Starting phenix.real_space_refine on Tue Aug 6 12:38:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wzj_37954/08_2024/8wzj_37954.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wzj_37954/08_2024/8wzj_37954.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wzj_37954/08_2024/8wzj_37954.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wzj_37954/08_2024/8wzj_37954.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wzj_37954/08_2024/8wzj_37954.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wzj_37954/08_2024/8wzj_37954.cif" } resolution = 2.7 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= 0.012 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 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 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 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 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: 0.04s 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: 8.55, per 1000 atoms: 0.52 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: 5.92 Conformation dependent library (CDL) restraints added in 2.6 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, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.88 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: 3.657A 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: 3.893A 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: 3.915A pdb=" N PHE B 356 " --> pdb=" O GLN B 352 " (cutoff:3.500A) removed outlier: 3.527A 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: 3.650A 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: 3.657A 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: 3.894A 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: 3.914A pdb=" N PHE A 356 " --> pdb=" O GLN A 352 " (cutoff:3.500A) removed outlier: 3.527A 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: 3.649A 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: 3.658A 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: 3.894A 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: 3.914A pdb=" N PHE C 356 " --> pdb=" O GLN C 352 " (cutoff:3.500A) removed outlier: 3.527A 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: 3.650A 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: 3.658A 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: 3.894A 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: 3.914A pdb=" N PHE D 356 " --> pdb=" O GLN D 352 " (cutoff:3.500A) removed outlier: 3.528A 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: 3.650A 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 Processing sheet with id=AA2, first strand: chain 'B' and resid 343 through 345 removed outlier: 5.988A pdb=" N ILE B 281 " --> pdb=" O PRO B 312 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N LEU B 316 " --> pdb=" O GLU B 86 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N GLU B 86 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LEU B 318 " --> pdb=" O TYR B 84 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N TYR B 84 " --> pdb=" O LEU B 318 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 429 through 431 Processing sheet with id=AA4, first strand: chain 'A' and resid 42 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 343 through 345 removed outlier: 5.987A pdb=" N ILE A 281 " --> pdb=" O PRO A 312 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N LEU A 316 " --> pdb=" O GLU A 86 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLU A 86 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N LEU A 318 " --> pdb=" O TYR A 84 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N TYR A 84 " --> pdb=" O LEU A 318 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 429 through 431 Processing sheet with id=AA7, first strand: chain 'C' and resid 343 through 345 removed outlier: 5.987A pdb=" N ILE C 281 " --> pdb=" O PRO C 312 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N LEU C 316 " --> pdb=" O GLU C 86 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLU C 86 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LEU C 318 " --> pdb=" O TYR C 84 " (cutoff:3.500A) removed outlier: 7.163A 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: 5.988A pdb=" N ILE D 281 " --> pdb=" O PRO D 312 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N LEU D 316 " --> pdb=" O GLU D 86 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLU D 86 " --> pdb=" O LEU D 316 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N LEU D 318 " --> pdb=" O TYR D 84 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N TYR D 84 " --> pdb=" O LEU D 318 " (cutoff:3.500A) 656 hydrogen bonds defined for protein. 1872 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: 4.88 Time building geometry restraints manager: 6.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.39: 6777 1.39 - 1.57: 9987 1.57 - 1.75: 20 1.75 - 1.93: 92 1.93 - 2.11: 12 Bond restraints: 16888 Sorted by residual: bond pdb=" O2B NDP D3002 " pdb=" P2B NDP D3002 " ideal model delta sigma weight residual 1.833 1.621 0.212 3.80e-02 6.93e+02 3.10e+01 bond pdb=" O2B NDP B3002 " pdb=" P2B NDP B3002 " ideal model delta sigma weight residual 1.833 1.622 0.211 3.80e-02 6.93e+02 3.09e+01 bond pdb=" O2B NDP C3002 " pdb=" P2B NDP C3002 " ideal model delta sigma weight residual 1.833 1.622 0.211 3.80e-02 6.93e+02 3.09e+01 bond pdb=" O2B NDP A3002 " pdb=" P2B NDP A3002 " ideal model delta sigma weight residual 1.833 1.622 0.211 3.80e-02 6.93e+02 3.08e+01 bond pdb=" O5D NDP A3002 " pdb=" PN NDP A3002 " ideal model delta sigma weight residual 1.757 1.602 0.155 3.50e-02 8.16e+02 1.95e+01 ... (remaining 16883 not shown) Histogram of bond angle deviations from ideal: 86.78 - 104.81: 512 104.81 - 122.84: 18208 122.84 - 140.87: 4312 140.87 - 158.89: 0 158.89 - 176.92: 8 Bond angle restraints: 23040 Sorted by residual: angle pdb=" PA NDP C3002 " pdb=" O3 NDP C3002 " pdb=" PN NDP C3002 " ideal model delta sigma weight residual 107.74 131.37 -23.63 1.95e+00 2.62e-01 1.46e+02 angle pdb=" PA NDP D3002 " pdb=" O3 NDP D3002 " pdb=" PN NDP D3002 " ideal model delta sigma weight residual 107.74 131.36 -23.62 1.95e+00 2.62e-01 1.46e+02 angle pdb=" PA NDP A3002 " pdb=" O3 NDP A3002 " pdb=" PN NDP A3002 " ideal model delta sigma weight residual 107.74 131.33 -23.59 1.95e+00 2.62e-01 1.46e+02 angle pdb=" PA NDP B3002 " pdb=" O3 NDP B3002 " pdb=" PN NDP B3002 " ideal model delta sigma weight residual 107.74 131.33 -23.59 1.95e+00 2.62e-01 1.46e+02 angle pdb=" C5B NDP C3002 " pdb=" O5B NDP C3002 " pdb=" PA NDP C3002 " ideal model delta sigma weight residual 103.84 120.50 -16.66 1.91e+00 2.73e-01 7.57e+01 ... (remaining 23035 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.88: 9054 18.88 - 37.76: 622 37.76 - 56.64: 124 56.64 - 75.52: 48 75.52 - 94.40: 12 Dihedral angle restraints: 9860 sinusoidal: 4080 