb=" O2B NDP A3002 " pdb=" P2B NDP A3002 " ideal model delta sigma weight residual 1.833 1.620 0.213 3.80e-02 6.93e+02 3.13e+01 bond pdb=" O2B NDP C3002 " pdb=" P2B NDP C3002 " ideal model delta sigma weight residual 1.833 1.620 0.213 3.80e-02 6.93e+02 3.13e+01 bond pdb=" O2B NDP B3002 " pdb=" P2B NDP B3002 " ideal model delta sigma weight residual 1.833 1.621 0.212 3.80e-02 6.93e+02 3.11e+01 bond pdb=" C VAL D 111 " pdb=" O VAL D 111 " ideal model delta sigma weight residual 1.236 1.283 -0.047 1.02e-02 9.61e+03 2.10e+01 ... (remaining 16883 not shown) Histogram of bond angle deviations from ideal: 88.14 - 105.95: 699 105.95 - 123.76: 19700 123.76 - 141.57: 2633 141.57 - 159.38: 0 159.38 - 177.19: 8 Bond angle restraints: 23040 Sorted by residual: angle pdb=" PA NDP B3002 " pdb=" O3 NDP B3002 " pdb=" PN NDP B3002 " ideal model delta sigma weight residual 107.74 129.97 -22.23 1.95e+00 2.62e-01 1.29e+02 angle pdb=" PA NDP D3002 " pdb=" O3 NDP D3002 " pdb=" PN NDP D3002 " ideal model delta sigma weight residual 107.74 129.97 -22.23 1.95e+00 2.62e-01 1.29e+02 angle pdb=" PA NDP C3002 " pdb=" O3 NDP C3002 " pdb=" PN NDP C3002 " ideal model delta sigma weight residual 107.74 129.96 -22.22 1.95e+00 2.62e-01 1.29e+02 angle pdb=" PA NDP A3002 " pdb=" O3 NDP A3002 " pdb=" PN NDP A3002 " ideal model delta sigma weight residual 107.74 129.96 -22.22 1.95e+00 2.62e-01 1.29e+02 angle pdb=" C5B NDP B3002 " pdb=" O5B NDP B3002 " pdb=" PA NDP B3002 " ideal model delta sigma weight residual 103.84 121.48 -17.64 1.91e+00 2.73e-01 8.48e+01 ... (remaining 23035 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.79: 9102 19.79 - 39.59: 589 39.59 - 59.38: 113 59.38 - 79.17: 40 79.17 - 98.96: 16 Dihedral angle restraints: 9860 sinusoidal: 4080 harmonic: 5780 Sorted by residual: dihedral pdb=" CA ASP A 389 " pdb=" C ASP A 389 " pdb=" N GLY A 390 " pdb=" CA GLY A 390 " ideal model delta harmonic sigma weight residual 180.00 154.53 25.47 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA ASP C 389 " pdb=" C ASP C 389 " pdb=" N GLY C 390 " pdb=" CA GLY C 390 " ideal model delta harmonic sigma weight residual 180.00 154.57 25.43 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA ASP B 389 " pdb=" C ASP B 389 " pdb=" N GLY B 390 " pdb=" CA GLY B 390 " ideal model delta harmonic sigma weight residual 180.00 154.57 25.43 0 5.00e+00 4.00e-02 2.59e+01 ... (remaining 9857 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 971 0.048 - 0.096: 759 0.096 - 0.144: 443 0.144 - 0.192: 120 0.192 - 0.241: 35 Chirality restraints: 2328 Sorted by residual: chirality pdb=" CA ILE B 311 " pdb=" N ILE B 311 " pdb=" C ILE B 311 " pdb=" CB ILE B 311 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CA ILE D 311 " pdb=" N ILE D 311 " pdb=" C ILE D 311 " pdb=" CB ILE D 311 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA ILE A 311 " pdb=" N ILE A 311 " pdb=" C ILE A 311 " pdb=" CB ILE A 311 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 2325 not shown) Planarity restraints: 3052 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C HEM D3001 " 0.072 2.00e-02 2.50e+03 4.02e-02 3.63e+01 pdb=" C2C HEM D3001 " 0.049 2.00e-02 2.50e+03 pdb=" C3C HEM D3001 " 0.006 2.00e-02 2.50e+03 pdb=" C4C HEM D3001 " -0.014 2.00e-02 2.50e+03 pdb=" CAC HEM D3001 " -0.040 2.00e-02 2.50e+03 pdb=" CHC HEM D3001 " -0.071 2.00e-02 2.50e+03 pdb=" CHD HEM D3001 " 0.005 2.00e-02 2.50e+03 pdb=" CMC HEM D3001 " -0.004 2.00e-02 2.50e+03 pdb=" NC HEM D3001 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEM B3001 " 0.072 2.00e-02 2.50e+03 4.00e-02 3.59e+01 pdb=" C2C HEM B3001 " 0.049 2.00e-02 2.50e+03 pdb=" C3C HEM B3001 " 0.007 2.00e-02 2.50e+03 pdb=" C4C HEM B3001 " -0.014 2.00e-02 2.50e+03 pdb=" CAC HEM B3001 " -0.040 2.00e-02 2.50e+03 pdb=" CHC HEM B3001 " -0.070 2.00e-02 2.50e+03 pdb=" CHD HEM B3001 " 0.005 2.00e-02 2.50e+03 pdb=" CMC HEM B3001 " -0.004 2.00e-02 2.50e+03 pdb=" NC HEM B3001 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEM C3001 " -0.072 2.00e-02 2.50e+03 3.99e-02 3.58e+01 pdb=" C2C HEM C3001 " -0.049 2.00e-02 2.50e+03 pdb=" C3C HEM C3001 " -0.006 2.00e-02 2.50e+03 pdb=" C4C HEM C3001 " 0.014 2.00e-02 2.50e+03 pdb=" CAC HEM C3001 " 0.039 2.00e-02 2.50e+03 pdb=" CHC HEM C3001 " 0.070 2.00e-02 2.50e+03 pdb=" CHD HEM C3001 " -0.005 2.00e-02 2.50e+03 pdb=" CMC HEM C3001 " 0.004 2.00e-02 2.50e+03 pdb=" NC HEM C3001 " 0.005 2.00e-02 2.50e+03 ... (remaining 3049 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 5403 2.88 - 3.39: 15743 3.39 - 3.89: 30676 3.89 - 4.40: 35266 4.40 - 4.90: 57765 Nonbonded interactions: 144853 Sorted by model distance: nonbonded pdb=" O ARG D 388 " pdb=" O ASP D 389 " model vdw 2.379 3.040 nonbonded pdb=" O ARG A 388 " pdb=" O ASP A 389 " model vdw 2.379 3.040 nonbonded pdb=" O ARG B 388 " pdb=" O ASP B 389 " model vdw 2.380 3.040 nonbonded pdb=" O ARG C 388 " pdb=" O ASP C 389 " model vdw 2.380 3.040 nonbonded pdb=" OD1 ASP A 298 " pdb=" OG1 THR A 300 " model vdw 2.389 3.040 ... (remaining 144848 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.650 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 41.840 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 55.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6515 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 : 0.016 0.213 16888 Z= 1.035 Angle : 1.797 22.233 23040 Z= 1.232 Chirality : 0.082 0.241 2328 Planarity : 0.009 0.045 3052 Dihedral : 14.605 98.964 6148 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.84 % Favored : 95.96 % Rotamer: Outliers : 1.87 % Allowed : 4.67 % Favored : 93.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.17), residues: 1980 helix: -0.51 (0.17), residues: 684 sheet: -0.29 (0.31), residues: 276 loop : -1.06 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.012 TRP C 277 HIS 0.031 0.006 HIS B 218 PHE 0.046 0.009 PHE B 334 TYR 0.038 0.009 TYR A 236 ARG 0.034 0.003 ARG C 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 332 time to evaluate : 1.754 Fit side-chains REVERT: B 12 MET cc_start: 0.6025 (OUTLIER) cc_final: 0.5776 (mtm) REVERT: B 93 LYS cc_start: 0.6283 (ptmt) cc_final: 0.5971 (mtpt) REVERT: B 94 TYR cc_start: 0.6983 (m-80) cc_final: 0.6775 (m-80) REVERT: B 98 LYS cc_start: 0.6813 (mttt) cc_final: 0.6305 (mtpt) REVERT: B 139 GLU cc_start: 0.5948 (mm-30) cc_final: 0.5400 (mt-10) REVERT: B 140 ASP cc_start: 0.6392 (m-30) cc_final: 0.6190 (m-30) REVERT: B 228 GLU cc_start: 0.5895 (mp0) cc_final: 0.5649 (tt0) REVERT: B 232 CYS cc_start: 0.7278 (t) cc_final: 0.6705 (p) REVERT: B 256 GLU cc_start: 0.6407 (mm-30) cc_final: 0.6185 (mt-10) REVERT: B 273 LYS cc_start: 0.5473 (mtmm) cc_final: 0.5262 (mmtm) REVERT: B 306 LYS cc_start: 0.6350 (mppt) cc_final: 0.6143 (mppt) REVERT: B 389 ASP cc_start: 0.5162 (OUTLIER) cc_final: 0.4598 (m-30) REVERT: B 396 ASP cc_start: 0.5060 (p0) cc_final: 0.4731 (p0) REVERT: B 422 SER cc_start: 0.6995 (p) cc_final: 0.6763 (t) REVERT: B 423 ILE cc_start: 0.6283 (OUTLIER) cc_final: 0.5850 (mp) REVERT: B 428 GLU cc_start: 0.6026 (mp0) cc_final: 0.5818 (mt-10) REVERT: B 453 GLU cc_start: 0.5781 (tp30) cc_final: 0.5378 (tp30) REVERT: B 466 HIS cc_start: 0.7133 (t-90) cc_final: 0.6832 (t-90) REVERT: B 484 GLU cc_start: 0.6868 (tt0) cc_final: 0.6454 (tt0) REVERT: A 12 MET cc_start: 0.6021 (OUTLIER) cc_final: 0.5767 (mtm) REVERT: A 93 LYS cc_start: 0.6289 (ptmt) cc_final: 0.5978 (mtpt) REVERT: A 94 TYR cc_start: 0.6984 (m-80) cc_final: 0.6781 (m-80) REVERT: A 98 LYS cc_start: 0.6816 (mttt) cc_final: 0.6313 (mtpt) REVERT: A 139 GLU cc_start: 0.5948 (mm-30) cc_final: 0.5400 (mt-10) REVERT: A 140 ASP cc_start: 0.6395 (m-30) cc_final: 0.6192 (m-30) REVERT: A 228 GLU cc_start: 0.5927 (mp0) cc_final: 0.5683 (tt0) REVERT: A 232 CYS cc_start: 0.7280 (t) cc_final: 0.6703 (p) REVERT: A 256 GLU cc_start: 0.6416 (mm-30) cc_final: 0.6197 (mt-10) REVERT: A 273 LYS cc_start: 0.5475 (mtmm) cc_final: 0.5264 (mmtm) REVERT: A 306 LYS cc_start: 0.6350 (mppt) cc_final: 0.6143 (mppt) REVERT: A 389 ASP cc_start: 0.5158 (OUTLIER) cc_final: 0.4596 (m-30) REVERT: A 396 ASP cc_start: 0.5055 (p0) cc_final: 0.4727 (p0) REVERT: A 422 SER cc_start: 0.6994 (p) cc_final: 0.6755 (t) REVERT: A 423 ILE cc_start: 0.6162 (OUTLIER) cc_final: 0.5732 (mp) REVERT: A 428 GLU cc_start: 0.6028 (mp0) cc_final: 0.5818 (mt-10) REVERT: A 453 GLU cc_start: 0.5777 (tp30) cc_final: 0.5374 (tp30) REVERT: A 466 HIS cc_start: 0.7134 (t-90) cc_final: 0.6832 (t-90) REVERT: A 484 GLU cc_start: 0.6884 (tt0) cc_final: 0.6468 (tt0) REVERT: C 12 MET cc_start: 0.6020 (OUTLIER) cc_final: 0.5763 (mtm) REVERT: C 93 LYS cc_start: 0.6282 (ptmt) cc_final: 0.5971 (mtpt) REVERT: C 94 TYR cc_start: 0.6981 (m-80) cc_final: 0.6776 (m-80) REVERT: C 98 LYS cc_start: 0.6818 (mttt) cc_final: 0.6477 (mttm) REVERT: C 139 GLU cc_start: 0.5950 (mm-30) cc_final: 0.5420 (mt-10) REVERT: C 228 GLU cc_start: 0.5926 (mp0) cc_final: 0.5684 (tt0) REVERT: C 232 CYS cc_start: 0.7279 (t) cc_final: 0.6703 (p) REVERT: C 256 GLU cc_start: 0.6408 (mm-30) cc_final: 0.6187 (mt-10) REVERT: C 273 LYS cc_start: 0.5474 (mtmm) cc_final: 0.5262 (mmtm) REVERT: C 306 LYS cc_start: 0.6351 (mppt) cc_final: 0.6142 (mppt) REVERT: C 389 ASP cc_start: 0.5161 (OUTLIER) cc_final: 0.4598 (m-30) REVERT: C 396 ASP cc_start: 0.5057 (p0) cc_final: 0.4729 (p0) REVERT: C 422 SER cc_start: 0.6998 (p) cc_final: 0.6762 (t) REVERT: C 423 ILE cc_start: 0.6164 (OUTLIER) cc_final: 0.5733 (mp) REVERT: C 428 GLU cc_start: 0.6025 (mp0) cc_final: 0.5801 (mt-10) REVERT: C 453 GLU cc_start: 0.5778 (tp30) cc_final: 0.5376 (tp30) REVERT: C 466 HIS cc_start: 0.7133 (t-90) cc_final: 0.6834 (t-90) REVERT: C 484 GLU cc_start: 0.6867 (tt0) cc_final: 0.6454 (tt0) REVERT: D 12 MET cc_start: 0.6021 (OUTLIER) cc_final: 0.5771 (mtm) REVERT: D 93 LYS cc_start: 0.6280 (ptmt) cc_final: 0.5970 (mtpt) REVERT: D 94 TYR cc_start: 0.6980 (m-80) cc_final: 0.6774 (m-80) REVERT: D 98 LYS cc_start: 0.6816 (mttt) cc_final: 0.6475 (mttm) REVERT: D 139 GLU cc_start: 0.5952 (mm-30) cc_final: 0.5423 (mt-10) REVERT: D 228 GLU cc_start: 0.5928 (mp0) cc_final: 0.5685 (tt0) REVERT: D 232 CYS cc_start: 0.7279 (t) cc_final: 0.6704 (p) REVERT: D 256 GLU cc_start: 0.6406 (mm-30) cc_final: 0.6193 (mt-10) REVERT: D 273 LYS cc_start: 0.5475 (mtmm) cc_final: 0.5263 (mmtm) REVERT: D 306 LYS cc_start: 0.6351 (mppt) cc_final: 0.6143 (mppt) REVERT: D 389 ASP cc_start: 0.5163 (OUTLIER) cc_final: 0.4599 (m-30) REVERT: D 396 ASP cc_start: 0.5058 (p0) cc_final: 0.4701 (p0) REVERT: D 422 SER cc_start: 0.6998 (p) cc_final: 0.6761 (t) REVERT: D 423 ILE cc_start: 0.6166 (OUTLIER) cc_final: 0.5734 (mp) REVERT: D 428 GLU cc_start: 0.6027 (mp0) cc_final: 0.5816 (mt-10) REVERT: D 453 GLU cc_start: 0.5778 (tp30) cc_final: 0.5376 (tp30) REVERT: D 466 HIS cc_start: 0.7134 (t-90) cc_final: 0.6833 (t-90) REVERT: D 484 GLU cc_start: 0.6867 (tt0) cc_final: 0.6454 (tt0) outliers start: 32 outliers final: 8 residues processed: 348 average time/residue: 1.2472 time to fit residues: 481.1155 Evaluate side-chains 264 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 244 time to evaluate : 1.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 MET Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 368 PRO Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 368 PRO Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain C residue 12 MET Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 368 PRO Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain D residue 12 MET Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 368 PRO Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 423 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 0.9990 chunk 148 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 100 optimal weight: 0.4980 chunk 79 optimal weight: 5.9990 chunk 153 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 114 optimal weight: 0.9990 chunk 177 optimal weight: 8.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 ASN ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 ASN ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 ASN ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 407 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6476 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16888 Z= 0.176 Angle : 0.584 6.424 23040 Z= 0.295 Chirality : 0.044 0.145 2328 Planarity : 0.004 0.040 3052 Dihedral : 8.863 107.183 2300 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.17 % Allowed : 9.11 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.19), residues: 1980 helix: 1.29 (0.20), residues: 688 sheet: 0.66 (0.31), residues: 300 loop : -0.43 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 15 HIS 0.003 0.001 HIS C 466 PHE 0.012 0.002 PHE D 57 TYR 0.019 0.001 TYR D 236 ARG 0.003 0.000 ARG C 363 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 275 time to evaluate : 1.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 12 MET cc_start: 0.5940 (mtm) cc_final: 0.5455 (mtm) REVERT: B 93 LYS cc_start: 0.6147 (ptmt) cc_final: 0.5916 (mtmt) REVERT: B 94 TYR cc_start: 0.6942 (m-80) cc_final: 0.6704 (m-80) REVERT: B 98 LYS cc_start: 0.6851 (mttt) cc_final: 0.6594 (mttm) REVERT: B 139 GLU cc_start: 0.6072 (mm-30) cc_final: 0.5694 (mm-30) REVERT: B 180 ASP cc_start: 0.7074 (OUTLIER) cc_final: 0.6786 (m-30) REVERT: B 228 GLU cc_start: 0.6060 (mp0) cc_final: 0.5728 (tt0) REVERT: B 232 CYS cc_start: 0.7284 (t) cc_final: 0.6701 (p) REVERT: B 256 GLU cc_start: 0.6290 (mm-30) cc_final: 0.6054 (mt-10) REVERT: B 259 ASP cc_start: 0.7515 (m-30) cc_final: 0.7314 (m-30) REVERT: B 389 ASP cc_start: 0.4982 (OUTLIER) cc_final: 0.4209 (m-30) REVERT: B 396 ASP cc_start: 0.5225 (p0) cc_final: 0.4619 (p0) REVERT: B 422 SER cc_start: 0.6866 (p) cc_final: 0.6580 (t) REVERT: B 423 ILE cc_start: 0.5995 (mm) cc_final: 0.5506 (mp) REVERT: B 428 GLU cc_start: 0.6078 (mp0) cc_final: 0.5764 (mt-10) REVERT: B 453 GLU cc_start: 0.5897 (tp30) cc_final: 0.5625 (tp30) REVERT: A 12 MET cc_start: 0.5936 (mtm) cc_final: 0.5451 (mtm) REVERT: A 93 LYS cc_start: 0.6144 (ptmt) cc_final: 0.5917 (mtmt) REVERT: A 94 TYR cc_start: 0.6943 (m-80) cc_final: 0.6711 (m-80) REVERT: A 98 LYS cc_start: 0.6851 (mttt) cc_final: 0.6596 (mttm) REVERT: A 139 GLU cc_start: 0.6074 (mm-30) cc_final: 0.5695 (mm-30) REVERT: A 180 ASP cc_start: 0.7072 (OUTLIER) cc_final: 0.6789 (m-30) REVERT: A 228 GLU cc_start: 0.6059 (mp0) cc_final: 0.5726 (tt0) REVERT: A 232 CYS cc_start: 0.7286 (t) cc_final: 0.6702 (p) REVERT: A 256 GLU cc_start: 0.6286 (mm-30) cc_final: 0.6046 (mt-10) REVERT: A 389 ASP cc_start: 0.4979 (OUTLIER) cc_final: 0.4207 (m-30) REVERT: A 396 ASP cc_start: 0.5226 (p0) cc_final: 0.4619 (p0) REVERT: A 422 SER cc_start: 0.6857 (p) cc_final: 0.6578 (t) REVERT: A 423 ILE cc_start: 0.5995 (mm) cc_final: 0.5506 (mp) REVERT: A 428 GLU cc_start: 0.6079 (mp0) cc_final: 0.5767 (mt-10) REVERT: A 453 GLU cc_start: 0.5898 (tp30) cc_final: 0.5626 (tp30) REVERT: C 12 MET cc_start: 0.5927 (mtm) cc_final: 0.5439 (mtm) REVERT: C 93 LYS cc_start: 0.6147 (ptmt) cc_final: 0.5918 (mtmt) REVERT: C 94 TYR cc_start: 0.6941 (m-80) cc_final: 0.6706 (m-80) REVERT: C 98 LYS cc_start: 0.6831 (mttt) cc_final: 0.6334 (mtpp) REVERT: C 139 GLU cc_start: 0.6301 (mm-30) cc_final: 0.5904 (mm-30) REVERT: C 180 ASP cc_start: 0.7074 (OUTLIER) cc_final: 0.6789 (m-30) REVERT: C 228 GLU cc_start: 0.6057 (mp0) cc_final: 0.5727 (tt0) REVERT: C 232 CYS cc_start: 0.7285 (t) cc_final: 0.6700 (p) REVERT: C 256 GLU cc_start: 0.6293 (mm-30) cc_final: 0.6056 (mt-10) REVERT: C 259 ASP cc_start: 0.7514 (m-30) cc_final: 0.7313 (m-30) REVERT: C 389 ASP cc_start: 0.4981 (OUTLIER) cc_final: 0.4207 (m-30) REVERT: C 396 ASP cc_start: 0.5224 (p0) cc_final: 0.4619 (p0) REVERT: C 422 SER cc_start: 0.6862 (p) cc_final: 0.6585 (t) REVERT: C 423 ILE cc_start: 0.5997 (mm) cc_final: 0.5482 (mp) REVERT: C 428 GLU cc_start: 0.6063 (mp0) cc_final: 0.5751 (mt-10) REVERT: C 453 GLU cc_start: 0.5851 (tp30) cc_final: 0.5593 (tp30) REVERT: D 12 MET cc_start: 0.5936 (mtm) cc_final: 0.5458 (mtm) REVERT: D 93 LYS cc_start: 0.6143 (ptmt) cc_final: 0.5915 (mtmt) REVERT: D 94 TYR cc_start: 0.6941 (m-80) cc_final: 0.6705 (m-80) REVERT: D 98 LYS cc_start: 0.6816 (mttt) cc_final: 0.6312 (mtpt) REVERT: D 139 GLU cc_start: 0.6304 (mm-30) cc_final: 0.5926 (mm-30) REVERT: D 180 ASP cc_start: 0.7071 (OUTLIER) cc_final: 0.6785 (m-30) REVERT: D 228 GLU cc_start: 0.6059 (mp0) cc_final: 0.5727 (tt0) REVERT: D 232 CYS cc_start: 0.7287 (t) cc_final: 0.6700 (p) REVERT: D 256 GLU cc_start: 0.6288 (mm-30) cc_final: 0.6052 (mt-10) REVERT: D 259 ASP cc_start: 0.7514 (m-30) cc_final: 0.7314 (m-30) REVERT: D 389 ASP cc_start: 0.4979 (OUTLIER) cc_final: 0.4208 (m-30) REVERT: D 396 ASP cc_start: 0.5224 (p0) cc_final: 0.4617 (p0) REVERT: D 422 SER cc_start: 0.6861 (p) cc_final: 0.6589 (t) REVERT: D 423 ILE cc_start: 0.6001 (mm) cc_final: 0.5486 (mp) REVERT: D 428 GLU cc_start: 0.6080 (mp0) cc_final: 0.5771 (mt-10) REVERT: D 453 GLU cc_start: 0.5851 (tp30) cc_final: 0.5593 (tp30) outliers start: 20 outliers final: 8 residues processed: 283 average time/residue: 1.2139 time to fit residues: 382.3639 Evaluate side-chains 256 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 240 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 389 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 7.9990 chunk 55 optimal weight: 7.9990 chunk 148 optimal weight: 10.0000 chunk 121 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 chunk 178 optimal weight: 7.9990 chunk 192 optimal weight: 1.9990 chunk 158 optimal weight: 0.0370 chunk 176 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 chunk 143 optimal weight: 1.9990 overall best weight: 3.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 369 ASN B 421 HIS ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 369 ASN A 421 HIS ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 369 ASN C 421 HIS ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 369 ASN D 421 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6514 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 16888 Z= 0.353 Angle : 0.768 15.072 23040 Z= 0.373 Chirality : 0.049 0.137 2328 Planarity : 0.006 0.051 3052 Dihedral : 9.943 130.464 2268 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.59 % Favored : 96.21 % Rotamer: Outliers : 1.93 % Allowed : 9.87 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.19), residues: 1980 helix: 0.83 (0.20), residues: 708 sheet: 0.85 (0.31), residues: 300 loop : -0.61 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 15 HIS 0.006 0.002 HIS C 218 PHE 0.022 0.003 PHE A 136 TYR 0.025 0.002 TYR C 236 ARG 0.007 0.001 ARG C 363 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 242 time to evaluate : 1.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 12 MET cc_start: 0.5874 (mtm) cc_final: 0.5409 (mtm) REVERT: B 139 GLU cc_start: 0.6175 (mm-30) cc_final: 0.5621 (pt0) REVERT: B 180 ASP cc_start: 0.7125 (m-30) cc_final: 0.6842 (m-30) REVERT: B 228 GLU cc_start: 0.6061 (mp0) cc_final: 0.5673 (tt0) REVERT: B 256 GLU cc_start: 0.6431 (mm-30) cc_final: 0.6131 (mt-10) REVERT: B 422 SER cc_start: 0.6785 (p) cc_final: 0.6466 (t) REVERT: B 423 ILE cc_start: 0.6065 (mm) cc_final: 0.5538 (mp) REVERT: B 428 GLU cc_start: 0.6216 (mp0) cc_final: 0.5784 (mt-10) REVERT: A 12 MET cc_start: 0.5876 (mtm) cc_final: 0.5417 (mtm) REVERT: A 139 GLU cc_start: 0.6175 (mm-30) cc_final: 0.5622 (pt0) REVERT: A 180 ASP cc_start: 0.7124 (m-30) cc_final: 0.6844 (m-30) REVERT: A 228 GLU cc_start: 0.6092 (mp0) cc_final: 0.5732 (tt0) REVERT: A 256 GLU cc_start: 0.6302 (mm-30) cc_final: 0.6002 (mt-10) REVERT: A 422 SER cc_start: 0.6785 (p) cc_final: 0.6466 (t) REVERT: A 423 ILE cc_start: 0.6059 (mm) cc_final: 0.5536 (mp) REVERT: A 428 GLU cc_start: 0.6219 (mp0) cc_final: 0.5788 (mt-10) REVERT: C 12 MET cc_start: 0.5899 (mtm) cc_final: 0.5448 (mtm) REVERT: C 139 GLU cc_start: 0.6187 (mm-30) cc_final: 0.5663 (pt0) REVERT: C 180 ASP cc_start: 0.7126 (m-30) cc_final: 0.6841 (m-30) REVERT: C 228 GLU cc_start: 0.6100 (mp0) cc_final: 0.5717 (tt0) REVERT: C 256 GLU cc_start: 0.6430 (mm-30) cc_final: 0.6130 (mt-10) REVERT: C 422 SER cc_start: 0.6781 (p) cc_final: 0.6459 (t) REVERT: C 423 ILE cc_start: 0.6064 (mm) cc_final: 0.5530 (mp) REVERT: C 428 GLU cc_start: 0.6212 (mp0) cc_final: 0.5778 (mt-10) REVERT: D 12 MET cc_start: 0.5893 (mtm) cc_final: 0.5443 (mtm) REVERT: D 139 GLU cc_start: 0.6190 (mm-30) cc_final: 0.5665 (pt0) REVERT: D 180 ASP cc_start: 0.7124 (m-30) cc_final: 0.6839 (m-30) REVERT: D 228 GLU cc_start: 0.6063 (mp0) cc_final: 0.5673 (tt0) REVERT: D 256 GLU cc_start: 0.6429 (mm-30) cc_final: 0.6130 (mt-10) REVERT: D 422 SER cc_start: 0.6785 (p) cc_final: 0.6467 (t) REVERT: D 423 ILE cc_start: 0.6065 (mm) cc_final: 0.5540 (mp) REVERT: D 428 GLU cc_start: 0.6218 (mp0) cc_final: 0.5788 (mt-10) outliers start: 33 outliers final: 20 residues processed: 271 average time/residue: 1.1789 time to fit residues: 357.8836 Evaluate side-chains 226 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 206 time to evaluate : 1.