harmonic: 5780 Sorted by residual: 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 180.00 158.93 21.07 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA ASP D 389 " pdb=" C ASP D 389 " pdb=" N GLY D 390 " pdb=" CA GLY D 390 " ideal model delta harmonic sigma weight residual 180.00 158.94 21.06 0 5.00e+00 4.00e-02 1.77e+01 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 180.00 158.97 21.03 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 9857 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 932 0.045 - 0.090: 777 0.090 - 0.136: 466 0.136 - 0.181: 142 0.181 - 0.226: 11 Chirality restraints: 2328 Sorted by residual: chirality pdb=" C4D NDP C3002 " pdb=" C3D NDP C3002 " pdb=" C5D NDP C3002 " pdb=" O4D NDP C3002 " both_signs ideal model delta sigma weight residual False -2.71 -2.49 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" C4D NDP B3002 " pdb=" C3D NDP B3002 " pdb=" C5D NDP B3002 " pdb=" O4D NDP B3002 " both_signs ideal model delta sigma weight residual False -2.71 -2.49 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" C4D NDP A3002 " pdb=" C3D NDP A3002 " pdb=" C5D NDP A3002 " pdb=" O4D NDP A3002 " both_signs ideal model delta sigma weight residual False -2.71 -2.49 -0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 2325 not shown) Planarity restraints: 3052 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2N NDP A3002 " -0.054 2.00e-02 2.50e+03 3.42e-02 1.46e+01 pdb=" C3N NDP A3002 " -0.012 2.00e-02 2.50e+03 pdb=" C4N NDP A3002 " -0.007 2.00e-02 2.50e+03 pdb=" C7N NDP A3002 " 0.030 2.00e-02 2.50e+03 pdb=" N1N NDP A3002 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEM B3001 " 0.044 2.00e-02 2.50e+03 2.54e-02 1.46e+01 pdb=" C2C HEM B3001 " 0.023 2.00e-02 2.50e+03 pdb=" C3C HEM B3001 " 0.013 2.00e-02 2.50e+03 pdb=" C4C HEM B3001 " 0.003 2.00e-02 2.50e+03 pdb=" CAC HEM B3001 " -0.027 2.00e-02 2.50e+03 pdb=" CHC HEM B3001 " -0.049 2.00e-02 2.50e+03 pdb=" CHD HEM B3001 " -0.008 2.00e-02 2.50e+03 pdb=" CMC HEM B3001 " -0.001 2.00e-02 2.50e+03 pdb=" NC HEM B3001 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2N NDP D3002 " 0.054 2.00e-02 2.50e+03 3.41e-02 1.45e+01 pdb=" C3N NDP D3002 " 0.012 2.00e-02 2.50e+03 pdb=" C4N NDP D3002 " 0.007 2.00e-02 2.50e+03 pdb=" C7N NDP D3002 " -0.030 2.00e-02 2.50e+03 pdb=" N1N NDP D3002 " -0.043 2.00e-02 2.50e+03 ... (remaining 3049 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 5036 2.87 - 3.38: 15764 3.38 - 3.89: 30616 3.89 - 4.39: 35341 4.39 - 4.90: 58001 Nonbonded interactions: 144758 Sorted by model distance: nonbonded pdb=" OD1 ASP D 298 " pdb=" OG1 THR D 300 " model vdw 2.368 3.040 nonbonded pdb=" OD1 ASP C 298 " pdb=" OG1 THR C 300 " model vdw 2.368 3.040 nonbonded pdb=" OD1 ASP B 298 " pdb=" OG1 THR B 300 " model vdw 2.368 3.040 nonbonded pdb=" OD1 ASP A 298 " pdb=" OG1 THR A 300 " model vdw 2.369 3.040 nonbonded pdb=" O ARG A 388 " pdb=" O ASP A 389 " model vdw 2.369 3.040 ... (remaining 144753 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: 0.760 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: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 42.510 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 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 : 0.014 0.212 16888 Z= 0.916 Angle : 1.675 23.631 23040 Z= 1.177 Chirality : 0.076 0.226 2328 Planarity : 0.005 0.035 3052 Dihedral : 14.337 94.395 6148 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.04 % Favored : 95.76 % Rotamer: Outliers : 0.99 % Allowed : 4.38 % Favored : 94.63 % 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: -1.14 (0.17), residues: 1980 helix: -0.22 (0.17), residues: 680 sheet: -0.64 (0.29), residues: 276 loop : -1.11 (0.17), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.004 TRP A 15 HIS 0.014 0.003 HIS C 218 PHE 0.031 0.004 PHE D 334 TYR 0.025 0.004 TYR D 236 ARG 0.022 0.002 ARG B 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 330 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 313 time to evaluate : 1.794 Fit side-chains REVERT: B 106 LYS cc_start: 0.7418 (mttt) cc_final: 0.7085 (mtmt) REVERT: B 201 SER cc_start: 0.7911 (t) cc_final: 0.7677 (p) REVERT: B 249 ASP cc_start: 0.6827 (m-30) cc_final: 0.6553 (t0) REVERT: B 255 GLN cc_start: 0.7417 (pt0) cc_final: 0.7117 (pp30) REVERT: B 392 MET cc_start: 0.8519 (mmm) cc_final: 0.7934 (mmm) REVERT: B 394 MET cc_start: 0.6569 (mpp) cc_final: 0.5721 (mpp) REVERT: B 428 GLU cc_start: 0.6028 (mp0) cc_final: 0.5637 (mp0) REVERT: B 457 LYS cc_start: 0.7312 (ttpt) cc_final: 0.6825 (ttmm) REVERT: B 476 LYS cc_start: 0.7055 (mttp) cc_final: 0.6851 (mptp) REVERT: B 488 ASP cc_start: 0.6799 (m-30) cc_final: 0.6400 (m-30) REVERT: B 492 HIS cc_start: 0.7138 (t-170) cc_final: 0.6854 (t-90) REVERT: B 499 LYS cc_start: 0.7043 (tttp) cc_final: 0.6351 (ttpp) REVERT: A 106 LYS cc_start: 0.7400 (mttt) cc_final: 0.7081 (mtmt) REVERT: A 201 SER cc_start: 0.7911 (t) cc_final: 0.7666 (p) REVERT: A 249 ASP cc_start: 0.6832 (m-30) cc_final: 0.6555 (t0) REVERT: A 255 GLN cc_start: 0.7409 (pt0) cc_final: 0.7119 (pp30) REVERT: A 392 MET cc_start: 0.8524 (mmm) cc_final: 0.8113 (mmm) REVERT: A 394 MET cc_start: 0.6546 (mpp) cc_final: 0.5724 (mpp) REVERT: A 428 GLU cc_start: 0.6063 (mp0) cc_final: 0.5676 (mp0) REVERT: A 457 LYS cc_start: 0.7133 (ttpt) cc_final: 0.6706 (ttmm) REVERT: A 476 LYS cc_start: 0.7000 (mttp) cc_final: 0.6791 (mptp) REVERT: A 492 HIS cc_start: 0.7173 (t-170) cc_final: 0.6951 (t-90) REVERT: A 499 LYS cc_start: 0.7029 (tttp) cc_final: 0.6343 (ttpp) REVERT: C 106 LYS cc_start: 0.7398 (mttt) cc_final: 0.7079 (mtmt) REVERT: C 201 SER cc_start: 0.7918 (t) cc_final: 0.7669 (p) REVERT: C 249 ASP cc_start: 0.6807 (m-30) cc_final: 0.6536 (t0) REVERT: C 255 GLN cc_start: 0.7407 (pt0) cc_final: 0.7173 (pp30) REVERT: C 392 MET cc_start: 0.8514 (mmm) cc_final: 0.8103 (mmm) REVERT: C 394 MET cc_start: 0.6454 (mpp) cc_final: 0.5673 (mpp) REVERT: C 428 GLU cc_start: 0.6082 (mp0) cc_final: 0.5711 (mp0) REVERT: C 457 LYS cc_start: 0.7138 (ttpt) cc_final: 0.6681 (ttmm) REVERT: C 471 GLN cc_start: 0.7281 (mt0) cc_final: 0.7031 (mt0) REVERT: C 476 LYS cc_start: 0.6905 (mttp) cc_final: 0.6699 (mptp) REVERT: C 488 ASP cc_start: 0.6795 (m-30) cc_final: 0.6385 (m-30) REVERT: C 492 HIS cc_start: 0.7136 (t-170) cc_final: 0.6842 (t-90) REVERT: C 499 LYS cc_start: 0.7039 (tttp) cc_final: 0.6352 (ttpp) REVERT: D 106 LYS cc_start: 0.7363 (mttt) cc_final: 0.7028 (mtmt) REVERT: D 201 SER cc_start: 0.7915 (t) cc_final: 0.7679 (p) REVERT: D 249 ASP cc_start: 0.6802 (m-30) cc_final: 0.6536 (t0) REVERT: D 255 GLN cc_start: 0.7407 (pt0) cc_final: 0.7147 (pp30) REVERT: D 392 MET cc_start: 0.8510 (mmm) cc_final: 0.7908 (mmm) REVERT: D 394 MET cc_start: 0.6578 (mpp) cc_final: 0.5721 (mpp) REVERT: D 428 GLU cc_start: 0.6063 (mp0) cc_final: 0.5691 (mp0) REVERT: D 457 LYS cc_start: 0.7340 (ttpt) cc_final: 0.6866 (ttmm) REVERT: D 471 GLN cc_start: 0.7287 (mt0) cc_final: 0.7042 (mt0) REVERT: D 488 ASP cc_start: 0.6797 (m-30) cc_final: 0.6389 (m-30) REVERT: D 492 HIS cc_start: 0.7194 (t-170) cc_final: 0.6914 (t-90) REVERT: D 499 LYS cc_start: 0.7105 (tttp) cc_final: 0.6406 (ttpp) outliers start: 17 outliers final: 4 residues processed: 321 average time/residue: 1.5452 time to fit residues: 540.0308 Evaluate side-chains 183 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 179 time to evaluate : 1.