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 389 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 178 optimal weight: 0.7980 chunk 189 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 chunk 169 optimal weight: 9.9990 chunk 51 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 GLN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 53 GLN ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 GLN ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 GLN ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6496 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16888 Z= 0.227 Angle : 0.646 10.644 23040 Z= 0.316 Chirality : 0.045 0.142 2328 Planarity : 0.005 0.046 3052 Dihedral : 9.422 128.511 2268 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.75 % Allowed : 10.28 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.19), residues: 1980 helix: 1.25 (0.21), residues: 688 sheet: 0.74 (0.32), residues: 292 loop : -0.35 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 183 HIS 0.006 0.001 HIS C 218 PHE 0.016 0.002 PHE A 136 TYR 0.021 0.002 TYR D 236 ARG 0.004 0.000 ARG D 363 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 207 time to evaluate : 2.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 12 MET cc_start: 0.5758 (mtm) cc_final: 0.5329 (mtm) REVERT: B 139 GLU cc_start: 0.6095 (mm-30) cc_final: 0.5456 (pt0) REVERT: B 180 ASP cc_start: 0.7196 (m-30) cc_final: 0.6918 (m-30) REVERT: B 228 GLU cc_start: 0.6035 (mp0) cc_final: 0.5606 (tt0) REVERT: B 232 CYS cc_start: 0.7335 (OUTLIER) cc_final: 0.7012 (p) REVERT: B 237 LYS cc_start: 0.6828 (OUTLIER) cc_final: 0.6511 (mtpm) REVERT: B 256 GLU cc_start: 0.6334 (mm-30) cc_final: 0.6082 (mt-10) REVERT: B 422 SER cc_start: 0.6929 (p) cc_final: 0.6587 (t) REVERT: B 423 ILE cc_start: 0.6174 (mm) cc_final: 0.5780 (mp) REVERT: B 428 GLU cc_start: 0.6415 (mp0) cc_final: 0.6164 (pt0) REVERT: A 12 MET cc_start: 0.5757 (mtm) cc_final: 0.5330 (mtm) REVERT: A 139 GLU cc_start: 0.6098 (mm-30) cc_final: 0.5458 (pt0) REVERT: A 180 ASP cc_start: 0.7179 (m-30) cc_final: 0.6901 (m-30) REVERT: A 228 GLU cc_start: 0.6038 (mp0) cc_final: 0.5621 (tt0) REVERT: A 232 CYS cc_start: 0.7332 (OUTLIER) cc_final: 0.7010 (p) REVERT: A 237 LYS cc_start: 0.6825 (OUTLIER) cc_final: 0.6509 (mtpm) REVERT: A 256 GLU cc_start: 0.6388 (mm-30) cc_final: 0.6135 (mt-10) REVERT: A 422 SER cc_start: 0.6928 (p) cc_final: 0.6580 (t) REVERT: A 423 ILE cc_start: 0.6176 (mm) cc_final: 0.5781 (mp) REVERT: A 428 GLU cc_start: 0.6419 (mp0) cc_final: 0.6176 (pt0) REVERT: C 12 MET cc_start: 0.5757 (mtm) cc_final: 0.5329 (mtm) REVERT: C 139 GLU cc_start: 0.6095 (mm-30) cc_final: 0.5478 (pt0) REVERT: C 180 ASP cc_start: 0.7182 (m-30) cc_final: 0.6904 (m-30) REVERT: C 228 GLU cc_start: 0.6037 (mp0) cc_final: 0.5621 (tt0) REVERT: C 232 CYS cc_start: 0.7335 (OUTLIER) cc_final: 0.7012 (p) REVERT: C 237 LYS cc_start: 0.6827 (OUTLIER) cc_final: 0.6509 (mtpm) REVERT: C 256 GLU cc_start: 0.6334 (mm-30) cc_final: 0.6081 (mt-10) REVERT: C 422 SER cc_start: 0.6924 (p) cc_final: 0.6583 (t) REVERT: C 423 ILE cc_start: 0.6176 (mm) cc_final: 0.5779 (mp) REVERT: C 428 GLU cc_start: 0.6408 (mp0) cc_final: 0.6132 (pt0) REVERT: D 12 MET cc_start: 0.5758 (mtm) cc_final: 0.5329 (mtm) REVERT: D 139 GLU cc_start: 0.6099 (mm-30) cc_final: 0.5481 (pt0) REVERT: D 180 ASP cc_start: 0.7178 (m-30) cc_final: 0.6902 (m-30) REVERT: D 228 GLU cc_start: 0.6039 (mp0) cc_final: 0.5621 (tt0) REVERT: D 232 CYS cc_start: 0.7333 (OUTLIER) cc_final: 0.7010 (p) REVERT: D 237 LYS cc_start: 0.6829 (OUTLIER) cc_final: 0.6512 (mtpm) REVERT: D 256 GLU cc_start: 0.6332 (mm-30) cc_final: 0.6081 (mt-10) REVERT: D 422 SER cc_start: 0.6928 (p) cc_final: 0.6582 (t) REVERT: D 423 ILE cc_start: 0.6179 (mm) cc_final: 0.5783 (mp) REVERT: D 428 GLU cc_start: 0.6422 (mp0) cc_final: 0.6182 (pt0) outliers start: 47 outliers final: 28 residues processed: 246 average time/residue: 1.2661 time to fit residues: 347.5154 Evaluate side-chains 233 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 197 time to evaluate : 1.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 232 CYS Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 237 LYS Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 237 LYS Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 93 LYS Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 232 CYS Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 237 LYS Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 93 LYS Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 232 CYS Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 237 LYS Chi-restraints excluded: chain D residue 254 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 141 optimal weight: 10.0000 chunk 78 optimal weight: 2.9990 chunk 161 optimal weight: 7.9990 chunk 130 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 96 optimal weight: 7.9990 chunk 170 optimal weight: 0.8980 chunk 47 optimal weight: 7.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 HIS ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 HIS C 22 GLN C 33 ASN C 173 GLN C 466 HIS D 33 ASN ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 466 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6503 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 16888 Z= 0.284 Angle : 0.702 13.587 23040 Z= 0.339 Chirality : 0.047 0.136 2328 Planarity : 0.005 0.048 3052 Dihedral : 9.685 133.752 2260 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.04 % Allowed : 10.11 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.19), residues: 1980 helix: 1.11 (0.21), residues: 688 sheet: 0.83 (0.31), residues: 300 loop : -0.51 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 183 HIS 0.006 0.001 HIS D 218 PHE 0.019 0.002 PHE B 136 TYR 0.023 0.002 TYR B 236 ARG 0.005 0.001 ARG D 363 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 198 time to evaluate : 1.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 12 MET cc_start: 0.6022 (mtm) cc_final: 0.5658 (mtm) REVERT: B 139 GLU cc_start: 0.5878 (mm-30) cc_final: 0.5398 (pt0) REVERT: B 180 ASP cc_start: 0.7112 (m-30) cc_final: 0.6829 (m-30) REVERT: B 228 GLU cc_start: 0.6063 (mp0) cc_final: 0.5644 (tt0) REVERT: B 237 LYS cc_start: 0.6870 (OUTLIER) cc_final: 0.6556 (mtpm) REVERT: B 256 GLU cc_start: 0.6551 (mm-30) cc_final: 0.6250 (mt-10) REVERT: B 389 ASP cc_start: 0.4663 (OUTLIER) cc_final: 0.4188 (m-30) REVERT: B 422 SER cc_start: 0.6909 (p) cc_final: 0.6573 (t) REVERT: B 423 ILE cc_start: 0.6060 (mm) cc_final: 0.5714 (mp) REVERT: B 428 GLU cc_start: 0.6316 (mp0) cc_final: 0.6076 (pt0) REVERT: A 12 MET cc_start: 0.6022 (mtm) cc_final: 0.5660 (mtm) REVERT: A 139 GLU cc_start: 0.5880 (mm-30) cc_final: 0.5400 (pt0) REVERT: A 180 ASP cc_start: 0.7110 (m-30) cc_final: 0.6828 (m-30) REVERT: A 228 GLU cc_start: 0.6065 (mp0) cc_final: 0.5659 (tt0) REVERT: A 237 LYS cc_start: 0.6894 (OUTLIER) cc_final: 0.6572 (mtpm) REVERT: A 256 GLU cc_start: 0.6549 (mm-30) cc_final: 0.6232 (mt-10) REVERT: A 389 ASP cc_start: 0.4662 (OUTLIER) cc_final: 0.4187 (m-30) REVERT: A 422 SER cc_start: 0.6911 (p) cc_final: 0.6577 (t) REVERT: A 423 ILE cc_start: 0.6031 (mm) cc_final: 0.5686 (mp) REVERT: A 428 GLU cc_start: 0.6319 (mp0) cc_final: 0.6078 (pt0) REVERT: C 12 MET cc_start: 0.6007 (mtm) cc_final: 0.5624 (mtm) REVERT: C 139 GLU cc_start: 0.6047 (mm-30) cc_final: 0.5628 (pt0) REVERT: C 180 ASP cc_start: 0.7111 (m-30) cc_final: 0.6831 (m-30) REVERT: C 228 GLU cc_start: 0.6065 (mp0) cc_final: 0.5659 (tt0) REVERT: C 237 LYS cc_start: 0.6868 (OUTLIER) cc_final: 0.6594 (mtpm) REVERT: C 256 GLU cc_start: 0.6550 (mm-30) cc_final: 0.6249 (mt-10) REVERT: C 389 ASP cc_start: 0.4662 (OUTLIER) cc_final: 0.4186 (m-30) REVERT: C 422 SER cc_start: 0.6913 (p) cc_final: 0.6578 (t) REVERT: C 423 ILE cc_start: 0.6032 (mm) cc_final: 0.5686 (mp) REVERT: C 428 GLU cc_start: 0.6324 (mp0) cc_final: 0.6078 (pt0) REVERT: D 12 MET cc_start: 0.6022 (mtm) cc_final: 0.5659 (mtm) REVERT: D 139 GLU cc_start: 0.6051 (mm-30) cc_final: 0.5631 (pt0) REVERT: D 180 ASP cc_start: 0.7108 (m-30) cc_final: 0.6827 (m-30) REVERT: D 228 GLU cc_start: 0.6066 (mp0) cc_final: 0.5659 (tt0) REVERT: D 237 LYS cc_start: 0.6869 (OUTLIER) cc_final: 0.6596 (mtpm) REVERT: D 256 GLU cc_start: 0.6543 (mm-30) cc_final: 0.6238 (mt-10) REVERT: D 389 ASP cc_start: 0.4660 (OUTLIER) cc_final: 0.4188 (m-30) REVERT: D 422 SER cc_start: 0.6909 (p) cc_final: 0.6576 (t) REVERT: D 423 ILE cc_start: 0.6033 (mm) cc_final: 0.5688 (mp) REVERT: D 428 GLU cc_start: 0.6320 (mp0) cc_final: 0.6080 (pt0) outliers start: 52 outliers final: 33 residues processed: 242 average time/residue: 1.2646 time to fit residues: 340.3755 Evaluate side-chains 235 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 194 time to evaluate : 1.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 232 CYS Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 237 LYS Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 237 LYS Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain C residue 22 GLN Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 93 LYS Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 232 CYS Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 237 LYS Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 93 LYS Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 232 CYS Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 237 LYS Chi-restraints excluded: chain D residue 254 SER Chi-restraints excluded: chain D residue 389 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 0.9990 chunk 170 optimal weight: 0.1980 chunk 37 optimal weight: 0.0010 chunk 111 optimal weight: 0.7980 chunk 46 optimal weight: 7.9990 chunk 189 optimal weight: 4.9990 chunk 157 optimal weight: 6.9990 chunk 87 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 62 optimal weight: 7.9990 chunk 99 optimal weight: 8.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 GLN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 HIS A 22 GLN ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 HIS C 466 HIS D 22 GLN ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 466 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6462 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16888 Z= 0.152 Angle : 0.548 6.535 23040 Z= 0.276 Chirality : 0.043 0.145 2328 Planarity : 0.005 0.046 3052 Dihedral : 8.457 118.138 2260 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.39 % Allowed : 11.80 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.19), residues: 1980 helix: 1.51 (0.21), residues: 688 sheet: 0.86 (0.32), residues: 292 loop : -0.20 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 183 HIS 0.003 0.001 HIS A 466 PHE 0.013 0.001 PHE B 136 TYR 0.016 0.001 TYR A 236 ARG 0.007 0.000 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 220 time to evaluate : 1.847 Fit side-chains REVERT: B 12 MET cc_start: 0.5700 (mtm) cc_final: 0.5416 (mtm) REVERT: B 139 GLU cc_start: 0.6084 (mm-30) cc_final: 0.5617 (pt0) REVERT: B 180 ASP cc_start: 0.7273 (m-30) cc_final: 0.7003 (m-30) REVERT: B 228 GLU cc_start: 0.6191 (mp0) cc_final: 0.5760 (tt0) REVERT: B 232 CYS cc_start: 0.7342 (OUTLIER) cc_final: 0.6991 (p) REVERT: B 237 LYS cc_start: 0.6797 (OUTLIER) cc_final: 0.6459 (mmtt) REVERT: B 256 GLU cc_start: 0.6476 (mm-30) cc_final: 0.6143 (mt-10) REVERT: B 389 ASP cc_start: 0.4793 (OUTLIER) cc_final: 0.4323 (m-30) REVERT: B 422 SER cc_start: 0.6947 (p) cc_final: 0.6596 (t) REVERT: B 423 ILE cc_start: 0.6102 (mm) cc_final: 0.5762 (mp) REVERT: A 12 MET cc_start: 0.5691 (mtm) cc_final: 0.5406 (mtm) REVERT: A 139 GLU cc_start: 0.6084 (mm-30) cc_final: 0.5617 (pt0) REVERT: A 180 ASP cc_start: 0.7273 (m-30) cc_final: 0.7005 (m-30) REVERT: A 228 GLU cc_start: 0.6191 (mp0) cc_final: 0.5760 (tt0) REVERT: A 232 CYS cc_start: 0.7341 (OUTLIER) cc_final: 0.6991 (p) REVERT: A 237 LYS cc_start: 0.6795 (OUTLIER) cc_final: 0.6457 (mmtt) REVERT: A 256 GLU cc_start: 0.6469 (mm-30) cc_final: 0.6105 (mt-10) REVERT: A 389 ASP cc_start: 0.4737 (OUTLIER) cc_final: 0.4244 (m-30) REVERT: A 422 SER cc_start: 0.6949 (p) cc_final: 0.6600 (t) REVERT: A 423 ILE cc_start: 0.6107 (mm) cc_final: 0.5762 (mp) REVERT: C 12 MET cc_start: 0.5735 (mtm) cc_final: 0.5422 (mtm) REVERT: C 139 GLU cc_start: 0.5747 (mm-30) cc_final: 0.5437 (pt0) REVERT: C 140 ASP cc_start: 0.7068 (OUTLIER) cc_final: 0.6197 (t0) REVERT: C 180 ASP cc_start: 0.7271 (m-30) cc_final: 0.7002 (m-30) REVERT: C 228 GLU cc_start: 0.6191 (mp0) cc_final: 0.5761 (tt0) REVERT: C 232 CYS cc_start: 0.7343 (OUTLIER) cc_final: 0.6995 (p) REVERT: C 237 LYS cc_start: 0.6799 (OUTLIER) cc_final: 0.6464 (mmtt) REVERT: C 256 GLU cc_start: 0.6474 (mm-30) cc_final: 0.6142 (mt-10) REVERT: C 389 ASP cc_start: 0.4807 (OUTLIER) cc_final: 0.4319 (m-30) REVERT: C 422 SER cc_start: 0.6949 (p) cc_final: 0.6599 (t) REVERT: C 423 ILE cc_start: 0.6105 (mm) cc_final: 0.5760 (mp) REVERT: D 12 MET cc_start: 0.5702 (mtm) cc_final: 0.5392 (mtm) REVERT: D 139 GLU cc_start: 0.5751 (mm-30) cc_final: 0.5440 (pt0) REVERT: D 140 ASP cc_start: 0.7074 (OUTLIER) cc_final: 0.6206 (t0) REVERT: D 180 ASP cc_start: 0.7271 (m-30) cc_final: 0.7004 (m-30) REVERT: D 228 GLU cc_start: 0.6194 (mp0) cc_final: 0.5762 (tt0) REVERT: D 232 CYS cc_start: 0.7342 (OUTLIER) cc_final: 0.6989 (p) REVERT: D 237 LYS cc_start: 0.6801 (OUTLIER) cc_final: 0.6467 (mmtt) REVERT: D 256 GLU cc_start: 0.6475 (mm-30) cc_final: 0.6142 (mt-10) REVERT: D 389 ASP cc_start: 0.4792 (OUTLIER) cc_final: 0.4321 (m-30) REVERT: D 422 SER cc_start: 0.6947 (p) cc_final: 0.6599 (t) REVERT: D 423 ILE cc_start: 0.6108 (mm) cc_final: 0.5763 (mp) outliers start: 41 outliers final: 22 residues processed: 257 average time/residue: 1.1881 time to fit residues: 341.5025 Evaluate side-chains 230 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 194 time to evaluate : 1.