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 236 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 0.9980 chunk 148 optimal weight: 9.9990 chunk 82 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 153 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 114 optimal weight: 0.9990 chunk 177 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 GLN B 226 ASN B 338 ASN B 407 ASN A 22 GLN A 102 HIS A 226 ASN A 338 ASN A 407 ASN C 22 GLN C 102 HIS C 226 ASN C 338 ASN C 407 ASN D 22 GLN D 226 ASN D 338 ASN D 407 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16888 Z= 0.219 Angle : 0.583 5.965 23040 Z= 0.299 Chirality : 0.045 0.147 2328 Planarity : 0.004 0.035 3052 Dihedral : 8.783 114.133 2260 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.52 % Allowed : 10.51 % Favored : 87.97 % 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: 0.31 (0.18), residues: 1980 helix: 1.03 (0.20), residues: 688 sheet: 0.32 (0.31), residues: 284 loop : -0.34 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 303 HIS 0.005 0.001 HIS A 102 PHE 0.013 0.002 PHE C 57 TYR 0.017 0.001 TYR C 236 ARG 0.003 0.001 ARG C 365 *********************** 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 216 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 190 time to evaluate : 1.907 Fit side-chains REVERT: B 12 MET cc_start: 0.7340 (mmm) cc_final: 0.7084 (mtm) REVERT: B 19 ARG cc_start: 0.6730 (OUTLIER) cc_final: 0.5789 (ttm-80) REVERT: B 60 GLU cc_start: 0.6996 (tt0) cc_final: 0.6792 (tt0) REVERT: B 106 LYS cc_start: 0.7317 (mttt) cc_final: 0.6918 (mttp) REVERT: B 201 SER cc_start: 0.7950 (t) cc_final: 0.7606 (p) REVERT: B 389 ASP cc_start: 0.5667 (OUTLIER) cc_final: 0.5032 (m-30) REVERT: B 476 LYS cc_start: 0.6773 (mttp) cc_final: 0.6381 (mtpp) REVERT: B 499 LYS cc_start: 0.6988 (tttp) cc_final: 0.6306 (ttpp) REVERT: A 12 MET cc_start: 0.7310 (mmm) cc_final: 0.7073 (mtm) REVERT: A 19 ARG cc_start: 0.6737 (OUTLIER) cc_final: 0.5782 (ttm-80) REVERT: A 106 LYS cc_start: 0.7279 (mttt) cc_final: 0.6907 (mttp) REVERT: A 107 THR cc_start: 0.7260 (m) cc_final: 0.6622 (t) REVERT: A 201 SER cc_start: 0.7949 (t) cc_final: 0.7600 (p) REVERT: A 389 ASP cc_start: 0.5672 (OUTLIER) cc_final: 0.5147 (m-30) REVERT: A 476 LYS cc_start: 0.6781 (mttp) cc_final: 0.6399 (mtpp) REVERT: A 499 LYS cc_start: 0.6977 (tttp) cc_final: 0.6299 (ttpp) REVERT: C 12 MET cc_start: 0.7319 (mmm) cc_final: 0.7081 (mtm) REVERT: C 19 ARG cc_start: 0.6736 (OUTLIER) cc_final: 0.5778 (ttm-80) REVERT: C 106 LYS cc_start: 0.7279 (mttt) cc_final: 0.6910 (mttp) REVERT: C 107 THR cc_start: 0.7261 (m) cc_final: 0.6626 (t) REVERT: C 201 SER cc_start: 0.7917 (t) cc_final: 0.7635 (p) REVERT: C 389 ASP cc_start: 0.5668 (OUTLIER) cc_final: 0.5145 (m-30) REVERT: C 476 LYS cc_start: 0.6736 (mttp) cc_final: 0.6365 (mtpp) REVERT: C 499 LYS cc_start: 0.6951 (tttp) cc_final: 0.6291 (ttpp) REVERT: D 12 MET cc_start: 0.7345 (mmm) cc_final: 0.7094 (mtm) REVERT: D 19 ARG cc_start: 0.6741 (OUTLIER) cc_final: 0.5795 (ttm-80) REVERT: D 60 GLU cc_start: 0.6998 (tt0) cc_final: 0.6796 (tt0) REVERT: D 106 LYS cc_start: 0.7309 (mttt) cc_final: 0.6909 (mttp) REVERT: D 201 SER cc_start: 0.7988 (t) cc_final: 0.7651 (p) REVERT: D 255 GLN cc_start: 0.7303 (pt0) cc_final: 0.7093 (pp30) REVERT: D 389 ASP cc_start: 0.5668 (OUTLIER) cc_final: 0.5028 (m-30) REVERT: D 499 LYS cc_start: 0.6959 (tttp) cc_final: 0.6293 (ttpp) outliers start: 26 outliers final: 8 residues processed: 212 average time/residue: 1.3241 time to fit residues: 311.3493 Evaluate side-chains 176 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 160 time to evaluate : 1.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 ARG 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 19 ARG 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 19 ARG 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 19 ARG 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: 10.0000 chunk 55 optimal weight: 1.9990 chunk 148 optimal weight: 8.9990 chunk 121 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 178 optimal weight: 5.9990 chunk 192 optimal weight: 0.8980 chunk 158 optimal weight: 9.9990 chunk 176 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 143 optimal weight: 0.8980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 63 HIS B 226 ASN B 338 ASN A 63 HIS A 102 HIS A 226 ASN A 338 ASN C 63 HIS C 102 HIS C 226 ASN C 338 ASN D 63 HIS D 226 ASN D 338 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 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 : 0.004 0.064 16888 Z= 0.280 Angle : 0.605 6.786 23040 Z= 0.306 Chirality : 0.046 0.143 2328 Planarity : 0.004 0.040 3052 Dihedral : 8.966 122.583 2260 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.28 % Favored : 96.52 % Rotamer: Outliers : 2.63 % Allowed : 11.21 % Favored : 86.16 % 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: 0.37 (0.19), residues: 1980 helix: 1.02 (0.20), residues: 684 sheet: 0.49 (0.32), residues: 272 loop : -0.29 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 183 HIS 0.005 0.001 HIS C 372 PHE 0.014 0.002 PHE C 136 TYR 0.019 0.002 TYR B 236 ARG 0.004 0.001 ARG D 382 *********************** 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 227 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 182 time to evaluate : 2.044 Fit side-chains REVERT: B 12 MET cc_start: 0.7340 (mmm) cc_final: 0.6933 (mtm) REVERT: B 19 ARG cc_start: 0.6668 (OUTLIER) cc_final: 0.5827 (ttm-80) REVERT: B 60 GLU cc_start: 0.6971 (tt0) cc_final: 0.6727 (mt-10) REVERT: B 101 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7226 (tp30) REVERT: B 106 LYS cc_start: 0.7225 (mttt) cc_final: 0.6888 (mttp) REVERT: B 107 THR cc_start: 0.7264 (m) cc_final: 0.6631 (t) REVERT: B 424 GLN cc_start: 0.6554 (OUTLIER) cc_final: 0.5867 (tm-30) REVERT: B 437 ASP cc_start: 0.6407 (m-30) cc_final: 0.5920 (m-30) REVERT: B 499 LYS cc_start: 0.6958 (tttp) cc_final: 0.6305 (ttpp) REVERT: A 19 ARG cc_start: 0.6693 (OUTLIER) cc_final: 0.5838 (ttm-80) REVERT: A 101 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7215 (tp30) REVERT: A 106 LYS cc_start: 0.7217 (mttt) cc_final: 0.6884 (mttp) REVERT: A 107 THR cc_start: 0.7296 (m) cc_final: 0.6664 (t) REVERT: A 424 GLN cc_start: 0.6559 (OUTLIER) cc_final: 0.5867 (tm-30) REVERT: A 437 ASP cc_start: 0.6473 (m-30) cc_final: 0.6003 (m-30) REVERT: A 499 LYS cc_start: 0.6957 (tttp) cc_final: 0.6306 (ttpp) REVERT: C 12 MET cc_start: 0.7359 (mmm) cc_final: 0.6941 (mtm) REVERT: C 19 ARG cc_start: 0.6642 (OUTLIER) cc_final: 0.5810 (ttm-80) REVERT: C 101 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7223 (tp30) REVERT: C 106 LYS cc_start: 0.7217 (mttt) cc_final: 0.6887 (mttp) REVERT: C 107 THR cc_start: 0.7297 (m) cc_final: 0.6665 (t) REVERT: C 424 GLN cc_start: 0.6810 (OUTLIER) cc_final: 0.6437 (tm-30) REVERT: C 437 ASP cc_start: 0.6464 (m-30) cc_final: 0.5987 (m-30) REVERT: C 499 LYS cc_start: 0.6956 (tttp) cc_final: 0.6306 (ttpp) REVERT: D 12 MET cc_start: 0.7344 (mmm) cc_final: 0.6938 (mtm) REVERT: D 19 ARG cc_start: 0.6696 (OUTLIER) cc_final: 0.5843 (ttm-80) REVERT: D 60 GLU cc_start: 0.6965 (tt0) cc_final: 0.6723 (mt-10) REVERT: D 101 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7220 (tp30) REVERT: D 106 LYS cc_start: 0.7224 (mttt) cc_final: 0.6890 (mttp) REVERT: D 107 THR cc_start: 0.7273 (m) cc_final: 0.6641 (t) REVERT: D 424 GLN cc_start: 0.6577 (OUTLIER) cc_final: 0.5877 (tm-30) REVERT: D 437 ASP cc_start: 0.6482 (m-30) cc_final: 0.6008 (m-30) REVERT: D 499 LYS cc_start: 0.6955 (tttp) cc_final: 0.6304 (ttpp) outliers start: 45 outliers final: 16 residues processed: 213 average time/residue: 1.3126 time to fit residues: 309.3591 Evaluate side-chains 189 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 161 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain A residue 19 ARG Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 424 GLN Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 424 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 6.9990 chunk 134 optimal weight: 2.9990 chunk 92 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 178 optimal weight: 0.7980 chunk 189 optimal weight: 10.0000 chunk 93 optimal weight: 4.9990 chunk 169 optimal weight: 8.9990 chunk 51 optimal weight: 0.9980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 226 ASN B 305 HIS B 338 ASN A 102 HIS A 226 ASN A 305 HIS A 338 ASN C 102 HIS C 226 ASN C 305 HIS C 338 ASN D 226 ASN D 305 HIS D 338 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 16888 Z= 0.296 Angle : 0.608 7.002 23040 Z= 0.307 Chirality : 0.046 0.150 2328 Planarity : 0.005 0.045 3052 Dihedral : 9.137 126.973 2260 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.22 % Allowed : 12.50 % Favored : 85.28 % 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: 0.36 (0.19), residues: 1980 helix: 0.94 (0.20), residues: 684 sheet: 0.63 (0.33), residues: 272 loop : -0.29 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 183 HIS 0.004 0.001 HIS D 372 PHE 0.015 0.002 PHE C 136 TYR 0.019 0.002 TYR A 236 ARG 0.004 0.001 ARG A 72 *********************** 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 211 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 173 time to evaluate : 1.812 Fit side-chains REVERT: B 12 MET cc_start: 0.7442 (mmm) cc_final: 0.7070 (mtm) REVERT: B 60 GLU cc_start: 0.7119 (tt0) cc_final: 0.6877 (mt-10) REVERT: B 101 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7274 (tp30) REVERT: B 106 LYS cc_start: 0.7128 (mttt) cc_final: 0.6777 (mttp) REVERT: B 107 THR cc_start: 0.7279 (m) cc_final: 0.6665 (t) REVERT: B 201 SER cc_start: 0.7924 (OUTLIER) cc_final: 0.7639 (p) REVERT: B 249 ASP cc_start: 0.7002 (OUTLIER) cc_final: 0.6610 (t0) REVERT: B 424 GLN cc_start: 0.6593 (OUTLIER) cc_final: 0.5892 (tm-30) REVERT: B 437 ASP cc_start: 0.6575 (m-30) cc_final: 0.6057 (m-30) REVERT: B 499 LYS cc_start: 0.7004 (tttp) cc_final: 0.6358 (ttpp) REVERT: A 12 MET cc_start: 0.7431 (mmm) cc_final: 0.6972 (mtm) REVERT: A 101 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.6941 (tp30) REVERT: A 106 LYS cc_start: 0.7102 (mttt) cc_final: 0.6773 (mttp) REVERT: A 107 THR cc_start: 0.7282 (m) cc_final: 0.6671 (t) REVERT: A 201 SER cc_start: 0.7920 (OUTLIER) cc_final: 0.7640 (p) REVERT: A 249 ASP cc_start: 0.7110 (m-30) cc_final: 0.6532 (t0) REVERT: A 298 ASP cc_start: 0.7987 (t0) cc_final: 0.7650 (t0) REVERT: A 424 GLN cc_start: 0.6592 (OUTLIER) cc_final: 0.5912 (tm-30) REVERT: A 437 ASP cc_start: 0.6565 (m-30) cc_final: 0.6024 (m-30) REVERT: A 499 LYS cc_start: 0.7018 (tttp) cc_final: 0.6363 (ttpp) REVERT: C 12 MET cc_start: 0.7451 (mmm) cc_final: 0.7076 (mtm) REVERT: C 101 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7092 (tp30) REVERT: C 106 LYS cc_start: 0.7104 (mttt) cc_final: 0.6776 (mttp) REVERT: C 107 THR cc_start: 0.7285 (m) cc_final: 0.6673 (t) REVERT: C 119 GLU cc_start: 0.6738 (OUTLIER) cc_final: 0.6437 (mp0) REVERT: C 201 SER cc_start: 0.7931 (OUTLIER) cc_final: 0.7648 (p) REVERT: C 249 ASP cc_start: 0.7089 (m-30) cc_final: 0.6521 (t0) REVERT: C 298 ASP cc_start: 0.7984 (t0) cc_final: 0.7688 (t0) REVERT: C 437 ASP cc_start: 0.6565 (m-30) cc_final: 0.6012 (m-30) REVERT: C 499 LYS cc_start: 0.7009 (tttp) cc_final: 0.6365 (ttpp) REVERT: D 12 MET cc_start: 0.7445 (mmm) cc_final: 0.7072 (mtm) REVERT: D 60 GLU cc_start: 0.7115 (tt0) cc_final: 0.6871 (mt-10) REVERT: D 101 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7258 (tp30) REVERT: D 106 LYS cc_start: 0.7129 (mttt) cc_final: 0.6782 (mttp) REVERT: D 107 THR cc_start: 0.7283 (m) cc_final: 0.6673 (t) REVERT: D 201 SER cc_start: 0.7925 (OUTLIER) cc_final: 0.7644 (p) REVERT: D 298 ASP cc_start: 0.7984 (t0) cc_final: 0.7685 (t0) REVERT: D 424 GLN cc_start: 0.6593 (OUTLIER) cc_final: 0.5914 (tm-30) REVERT: D 437 ASP cc_start: 0.6570 (m-30) cc_final: 0.6028 (m-30) REVERT: D 499 LYS cc_start: 0.7003 (tttp) cc_final: 0.6358 (ttpp) outliers start: 38 outliers final: 16 residues processed: 205 average time/residue: 1.3568 time to fit residues: 307.7713 Evaluate side-chains 199 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 170 time to evaluate : 1.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 424 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 4.9990 chunk 107 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 chunk 78 optimal weight: 0.5980 chunk 161 optimal weight: 0.4980 chunk 130 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 96 optimal weight: 7.9990 chunk 170 optimal weight: 6.9990 chunk 47 optimal weight: 7.