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 GLN Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 232 CYS Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 237 LYS Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain A residue 22 GLN Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 237 LYS Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 93 LYS Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 232 CYS Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 237 LYS Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain D residue 22 GLN Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 93 LYS Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 232 CYS Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 237 LYS Chi-restraints excluded: chain D residue 389 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 8.9990 chunk 21 optimal weight: 4.9990 chunk 108 optimal weight: 10.0000 chunk 138 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 159 optimal weight: 0.9990 chunk 105 optimal weight: 6.9990 chunk 188 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 87 optimal weight: 9.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 HIS ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 HIS C 22 GLN C 466 HIS ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 466 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6491 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16888 Z= 0.215 Angle : 0.633 10.815 23040 Z= 0.308 Chirality : 0.045 0.147 2328 Planarity : 0.005 0.046 3052 Dihedral : 8.922 119.039 2260 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.39 % Allowed : 12.85 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.19), residues: 1980 helix: 1.37 (0.21), residues: 688 sheet: 0.75 (0.32), residues: 292 loop : -0.25 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 183 HIS 0.007 0.001 HIS C 218 PHE 0.016 0.002 PHE B 136 TYR 0.021 0.002 TYR B 236 ARG 0.006 0.000 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 192 time to evaluate : 1.822 Fit side-chains REVERT: B 12 MET cc_start: 0.5834 (mtm) cc_final: 0.5465 (mtm) REVERT: B 138 THR cc_start: 0.7161 (m) cc_final: 0.6793 (p) REVERT: B 139 GLU cc_start: 0.6016 (mm-30) cc_final: 0.5629 (pt0) REVERT: B 180 ASP cc_start: 0.7279 (m-30) cc_final: 0.7021 (m-30) REVERT: B 228 GLU cc_start: 0.6198 (mp0) cc_final: 0.5785 (tt0) REVERT: B 232 CYS cc_start: 0.7252 (OUTLIER) cc_final: 0.6882 (p) REVERT: B 237 LYS cc_start: 0.6737 (OUTLIER) cc_final: 0.6526 (mtpm) REVERT: B 256 GLU cc_start: 0.6431 (mm-30) cc_final: 0.6084 (mt-10) REVERT: B 389 ASP cc_start: 0.4714 (OUTLIER) cc_final: 0.4222 (m-30) REVERT: B 422 SER cc_start: 0.7038 (p) cc_final: 0.6593 (t) REVERT: B 423 ILE cc_start: 0.6094 (mm) cc_final: 0.5749 (mp) REVERT: A 12 MET cc_start: 0.5834 (mtm) cc_final: 0.5490 (mtm) REVERT: A 138 THR cc_start: 0.7162 (m) cc_final: 0.6795 (p) REVERT: A 139 GLU cc_start: 0.6058 (mm-30) cc_final: 0.5677 (pt0) REVERT: A 180 ASP cc_start: 0.7275 (m-30) cc_final: 0.7003 (m-30) REVERT: A 228 GLU cc_start: 0.6198 (mp0) cc_final: 0.5785 (tt0) REVERT: A 232 CYS cc_start: 0.7252 (OUTLIER) cc_final: 0.6884 (p) REVERT: A 237 LYS cc_start: 0.6735 (OUTLIER) cc_final: 0.6520 (mtpm) REVERT: A 389 ASP cc_start: 0.4713 (OUTLIER) cc_final: 0.4220 (m-30) REVERT: A 422 SER cc_start: 0.7042 (p) cc_final: 0.6679 (t) REVERT: C 12 MET cc_start: 0.5828 (mtm) cc_final: 0.5487 (mtm) REVERT: C 139 GLU cc_start: 0.5815 (mm-30) cc_final: 0.5426 (pt0) REVERT: C 140 ASP cc_start: 0.6834 (OUTLIER) cc_final: 0.6236 (t0) REVERT: C 180 ASP cc_start: 0.7270 (m-30) cc_final: 0.6982 (m-30) REVERT: C 228 GLU cc_start: 0.6200 (mp0) cc_final: 0.5787 (tt0) REVERT: C 232 CYS cc_start: 0.7254 (OUTLIER) cc_final: 0.6885 (p) REVERT: C 237 LYS cc_start: 0.6783 (OUTLIER) cc_final: 0.6573 (mtpm) REVERT: C 256 GLU cc_start: 0.6431 (mm-30) cc_final: 0.6075 (mt-10) REVERT: C 389 ASP cc_start: 0.4716 (OUTLIER) cc_final: 0.4220 (m-30) REVERT: C 422 SER cc_start: 0.7043 (p) cc_final: 0.6598 (t) REVERT: C 423 ILE cc_start: 0.6091 (mm) cc_final: 0.5745 (mp) REVERT: D 12 MET cc_start: 0.5833 (mtm) cc_final: 0.5468 (mtm) REVERT: D 139 GLU cc_start: 0.5816 (mm-30) cc_final: 0.5427 (pt0) REVERT: D 140 ASP cc_start: 0.6835 (OUTLIER) cc_final: 0.6203 (t0) REVERT: D 180 ASP cc_start: 0.7273 (m-30) cc_final: 0.6984 (m-30) REVERT: D 228 GLU cc_start: 0.6201 (mp0) cc_final: 0.5786 (tt0) REVERT: D 232 CYS cc_start: 0.7253 (OUTLIER) cc_final: 0.6882 (p) REVERT: D 237 LYS cc_start: 0.6784 (OUTLIER) cc_final: 0.6573 (mtpm) REVERT: D 256 GLU cc_start: 0.6429 (mm-30) cc_final: 0.6206 (mt-10) REVERT: D 389 ASP cc_start: 0.4713 (OUTLIER) cc_final: 0.4218 (m-30) REVERT: D 422 SER cc_start: 0.7043 (p) cc_final: 0.6599 (t) REVERT: D 423 ILE cc_start: 0.6097 (mm) cc_final: 0.5753 (mp) outliers start: 41 outliers final: 26 residues processed: 229 average time/residue: 1.1835 time to fit residues: 303.4210 Evaluate side-chains 232 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 192 time to evaluate : 1.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 232 CYS Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 237 LYS Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 237 LYS Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 93 LYS Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 232 CYS Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 237 LYS Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 93 LYS Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 232 CYS Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 237 LYS Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 389 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 7.9990 chunk 75 optimal weight: 8.9990 chunk 112 optimal weight: 0.9990 chunk 56 optimal weight: 9.9990 chunk 37 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 120 optimal weight: 9.9990 chunk 128 optimal weight: 6.9990 chunk 93 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 148 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 GLN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 HIS A 22 GLN ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 HIS C 466 HIS D 22 GLN ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 466 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6490 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16888 Z= 0.212 Angle : 0.631 10.187 23040 Z= 0.307 Chirality : 0.045 0.137 2328 Planarity : 0.005 0.047 3052 Dihedral : 8.731 111.536 2260 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.98 % Allowed : 12.97 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.19), residues: 1980 helix: 1.31 (0.21), residues: 688 sheet: 0.72 (0.32), residues: 292 loop : -0.21 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 183 HIS 0.006 0.001 HIS C 218 PHE 0.016 0.002 PHE B 136 TYR 0.019 0.002 TYR C 236 ARG 0.005 0.000 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 198 time to evaluate : 1.717 Fit side-chains REVERT: B 12 MET cc_start: 0.5814 (mtm) cc_final: 0.5457 (mtm) REVERT: B 138 THR cc_start: 0.7159 (m) cc_final: 0.6798 (p) REVERT: B 139 GLU cc_start: 0.6042 (mm-30) cc_final: 0.5652 (pt0) REVERT: B 180 ASP cc_start: 0.7169 (m-30) cc_final: 0.6880 (m-30) REVERT: B 228 GLU cc_start: 0.6148 (mp0) cc_final: 0.5735 (tt0) REVERT: B 256 GLU cc_start: 0.6492 (mm-30) cc_final: 0.6228 (mt-10) REVERT: B 328 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7120 (pt0) REVERT: B 389 ASP cc_start: 0.4649 (OUTLIER) cc_final: 0.4225 (m-30) REVERT: B 422 SER cc_start: 0.7046 (p) cc_final: 0.6601 (t) REVERT: B 423 ILE cc_start: 0.6153 (mm) cc_final: 0.5808 (mp) REVERT: A 12 MET cc_start: 0.5815 (mtm) cc_final: 0.5482 (mtm) REVERT: A 138 THR cc_start: 0.7156 (m) cc_final: 0.6805 (p) REVERT: A 139 GLU cc_start: 0.6042 (mm-30) cc_final: 0.5652 (pt0) REVERT: A 180 ASP cc_start: 0.7166 (m-30) cc_final: 0.6878 (m-30) REVERT: A 228 GLU cc_start: 0.6145 (mp0) cc_final: 0.5760 (tt0) REVERT: A 328 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7112 (pt0) REVERT: A 389 ASP cc_start: 0.4649 (OUTLIER) cc_final: 0.4225 (m-30) REVERT: A 422 SER cc_start: 0.6830 (p) cc_final: 0.6520 (t) REVERT: C 12 MET cc_start: 0.5808 (mtm) cc_final: 0.5447 (mtm) REVERT: C 139 GLU cc_start: 0.5889 (mm-30) cc_final: 0.5482 (pt0) REVERT: C 140 ASP cc_start: 0.6969 (OUTLIER) cc_final: 0.6377 (t0) REVERT: C 180 ASP cc_start: 0.7166 (m-30) cc_final: 0.6896 (m-30) REVERT: C 228 GLU cc_start: 0.6151 (mp0) cc_final: 0.5738 (tt0) REVERT: C 256 GLU cc_start: 0.6491 (mm-30) cc_final: 0.6228 (mt-10) REVERT: C 328 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7120 (pt0) REVERT: C 389 ASP cc_start: 0.4647 (OUTLIER) cc_final: 0.4231 (m-30) REVERT: C 422 SER cc_start: 0.7049 (p) cc_final: 0.6604 (t) REVERT: C 423 ILE cc_start: 0.6152 (mm) cc_final: 0.5807 (mp) REVERT: D 12 MET cc_start: 0.5815 (mtm) cc_final: 0.5458 (mtm) REVERT: D 139 GLU cc_start: 0.5890 (mm-30) cc_final: 0.5482 (pt0) REVERT: D 140 ASP cc_start: 0.6967 (OUTLIER) cc_final: 0.6377 (t0) REVERT: D 180 ASP cc_start: 0.7165 (m-30) cc_final: 0.6895 (m-30) REVERT: D 228 GLU cc_start: 0.6153 (mp0) cc_final: 0.5737 (tt0) REVERT: D 256 GLU cc_start: 0.6506 (mm-30) cc_final: 0.6244 (mt-10) REVERT: D 328 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7121 (pt0) REVERT: D 389 ASP cc_start: 0.4645 (OUTLIER) cc_final: 0.4224 (m-30) REVERT: D 422 SER cc_start: 0.7048 (p) cc_final: 0.6604 (t) REVERT: D 423 ILE cc_start: 0.6152 (mm) cc_final: 0.5806 (mp) outliers start: 51 outliers final: 40 residues processed: 245 average time/residue: 1.1415 time to fit residues: 314.3674 Evaluate side-chains 238 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 192 time to evaluate : 2.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 GLN Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 232 CYS Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain A residue 22 GLN Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 93 LYS Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 232 CYS Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain D residue 22 GLN Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 93 LYS Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 232 CYS Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 254 SER Chi-restraints excluded: chain D residue 389 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 7.9990 chunk 180 optimal weight: 3.9990 chunk 165 optimal weight: 0.9980 chunk 176 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 138 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 159 optimal weight: 7.9990 chunk 166 optimal weight: 0.9980 chunk 175 optimal weight: 5.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 GLN ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 HIS A 173 GLN ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 HIS ** C 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 HIS D 173 GLN ** D 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 466 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6492 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16888 Z= 0.220 Angle : 0.645 10.710 23040 Z= 0.312 Chirality : 0.045 0.137 2328 Planarity : 0.005 0.046 3052 Dihedral : 8.641 106.602 2260 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.98 % Allowed : 13.26 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.19), residues: 1980 helix: 1.30 (0.21), residues: 688 sheet: 0.71 (0.32), residues: 292 loop : -0.19 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 183 HIS 0.005 0.001 HIS A 218 PHE 0.016 0.002 PHE A 136 TYR 0.019 0.002 TYR D 236 ARG 0.005 0.000 ARG D 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 189 time to evaluate : 1.876 Fit side-chains REVERT: B 12 MET cc_start: 0.5802 (mtm) cc_final: 0.5446 (mtm) REVERT: B 138 THR cc_start: 0.7126 (m) cc_final: 0.6754 (p) REVERT: B 139 GLU cc_start: 0.6071 (mm-30) cc_final: 0.5664 (pt0) REVERT: B 180 ASP cc_start: 0.7170 (m-30) cc_final: 0.6881 (m-30) REVERT: B 228 GLU cc_start: 0.6157 (mp0) cc_final: 0.5736 (tt0) REVERT: B 256 GLU cc_start: 0.6532 (mm-30) cc_final: 0.6151 (mt-10) REVERT: B 389 ASP cc_start: 0.4634 (OUTLIER) cc_final: 0.4122 (m-30) REVERT: B 396 ASP cc_start: 0.5083 (OUTLIER) cc_final: 0.4877 (p0) REVERT: B 422 SER cc_start: 0.7053 (p) cc_final: 0.6606 (t) REVERT: B 423 ILE cc_start: 0.6185 (mm) cc_final: 0.5843 (mp) REVERT: A 12 MET cc_start: 0.5804 (mtm) cc_final: 0.5471 (mtm) REVERT: A 138 THR cc_start: 0.7161 (m) cc_final: 0.6799 (p) REVERT: A 139 GLU cc_start: 0.6037 (mm-30) cc_final: 0.5630 (pt0) REVERT: A 180 ASP cc_start: 0.7165 (m-30) cc_final: 0.6878 (m-30) REVERT: A 228 GLU cc_start: 0.6154 (mp0) cc_final: 0.5736 (tt0) REVERT: A 389 ASP cc_start: 0.4635 (OUTLIER) cc_final: 0.4122 (m-30) REVERT: A 396 ASP cc_start: 0.5088 (OUTLIER) cc_final: 0.4883 (p0) REVERT: A 422 SER cc_start: 0.6839 (p) cc_final: 0.6520 (t) REVERT: C 12 MET cc_start: 0.5802 (mtm) cc_final: 0.5445 (mtm) REVERT: C 139 GLU cc_start: 0.5894 (mm-30) cc_final: 0.5494 (pt0) REVERT: C 140 ASP cc_start: 0.6823 (OUTLIER) cc_final: 0.6283 (t0) REVERT: C 180 ASP cc_start: 0.7167 (m-30) cc_final: 0.6881 (m-30) REVERT: C 228 GLU cc_start: 0.6160 (mp0) cc_final: 0.5739 (tt0) REVERT: C 256 GLU cc_start: 0.6528 (mm-30) cc_final: 0.6142 (mt-10) REVERT: C 389 ASP cc_start: 0.4642 (OUTLIER) cc_final: 0.4215 (m-30) REVERT: C 396 ASP cc_start: 0.5109 (OUTLIER) cc_final: 0.4864 (p0) REVERT: C 422 SER cc_start: 0.7056 (p) cc_final: 0.6610 (t) REVERT: C 423 ILE cc_start: 0.6186 (mm) cc_final: 0.5844 (mp) REVERT: D 12 MET cc_start: 0.5803 (mtm) cc_final: 0.5447 (mtm) REVERT: D 139 GLU cc_start: 0.5895 (mm-30) cc_final: 0.5493 (pt0) REVERT: D 140 ASP cc_start: 0.6822 (OUTLIER) cc_final: 0.6282 (t0) REVERT: D 180 ASP cc_start: 0.7165 (m-30) cc_final: 0.6878 (m-30) REVERT: D 228 GLU cc_start: 0.6162 (mp0) cc_final: 0.5738 (tt0) REVERT: D 256 GLU cc_start: 0.6529 (mm-30) cc_final: 0.6149 (mt-10) REVERT: D 389 ASP cc_start: 0.4640 (OUTLIER) cc_final: 0.4212 (m-30) REVERT: D 396 ASP cc_start: 0.5096 (OUTLIER) cc_final: 0.4851 (p0) REVERT: D 422 SER cc_start: 0.7053 (p) cc_final: 0.6608 (t) REVERT: D 423 ILE cc_start: 0.6189 (mm) cc_final: 0.5845 (mp) outliers start: 51 outliers final: 37 residues processed: 236 average time/residue: 1.1626 time to fit residues: 308.1089 Evaluate side-chains 238 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 191 time to evaluate : 1.