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 226 ASN A 226 ASN C 226 ASN D 226 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 16888 Z= 0.265 Angle : 0.587 6.927 23040 Z= 0.295 Chirality : 0.045 0.148 2328 Planarity : 0.005 0.047 3052 Dihedral : 8.980 128.767 2260 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.80 % Allowed : 13.14 % 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: 0.36 (0.19), residues: 1980 helix: 0.95 (0.20), residues: 684 sheet: 0.57 (0.33), residues: 276 loop : -0.27 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 183 HIS 0.003 0.001 HIS B 75 PHE 0.014 0.002 PHE D 136 TYR 0.018 0.002 TYR B 236 ARG 0.003 0.000 ARG A 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 229 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 181 time to evaluate : 2.181 Fit side-chains REVERT: B 12 MET cc_start: 0.7399 (mmm) cc_final: 0.7096 (mtm) REVERT: B 23 LYS cc_start: 0.7165 (pttm) cc_final: 0.6946 (ptmt) REVERT: B 60 GLU cc_start: 0.7125 (tt0) cc_final: 0.6815 (mt-10) REVERT: B 101 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.6962 (tp30) REVERT: B 106 LYS cc_start: 0.7096 (mttt) cc_final: 0.6786 (mttp) REVERT: B 107 THR cc_start: 0.7263 (m) cc_final: 0.6673 (t) REVERT: B 119 GLU cc_start: 0.6807 (mt-10) cc_final: 0.6462 (mp0) REVERT: B 191 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.6907 (pm20) REVERT: B 249 ASP cc_start: 0.7017 (OUTLIER) cc_final: 0.6621 (t0) REVERT: B 298 ASP cc_start: 0.7982 (t0) cc_final: 0.7681 (t0) REVERT: B 424 GLN cc_start: 0.6620 (OUTLIER) cc_final: 0.5910 (tm-30) REVERT: B 437 ASP cc_start: 0.6585 (m-30) cc_final: 0.6040 (m-30) REVERT: B 499 LYS cc_start: 0.7021 (tttp) cc_final: 0.6365 (ttpp) REVERT: A 12 MET cc_start: 0.7398 (mmm) cc_final: 0.7076 (mtm) REVERT: A 101 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.6907 (tp30) REVERT: A 106 LYS cc_start: 0.7087 (mttt) cc_final: 0.6782 (mttp) REVERT: A 107 THR cc_start: 0.7268 (m) cc_final: 0.6665 (t) REVERT: A 119 GLU cc_start: 0.6789 (mt-10) cc_final: 0.6399 (mp0) REVERT: A 191 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.6908 (pm20) REVERT: A 249 ASP cc_start: 0.7051 (OUTLIER) cc_final: 0.6630 (t0) REVERT: A 298 ASP cc_start: 0.7982 (t0) cc_final: 0.7649 (t0) REVERT: A 424 GLN cc_start: 0.6618 (OUTLIER) cc_final: 0.5907 (tm-30) REVERT: A 437 ASP cc_start: 0.6579 (m-30) cc_final: 0.5998 (m-30) REVERT: A 458 ARG cc_start: 0.6812 (mtm-85) cc_final: 0.6377 (mtm180) REVERT: A 499 LYS cc_start: 0.7035 (tttp) cc_final: 0.6370 (ttpp) REVERT: C 12 MET cc_start: 0.7410 (mmm) cc_final: 0.7106 (mtm) REVERT: C 101 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.6934 (tp30) REVERT: C 106 LYS cc_start: 0.7090 (mttt) cc_final: 0.6785 (mttp) REVERT: C 107 THR cc_start: 0.7267 (m) cc_final: 0.6666 (t) REVERT: C 191 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.6909 (pm20) REVERT: C 249 ASP cc_start: 0.7045 (OUTLIER) cc_final: 0.6445 (t0) REVERT: C 298 ASP cc_start: 0.7984 (t0) cc_final: 0.7653 (t0) REVERT: C 437 ASP cc_start: 0.6580 (m-30) cc_final: 0.6015 (m-30) REVERT: C 458 ARG cc_start: 0.6907 (mtm-85) cc_final: 0.6466 (mtm180) REVERT: C 499 LYS cc_start: 0.7036 (tttp) cc_final: 0.6372 (ttpp) REVERT: D 12 MET cc_start: 0.7401 (mmm) cc_final: 0.7105 (mtm) REVERT: D 60 GLU cc_start: 0.7119 (tt0) cc_final: 0.6849 (mt-10) REVERT: D 101 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.6959 (tp30) REVERT: D 106 LYS cc_start: 0.7099 (mttt) cc_final: 0.6791 (mttp) REVERT: D 107 THR cc_start: 0.7269 (m) cc_final: 0.6680 (t) REVERT: D 119 GLU cc_start: 0.6807 (mt-10) cc_final: 0.6462 (mp0) REVERT: D 191 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.6907 (pm20) REVERT: D 298 ASP cc_start: 0.7984 (t0) cc_final: 0.7682 (t0) REVERT: D 424 GLN cc_start: 0.6618 (OUTLIER) cc_final: 0.5909 (tm-30) REVERT: D 437 ASP cc_start: 0.6585 (m-30) cc_final: 0.6016 (m-30) REVERT: D 458 ARG cc_start: 0.6913 (mtm-85) cc_final: 0.6475 (mtm180) REVERT: D 499 LYS cc_start: 0.7019 (tttp) cc_final: 0.6363 (ttpp) outliers start: 48 outliers final: 20 residues processed: 215 average time/residue: 1.3836 time to fit residues: 328.3964 Evaluate side-chains 210 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 176 time to evaluate : 1.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 424 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 1.9990 chunk 170 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 chunk 46 optimal weight: 8.9990 chunk 189 optimal weight: 3.9990 chunk 157 optimal weight: 4.9990 chunk 87 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 226 ASN B 235 HIS A 226 ASN A 235 HIS C 226 ASN C 235 HIS D 226 ASN D 235 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 16888 Z= 0.336 Angle : 0.636 7.792 23040 Z= 0.319 Chirality : 0.047 0.156 2328 Planarity : 0.005 0.047 3052 Dihedral : 9.434 136.203 2260 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.04 % Allowed : 12.21 % 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: 0.22 (0.19), residues: 1980 helix: 0.80 (0.20), residues: 684 sheet: 0.56 (0.33), residues: 272 loop : -0.35 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 183 HIS 0.004 0.001 HIS D 75 PHE 0.015 0.002 PHE D 136 TYR 0.020 0.002 TYR C 236 ARG 0.004 0.001 ARG C 72 *********************** 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 217 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 165 time to evaluate : 1.889 Fit side-chains REVERT: B 23 LYS cc_start: 0.7138 (pttm) cc_final: 0.6932 (ptmt) REVERT: B 60 GLU cc_start: 0.7134 (tt0) cc_final: 0.6817 (mt-10) REVERT: B 101 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.6987 (tp30) REVERT: B 106 LYS cc_start: 0.7091 (mttt) cc_final: 0.6812 (mttp) REVERT: B 107 THR cc_start: 0.7273 (m) cc_final: 0.6670 (t) REVERT: B 119 GLU cc_start: 0.6764 (OUTLIER) cc_final: 0.6450 (mp0) REVERT: B 191 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.6959 (pm20) REVERT: B 249 ASP cc_start: 0.7015 (OUTLIER) cc_final: 0.6607 (t0) REVERT: B 424 GLN cc_start: 0.6746 (OUTLIER) cc_final: 0.5991 (tm-30) REVERT: B 437 ASP cc_start: 0.6684 (m-30) cc_final: 0.6252 (m-30) REVERT: B 457 LYS cc_start: 0.7301 (OUTLIER) cc_final: 0.7012 (ttmm) REVERT: B 458 ARG cc_start: 0.6934 (ttp-170) cc_final: 0.6553 (mtm180) REVERT: B 499 LYS cc_start: 0.6933 (tttp) cc_final: 0.6302 (ttpp) REVERT: A 12 MET cc_start: 0.7478 (mmm) cc_final: 0.7106 (mtm) REVERT: A 101 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.6977 (tp30) REVERT: A 106 LYS cc_start: 0.7096 (mttt) cc_final: 0.6824 (mttp) REVERT: A 107 THR cc_start: 0.7278 (m) cc_final: 0.6681 (t) REVERT: A 119 GLU cc_start: 0.6760 (OUTLIER) cc_final: 0.6444 (mp0) REVERT: A 191 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.6960 (pm20) REVERT: A 249 ASP cc_start: 0.7047 (OUTLIER) cc_final: 0.6609 (t0) REVERT: A 298 ASP cc_start: 0.7992 (t0) cc_final: 0.7666 (t0) REVERT: A 424 GLN cc_start: 0.6743 (OUTLIER) cc_final: 0.5985 (tm-30) REVERT: A 437 ASP cc_start: 0.6678 (m-30) cc_final: 0.6228 (m-30) REVERT: A 458 ARG cc_start: 0.6853 (mtm-85) cc_final: 0.6417 (mtm180) REVERT: A 499 LYS cc_start: 0.7005 (tttp) cc_final: 0.6355 (ttpp) REVERT: C 12 MET cc_start: 0.7458 (mmm) cc_final: 0.7114 (mtm) REVERT: C 101 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.6981 (tp30) REVERT: C 106 LYS cc_start: 0.7099 (mttt) cc_final: 0.6827 (mttp) REVERT: C 107 THR cc_start: 0.7279 (m) cc_final: 0.6682 (t) REVERT: C 119 GLU cc_start: 0.6838 (OUTLIER) cc_final: 0.6504 (mp0) REVERT: C 191 