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 232 CYS Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 93 LYS Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 232 CYS Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 93 LYS Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 232 CYS Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 254 SER Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 396 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 10.0000 chunk 186 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 chunk 88 optimal weight: 0.4980 chunk 129 optimal weight: 8.9990 chunk 195 optimal weight: 5.9990 chunk 179 optimal weight: 8.9990 chunk 155 optimal weight: 0.0980 chunk 16 optimal weight: 0.9990 chunk 120 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 GLN B 466 HIS A 22 GLN A 466 HIS C 466 HIS D 22 GLN D 466 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6475 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16888 Z= 0.186 Angle : 0.614 11.718 23040 Z= 0.297 Chirality : 0.044 0.141 2328 Planarity : 0.005 0.046 3052 Dihedral : 8.220 96.531 2260 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.34 % Allowed : 13.90 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.19), residues: 1980 helix: 1.18 (0.20), residues: 712 sheet: 0.74 (0.32), residues: 292 loop : -0.11 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 183 HIS 0.004 0.001 HIS B 218 PHE 0.015 0.001 PHE A 136 TYR 0.018 0.001 TYR C 236 ARG 0.004 0.000 ARG C 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 195 time to evaluate : 1.750 Fit side-chains REVERT: B 12 MET cc_start: 0.5716 (mtm) cc_final: 0.5419 (mtm) REVERT: B 138 THR cc_start: 0.6969 (m) cc_final: 0.6746 (p) REVERT: B 139 GLU cc_start: 0.6027 (mm-30) cc_final: 0.5637 (pt0) REVERT: B 180 ASP cc_start: 0.7176 (m-30) cc_final: 0.6903 (m-30) REVERT: B 228 GLU cc_start: 0.6111 (mp0) cc_final: 0.5718 (tt0) REVERT: B 232 CYS cc_start: 0.7386 (OUTLIER) cc_final: 0.7028 (p) REVERT: B 256 GLU cc_start: 0.6517 (mm-30) cc_final: 0.6124 (mt-10) REVERT: B 328 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7323 (pt0) REVERT: B 389 ASP cc_start: 0.4706 (OUTLIER) cc_final: 0.4229 (m-30) REVERT: B 422 SER cc_start: 0.7076 (p) cc_final: 0.6627 (t) REVERT: B 423 ILE cc_start: 0.6109 (mm) cc_final: 0.5763 (mp) REVERT: A 12 MET cc_start: 0.5729 (mtm) cc_final: 0.5432 (mtm) REVERT: A 138 THR cc_start: 0.6964 (m) cc_final: 0.6743 (p) REVERT: A 139 GLU cc_start: 0.6024 (mm-30) cc_final: 0.5640 (pt0) REVERT: A 180 ASP cc_start: 0.7172 (m-30) cc_final: 0.6881 (m-30) REVERT: A 228 GLU cc_start: 0.6171 (mp0) cc_final: 0.5773 (tt0) REVERT: A 232 CYS cc_start: 0.7386 (OUTLIER) cc_final: 0.7030 (p) REVERT: A 255 GLN cc_start: 0.6820 (tm-30) cc_final: 0.6473 (tm-30) REVERT: A 290 GLU cc_start: 0.6306 (mm-30) cc_final: 0.5719 (mp0) REVERT: A 328 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7323 (pt0) REVERT: A 389 ASP cc_start: 0.4708 (OUTLIER) cc_final: 0.4230 (m-30) REVERT: A 422 SER cc_start: 0.6872 (p) cc_final: 0.6560 (t) REVERT: C 12 MET cc_start: 0.5707 (mtm) cc_final: 0.5448 (mtm) REVERT: C 139 GLU cc_start: 0.5854 (mm-30) cc_final: 0.5466 (pt0) REVERT: C 140 ASP cc_start: 0.6921 (OUTLIER) cc_final: 0.6396 (t0) REVERT: C 180 ASP cc_start: 0.7173 (m-30) cc_final: 0.6904 (m-30) REVERT: C 228 GLU cc_start: 0.6164 (mp0) cc_final: 0.5779 (tt0) REVERT: C 232 CYS cc_start: 0.7342 (OUTLIER) cc_final: 0.6977 (p) REVERT: C 256 GLU cc_start: 0.6513 (mm-30) cc_final: 0.6238 (mt-10) REVERT: C 328 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7322 (pt0) REVERT: C 389 ASP cc_start: 0.4769 (OUTLIER) cc_final: 0.4316 (m-30) REVERT: C 422 SER cc_start: 0.7078 (p) cc_final: 0.6630 (t) REVERT: C 423 ILE cc_start: 0.6109 (mm) cc_final: 0.5763 (mp) REVERT: D 12 MET cc_start: 0.5718 (mtm) cc_final: 0.5429 (mtm) REVERT: D 139 GLU cc_start: 0.5855 (mm-30) cc_final: 0.5466 (pt0) REVERT: D 140 ASP cc_start: 0.6919 (OUTLIER) cc_final: 0.6396 (t0) REVERT: D 180 ASP cc_start: 0.7159 (m-30) cc_final: 0.6865 (m-30) REVERT: D 228 GLU cc_start: 0.6166 (mp0) cc_final: 0.5779 (tt0) REVERT: D 232 CYS cc_start: 0.7342 (OUTLIER) cc_final: 0.6974 (p) REVERT: D 256 GLU cc_start: 0.6512 (mm-30) cc_final: 0.6121 (mt-10) REVERT: D 328 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7322 (pt0) REVERT: D 389 ASP cc_start: 0.4712 (OUTLIER) cc_final: 0.4234 (m-30) REVERT: D 422 SER cc_start: 0.6933 (p) cc_final: 0.6477 (t) REVERT: D 423 ILE cc_start: 0.6177 (mm) cc_final: 0.5839 (mp) outliers start: 40 outliers final: 25 residues processed: 231 average time/residue: 1.1264 time to fit residues: 292.1284 Evaluate side-chains 237 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 202 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 GLN Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 232 CYS Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain A residue 22 GLN Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 232 CYS Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain D residue 22 GLN Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 232 CYS Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 254 SER Chi-restraints excluded: chain D residue 389 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 4.9990 chunk 165 optimal weight: 0.8980 chunk 47 optimal weight: 9.9990 chunk 143 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 43 optimal weight: 9.9990 chunk 155 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 0.3980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 GLN B 466 HIS A 22 GLN A 466 HIS C 466 HIS D 22 GLN D 466 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.165289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.145363 restraints weight = 16325.484| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 1.00 r_work: 0.3503 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16888 Z= 0.198 Angle : 0.638 13.113 23040 Z= 0.306 Chirality : 0.044 0.139 2328 Planarity : 0.005 0.046 3052 Dihedral : 8.202 93.007 2260 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.39 % Allowed : 13.96 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.19), residues: 1980 helix: 1.15 (0.20), residues: 712 sheet: 0.72 (0.32), residues: 292 loop : -0.13 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 183 HIS 0.005 0.001 HIS A 466 PHE 0.015 0.002 PHE B 136 TYR 0.018 0.001 TYR A 236 ARG 0.004 0.000 ARG D 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5946.44 seconds wall clock time: 104 minutes 38.90 seconds (6278.90 seconds total)