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.6971 (pm20) REVERT: C 249 ASP cc_start: 0.7045 (OUTLIER) cc_final: 0.6604 (t0) REVERT: C 298 ASP cc_start: 0.7994 (t0) cc_final: 0.7673 (t0) REVERT: C 437 ASP cc_start: 0.6678 (m-30) cc_final: 0.6230 (m-30) REVERT: C 457 LYS cc_start: 0.7294 (OUTLIER) cc_final: 0.6980 (ttmm) REVERT: C 458 ARG cc_start: 0.6835 (mtm-85) cc_final: 0.6401 (mtm180) REVERT: C 499 LYS cc_start: 0.7006 (tttp) cc_final: 0.6357 (ttpp) REVERT: D 60 GLU cc_start: 0.7208 (tt0) cc_final: 0.6950 (mt-10) REVERT: D 101 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.6985 (tp30) REVERT: D 106 LYS cc_start: 0.7098 (mttt) cc_final: 0.6821 (mttp) REVERT: D 107 THR cc_start: 0.7279 (m) cc_final: 0.6677 (t) REVERT: D 119 GLU cc_start: 0.6763 (OUTLIER) cc_final: 0.6449 (mp0) REVERT: D 191 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.6960 (pm20) REVERT: D 249 ASP cc_start: 0.7041 (OUTLIER) cc_final: 0.6615 (t0) REVERT: D 298 ASP cc_start: 0.7994 (t0) cc_final: 0.7699 (t0) REVERT: D 424 GLN cc_start: 0.6743 (OUTLIER) cc_final: 0.5989 (tm-30) REVERT: D 437 ASP cc_start: 0.6683 (m-30) cc_final: 0.6230 (m-30) REVERT: D 457 LYS cc_start: 0.7291 (OUTLIER) cc_final: 0.6976 (ttmm) REVERT: D 458 ARG cc_start: 0.6840 (mtm-85) cc_final: 0.6411 (mtm180) REVERT: D 499 LYS cc_start: 0.6998 (tttp) cc_final: 0.6351 (ttpp) outliers start: 52 outliers final: 24 residues processed: 202 average time/residue: 1.4121 time to fit residues: 314.1003 Evaluate side-chains 213 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 167 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain B residue 457 LYS Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 457 LYS Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 249 ASP Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain D residue 361 THR Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 424 GLN Chi-restraints excluded: chain D residue 457 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 159 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 188 optimal weight: 9.9990 chunk 118 optimal weight: 6.9990 chunk 115 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 102 HIS B 226 ASN A 226 ASN C 226 ASN D 226 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16888 Z= 0.224 Angle : 0.569 7.397 23040 Z= 0.285 Chirality : 0.044 0.144 2328 Planarity : 0.004 0.044 3052 Dihedral : 8.940 133.077 2260 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.63 % Allowed : 12.73 % Favored : 84.64 % 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: 0.36 (0.19), residues: 1980 helix: 0.92 (0.20), residues: 684 sheet: 0.47 (0.33), residues: 276 loop : -0.21 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 183 HIS 0.004 0.001 HIS C 235 PHE 0.013 0.002 PHE A 136 TYR 0.017 0.002 TYR A 236 ARG 0.003 0.000 ARG C 363 *********************** 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 229 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 184 time to evaluate : 1.747 Fit side-chains REVERT: B 12 MET cc_start: 0.7330 (mmm) cc_final: 0.6888 (mtm) REVERT: B 23 LYS cc_start: 0.7174 (pttm) cc_final: 0.6935 (ptmt) REVERT: B 60 GLU cc_start: 0.7110 (tt0) cc_final: 0.6789 (mt-10) REVERT: B 101 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7040 (tp30) REVERT: B 106 LYS cc_start: 0.7076 (mttt) cc_final: 0.6813 (mttp) REVERT: B 107 THR cc_start: 0.7285 (m) cc_final: 0.6710 (t) REVERT: B 119 GLU cc_start: 0.6762 (mt-10) cc_final: 0.6428 (mp0) REVERT: B 249 ASP cc_start: 0.7017 (OUTLIER) cc_final: 0.6608 (t0) REVERT: B 298 ASP cc_start: 0.7973 (t0) cc_final: 0.7656 (t0) REVERT: B 424 GLN cc_start: 0.6725 (OUTLIER) cc_final: 0.5977 (tm-30) REVERT: B 437 ASP cc_start: 0.6600 (m-30) cc_final: 0.6039 (m-30) REVERT: B 458 ARG cc_start: 0.6973 (ttp-170) cc_final: 0.6549 (mtm180) REVERT: B 499 LYS cc_start: 0.7027 (tttp) cc_final: 0.6306 (ttpp) REVERT: A 106 LYS cc_start: 0.7075 (mttt) cc_final: 0.6812 (mttp) REVERT: A 107 THR cc_start: 0.7290 (m) cc_final: 0.6713 (t) REVERT: A 119 GLU cc_start: 0.6752 (mt-10) cc_final: 0.6410 (mp0) REVERT: A 298 ASP cc_start: 0.8003 (t0) cc_final: 0.7631 (t0) REVERT: A 424 GLN cc_start: 0.6725 (OUTLIER) cc_final: 0.5973 (tm-30) REVERT: A 437 ASP cc_start: 0.6594 (m-30) cc_final: 0.6034 (m-30) REVERT: A 499 LYS cc_start: 0.7034 (tttp) cc_final: 0.6312 (ttpp) REVERT: C 23 LYS cc_start: 0.7010 (pttm) cc_final: 0.6806 (ptmt) REVERT: C 101 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.6959 (tp30) REVERT: C 106 LYS cc_start: 0.7077 (mttt) cc_final: 0.6811 (mttp) REVERT: C 107 THR cc_start: 0.7288 (m) cc_final: 0.6711 (t) REVERT: C 298 ASP cc_start: 0.8000 (t0) cc_final: 0.7634 (t0) REVERT: C 394 MET cc_start: 0.7159 (tpp) cc_final: 0.6602 (mpt) REVERT: C 437 ASP cc_start: 0.6647 (m-30) cc_final: 0.6200 (m-30) REVERT: C 499 LYS cc_start: 0.7033 (tttp) cc_final: 0.6313 (ttpp) REVERT: D 12 MET cc_start: 0.7335 (mmm) cc_final: 0.6895 (mtm) REVERT: D 60 GLU cc_start: 0.7106 (tt0) cc_final: 0.6787 (mt-10) REVERT: D 101 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7051 (tp30) REVERT: D 106 LYS cc_start: 0.7076 (mttt) cc_final: 0.6814 (mttp) REVERT: D 107 THR cc_start: 0.7286 (m) cc_final: 0.6712 (t) REVERT: D 119 GLU cc_start: 0.6762 (mt-10) cc_final: 0.6430 (mp0) REVERT: D 249 ASP cc_start: 0.7045 (OUTLIER) cc_final: 0.6614 (t0) REVERT: D 298 ASP cc_start: 0.7973 (t0) cc_final: 0.7658 (t0) REVERT: D 394 MET cc_start: 0.7175 (OUTLIER) cc_final: 0.6531 (mpp) REVERT: D 424 GLN cc_start: 0.6724 (OUTLIER) cc_final: 0.5973 (tm-30) REVERT: D 437 ASP cc_start: 0.6651 (m-30) cc_final: 0.6201 (m-30) REVERT: D 457 LYS cc_start: 0.7261 (OUTLIER) cc_final: 0.6953 (ttmm) REVERT: D 499 LYS cc_start: 0.7024 (tttp) cc_final: 0.6306 (ttpp) outliers start: 45 outliers final: 24 residues processed: 213 average time/residue: 1.3030 time to fit residues: 307.9337 Evaluate side-chains 203 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 169 time to evaluate : 1.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 249 ASP Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain D residue 361 THR Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 394 MET Chi-restraints excluded: chain D residue 424 GLN Chi-restraints excluded: chain D residue 457 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 112 optimal weight: 8.9990 chunk 56 optimal weight: 0.1980 chunk 37 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 120 optimal weight: 9.9990 chunk 128 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 148 optimal weight: 0.3980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 226 ASN B 439 ASN A 102 HIS A 226 ASN A 439 ASN C 102 HIS C 226 ASN C 439 ASN D 226 ASN D 439 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16888 Z= 0.222 Angle : 0.570 9.648 23040 Z= 0.286 Chirality : 0.044 0.142 2328 Planarity : 0.004 0.044 3052 Dihedral : 8.909 132.953 2260 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.75 % Allowed : 12.85 % Favored : 84.40 % 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: 0.40 (0.19), residues: 1980 helix: 0.96 (0.20), residues: 684 sheet: 0.49 (0.33), residues: 276 loop : -0.20 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 183 HIS 0.004 0.001 HIS A 235 PHE 0.013 0.002 PHE C 136 TYR 0.017 0.002 TYR A 236 ARG 0.003 0.000 ARG D 382 *********************** 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 215 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 168 time to evaluate : 1.745 Fit side-chains REVERT: B 23 LYS cc_start: 0.7194 (pttm) cc_final: 0.6964 (ptmt) REVERT: B 60 GLU cc_start: 0.7104 (tt0) cc_final: 0.6814 (mt-10) REVERT: B 101 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7043 (tp30) REVERT: B 106 LYS cc_start: 0.7074 (mttt) cc_final: 0.6816 (mttp) REVERT: B 107 THR cc_start: 0.7188 (m) cc_final: 0.6616 (t) REVERT: B 119 GLU cc_start: 0.6762 (mt-10) cc_final: 0.6418 (mp0) REVERT: B 191 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.6863 (pm20) REVERT: B 249 ASP cc_start: 0.7016 (OUTLIER) cc_final: 0.6603 (t0) REVERT: B 298 ASP cc_start: 0.7930 (t0) cc_final: 0.7613 (t0) REVERT: B 424 GLN cc_start: 0.6719 (OUTLIER) cc_final: 0.5976 (tm-30) REVERT: B 437 ASP cc_start: 0.6657 (m-30) cc_final: 0.6184 (m-30) REVERT: B 458 ARG cc_start: 0.6991 (ttp-170) cc_final: 0.6525 (mtm180) REVERT: B 499 LYS cc_start: 0.6963 (tttp) cc_final: 0.6257 (ttpp) REVERT: A 101 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.6931 (tp30) REVERT: A 106 LYS cc_start: 0.7087 (mttt) cc_final: 0.6815 (mttp) REVERT: A 107 THR cc_start: 0.7194 (m) cc_final: 0.6614 (t) REVERT: A 119 GLU cc_start: 0.6756 (mt-10) cc_final: 0.6415 (mp0) REVERT: A 249 ASP cc_start: 0.7082 (OUTLIER) cc_final: 0.6626 (t0) REVERT: A 298 ASP cc_start: 0.7934 (t0) cc_final: 0.7616 (t0) REVERT: A 394 MET cc_start: 0.7219 (OUTLIER) cc_final: 0.6659 (mpp) REVERT: A 424 GLN cc_start: 0.6725 (OUTLIER) cc_final: 0.5979 (tm-30) REVERT: A 437 ASP cc_start: 0.6659 (m-30) cc_final: 0.6189 (m-30) REVERT: A 458 ARG cc_start: 0.7004 (mtp180) cc_final: 0.6645 (mtm180) REVERT: A 499 LYS cc_start: 0.7039 (tttp) cc_final: 0.6313 (ttpp) REVERT: C 12 MET cc_start: 0.7161 (OUTLIER) cc_final: 0.6960 (mtm) REVERT: C 101 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7047 (tp30) REVERT: C 106 LYS cc_start: 0.7088 (mttt) cc_final: 0.6821 (mttp) REVERT: C 107 THR cc_start: 0.7195 (m) cc_final: 0.6616 (t) REVERT: C 124 ASP cc_start: 0.7197 (t0) cc_final: 0.6928 (t0) REVERT: C 191 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.6866 (pm20) REVERT: C 249 ASP cc_start: 0.7079 (OUTLIER) cc_final: 0.6632 (t0) REVERT: C 298 ASP cc_start: 0.7937 (t0) cc_final: 0.7622 (t0) REVERT: C 437 ASP cc_start: 0.6668 (m-30) cc_final: 0.6197 (m-30) REVERT: C 457 LYS cc_start: 0.7272 (OUTLIER) cc_final: 0.6993 (ttmm) REVERT: C 458 ARG cc_start: 0.6985 (mtp180) cc_final: 0.6640 (mtm180) REVERT: C 499 LYS cc_start: 0.7040 (tttp) cc_final: 0.6315 (ttpp) REVERT: D 60 GLU cc_start: 0.7099 (tt0) cc_final: 0.6821 (mt-10) REVERT: D 101 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7054 (tp30) REVERT: D 106 LYS cc_start: 0.7145 (mttt) cc_final: 0.6857 (mttp) REVERT: D 107 THR cc_start: 0.7265 (m) cc_final: 0.6685 (t) REVERT: D 119 GLU cc_start: 0.6765 (mt-10) cc_final: 0.6420 (mp0) REVERT: D 191 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.6844 (pm20) REVERT: D 249 ASP cc_start: 0.7038 (OUTLIER) cc_final: 0.6604 (t0) REVERT: D 298 ASP cc_start: 0.7907 (t0) cc_final: 0.7610 (t0) REVERT: D 424 GLN cc_start: 0.6725 (OUTLIER) cc_final: 0.5980 (tm-30) REVERT: D 437 ASP cc_start: 0.6654 (m-30) cc_final: 0.6181 (m-30) REVERT: D 457 LYS cc_start: 0.7271 (OUTLIER) cc_final: 0.6988 (ttmm) REVERT: D 458 ARG cc_start: 0.6984 (mtp180) cc_final: 0.6640 (mtm180) REVERT: D 499 LYS cc_start: 0.6962 (tttp) cc_final: 0.6258 (ttpp) outliers start: 47 outliers final: 26 residues processed: 195 average time/residue: 1.4365 time to fit residues: 309.1236 Evaluate side-chains 211 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 167 time to evaluate : 1.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain C residue 12 MET Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 457 LYS Chi-restraints excluded: chain D residue 23 LYS Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 249 ASP Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain D residue 361 THR Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 424 GLN Chi-restraints excluded: chain D residue 457 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 10.0000 chunk 180 optimal weight: 0.0030 chunk 165 optimal weight: 2.9990 chunk 176 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 chunk 76 optimal weight: 0.4980 chunk 138 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 159 optimal weight: 2.9990 chunk 166 optimal weight: 0.6980 chunk 175 optimal weight: 0.9990 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 226 ASN A 226 ASN C 226 ASN D 102 HIS D 226 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 16888 Z= 0.151 Angle : 0.520 7.665 23040 Z= 0.260 Chirality : 0.043 0.137 2328 Planarity : 0.004 0.042 3052 Dihedral : 8.166 125.260 2260 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.87 % Allowed : 13.90 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.19), residues: 1980 helix: 1.19 (0.20), residues: 680 sheet: 0.65 (0.33), residues: 276 loop : -0.11 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 183 HIS 0.004 0.001 HIS D 102 PHE 0.011 0.001 PHE B 473 TYR 0.015 0.001 TYR A 236 ARG 0.003 0.000 ARG D 382 *********************** 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 229 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 197 time to evaluate : 1.884 Fit side-chains REVERT: B 60 GLU cc_start: 0.7021 (tt0) cc_final: 0.6768 (tt0) REVERT: B 106 LYS cc_start: 0.7096 (mttt) cc_final: 0.6834 (mttp) REVERT: B 107 THR cc_start: 0.7286 (m) cc_final: 0.6755 (t) REVERT: B 119 GLU cc_start: 0.6653 (mt-10) cc_final: 0.6388 (mp0) REVERT: B 249 ASP cc_start: 0.7073 (m-30) cc_final: 0.6595 (t0) REVERT: B 298 ASP cc_start: 0.7924 (t0) cc_final: 0.7592 (t0) REVERT: B 424 GLN cc_start: 0.6652 (OUTLIER) cc_final: 0.5909 (tm-30) REVERT: B 437 ASP cc_start: 0.6562 (m-30) cc_final: 0.5978 (m-30) REVERT: B 458 ARG cc_start: 0.6977 (ttp-170) cc_final: 0.6550 (mtm180) REVERT: B 499 LYS cc_start: 0.6939 (tttp) cc_final: 0.6245 (ttpp) REVERT: A 106 LYS cc_start: 0.7141 (mttt) cc_final: 0.6857 (mttp) REVERT: A 107 THR cc_start: 0.7286 (m) cc_final: 0.6748 (t) REVERT: A 119 GLU cc_start: 0.6641 (mt-10) cc_final: 0.6383 (mp0) REVERT: A 249 ASP cc_start: 0.7083 (m-30) cc_final: 0.6512 (t0) REVERT: A 298 ASP cc_start: 0.7853 (t0) cc_final: 0.7516 (t0) REVERT: A 424 GLN cc_start: 0.6664 (OUTLIER) cc_final: 0.5915 (tm-30) REVERT: A 437 ASP cc_start: 0.6564 (m-30) cc_final: 0.5985 (m-30) REVERT: A 458 ARG cc_start: 0.7055 (mtp180) cc_final: 0.6684 (mtm180) REVERT: A 499 LYS cc_start: 0.6969 (tttp) cc_final: 0.6275 (ttpp) REVERT: C 106 LYS cc_start: 0.7144 (mttt) cc_final: 0.6863 (mttp) REVERT: C 107 THR cc_start: 0.7285 (m) cc_final: 0.6746 (t) REVERT: C 249 ASP cc_start: 0.7078 (m-30) cc_final: 0.6511 (t0) REVERT: C 298 ASP cc_start: 0.7855 (t0) cc_final: 0.7519 (t0) REVERT: C 437 ASP cc_start: 0.6548 (m-30) cc_final: 0.5963 (m-30) REVERT: C 458 ARG cc_start: 0.7061 (mtp180) cc_final: 0.6690 (mtm180) REVERT: C 499 LYS cc_start: 0.6970 (tttp) cc_final: 0.6277 (ttpp) REVERT: D 60 GLU cc_start: 0.7067 (tt0) cc_final: 0.6820 (tt0) REVERT: D 106 LYS cc_start: 0.7142 (mttt) cc_final: 0.6864 (mttp) REVERT: D 107 THR cc_start: 0.7283 (m) cc_final: 0.6744 (t) REVERT: D 119 GLU cc_start: 0.6657 (mt-10) cc_final: 0.6391 (mp0) REVERT: D 249 ASP cc_start: 0.7070 (m-30) cc_final: 0.6528 (t0) REVERT: D 298 ASP cc_start: 0.7853 (t0) cc_final: 0.7514 (t0) REVERT: D 424 GLN cc_start: 0.6667 (OUTLIER) cc_final: 0.5917 (tm-30) REVERT: D 437 ASP cc_start: 0.6561 (m-30) cc_final: 0.5979 (m-30) REVERT: D 457 LYS cc_start: 0.7311 (OUTLIER) cc_final: 0.7020 (tttm) REVERT: D 458 ARG cc_start: 0.7051 (mtp180) cc_final: 0.6711 (mtm180) REVERT: D 499 LYS cc_start: 0.6938 (tttp) cc_final: 0.6245 (ttpp) outliers start: 32 outliers final: 19 residues processed: 217 average time/residue: 1.2805 time to fit residues: 308.6429 Evaluate side-chains 195 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 172 time to evaluate : 1.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 361 THR Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 424 GLN Chi-restraints excluded: chain D residue 457 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 3.9990 chunk 186 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 195 optimal weight: 0.9990 chunk 179 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 16 optimal weight: 0.0980 chunk 120 optimal weight: 7.9990 chunk 95 optimal weight: 9.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 102 HIS B 226 ASN A 226 ASN C 102 HIS C 226 ASN D 226 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 16888 Z= 0.229 Angle : 0.577 8.420 23040 Z= 0.288 Chirality : 0.044 0.141 2328 Planarity : 0.004 0.044 3052 Dihedral : 8.722 129.116 2260 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.64 % Allowed : 14.60 % 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: 0.56 (0.19), residues: 1980 helix: 1.10 (0.20), residues: 684 sheet: 0.58 (0.33), residues: 276 loop : -0.10 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 183 HIS 0.005 0.001 HIS C 102 PHE 0.014 0.002 PHE C 136 TYR 0.018 0.002 TYR B 236 ARG 0.003 0.000 ARG D 382 ********************** 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 194 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 166 time to evaluate : 1.851 Fit side-chains REVERT: B 60 GLU cc_start: 0.7096 (tt0) cc_final: 0.6832 (mt-10) REVERT: B 106 LYS cc_start: 0.7074 (mttt) cc_final: 0.6805 (mttp) REVERT: B 107 THR cc_start: 0.7224 (m) cc_final: 0.6650 (t) REVERT: B 119 GLU cc_start: 0.6718 (OUTLIER) cc_final: 0.6363 (mp0) REVERT: B 298 ASP cc_start: 0.7918 (t0) cc_final: 0.7633 (t0) REVERT: B 424 GLN cc_start: 0.6671 (OUTLIER) cc_final: 0.5925 (tm-30) REVERT: B 437 ASP cc_start: 0.6665 (m-30) cc_final: 0.6202 (m-30) REVERT: B 458 ARG cc_start: 0.6987 (ttp-170) cc_final: 0.6557 (mtm180) REVERT: B 499 LYS cc_start: 0.6930 (tttp) cc_final: 0.6251 (ttpp) REVERT: A 106 LYS cc_start: 0.7110 (mttt) cc_final: 0.6839 (mttp) REVERT: A 107 THR cc_start: 0.7229 (m) cc_final: 0.6648 (t) REVERT: A 119 GLU cc_start: 0.6705 (mt-10) cc_final: 0.6355 (mp0) REVERT: A 191 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.6838 (pm20) REVERT: A 298 ASP cc_start: 0.7946 (t0) cc_final: 0.7613 (t0) REVERT: A 424 GLN cc_start: 0.6690 (OUTLIER) cc_final: 0.5935 (tm-30) REVERT: A 437 ASP cc_start: 0.6661 (m-30) cc_final: 0.6198 (m-30) REVERT: A 458 ARG cc_start: 0.7066 (mtp180) cc_final: 0.6674 (mtm180) REVERT: A 499 LYS cc_start: 0.6939 (tttp) cc_final: 0.6258 (ttpp) REVERT: C 106 LYS cc_start: 0.7110 (mttt) cc_final: 0.6840 (mttp) REVERT: C 107 THR cc_start: 0.7229 (m) cc_final: 0.6651 (t) REVERT: C 298 ASP cc_start: 0.7947 (t0) cc_final: 0.7617 (t0) REVERT: C 437 ASP cc_start: 0.6644 (m-30) cc_final: 0.6194 (m-30) REVERT: C 458 ARG cc_start: 0.7051 (mtp180) cc_final: 0.6667 (mtm180) REVERT: C 499 LYS cc_start: 0.6942 (tttp) cc_final: 0.6262 (ttpp) REVERT: D 60 GLU cc_start: 0.7094 (tt0) cc_final: 0.6864 (mt-10) REVERT: D 106 LYS cc_start: 0.7113 (mttt) cc_final: 0.6839 (mttp) REVERT: D 107 THR cc_start: 0.7228 (m) cc_final: 0.6647 (t) REVERT: D 119 GLU cc_start: 0.6716 (OUTLIER) cc_final: 0.6297 (mp0) REVERT: D 298 ASP cc_start: 0.7924 (t0) cc_final: 0.7637 (t0) REVERT: D 424 GLN cc_start: 0.6688 (OUTLIER) cc_final: 0.5935 (tm-30) REVERT: D 437 ASP cc_start: 0.6662 (m-30) cc_final: 0.6198 (m-30) REVERT: D 457 LYS cc_start: 0.7254 (OUTLIER) cc_final: 0.6986 (ttmm) REVERT: D 499 LYS cc_start: 0.6930 (tttp) cc_final: 0.6252 (ttpp) outliers start: 28 outliers final: 20 residues processed: 185 average time/residue: 1.3340 time to fit residues: 273.9766 Evaluate side-chains 192 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 165 time to evaluate : 1.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 361 THR Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 424 GLN Chi-restraints excluded: chain D residue 457 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 5.9990 chunk 165 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 143 optimal weight: 0.9980 chunk 22 optimal weight: 9.9990 chunk 43 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 chunk 65 optimal weight: 0.5980 chunk 159 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 226 ASN A 226 ASN C 226 ASN D 226 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.132066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.112402 restraints weight = 18934.762| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.26 r_work: 0.3142 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16888 Z= 0.170 Angle : 0.533 6.553 23040 Z= 0.267 Chirality : 0.043 0.136 2328 Planarity : 0.004 0.042 3052 Dihedral : 8.244 124.572 2260 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.58 % Allowed : 14.54 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.19), residues: 1980 helix: 1.21 (0.20), residues: 680 sheet: 0.48 (0.32), residues: 304 loop : 0.06 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 183 HIS 0.003 0.001 HIS D 235 PHE 0.012 0.001 PHE D 409 TYR 0.016 0.001 TYR A 236 ARG 0.003 0.000 ARG D 382 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5629.99 seconds wall clock time: 99 minutes 22.00 seconds (5962.00 seconds total)