Starting phenix.real_space_refine on Sat Apr 6 17:34:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6avb_7008/04_2024/6avb_7008_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6avb_7008/04_2024/6avb_7008.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6avb_7008/04_2024/6avb_7008.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6avb_7008/04_2024/6avb_7008.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6avb_7008/04_2024/6avb_7008_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6avb_7008/04_2024/6avb_7008_updated.pdb" } resolution = 3.9 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 ------------------------------------------------------------------------------- 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 60 5.16 5 C 5469 2.51 5 N 1458 2.21 5 O 1680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 8673 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 2864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2864 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 19, 'TRANS': 347} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'SME:plan-1': 2, 'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 2864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2864 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 19, 'TRANS': 347} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'SME:plan-1': 2, 'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2864 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 19, 'TRANS': 347} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'SME:plan-1': 2, 'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.20, per 1000 atoms: 0.60 Number of scatterers: 8673 At special positions: 0 Unit cell: (86.403, 89.526, 135.33, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 60 16.00 P 6 15.00 O 1680 8.00 N 1458 7.00 C 5469 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=0, symmetry=0 Time building additional restraints: 3.67 Conformation dependent library (CDL) restraints added in 1.6 seconds 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2034 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 12 sheets defined 33.5% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'C' and resid 55 through 60 Processing helix chain 'C' and resid 80 through 90 removed outlier: 3.670A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE C 85 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TRP C 86 " --> pdb=" O MET C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 122 removed outlier: 3.633A pdb=" N MET C 119 " --> pdb=" O ASN C 115 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N THR C 120 " --> pdb=" O ARG C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 145 Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 182 through 193 removed outlier: 3.551A pdb=" N TYR C 188 " --> pdb=" O ASP C 184 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU C 189 " --> pdb=" O LEU C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 215 removed outlier: 4.213A pdb=" N ARG C 210 " --> pdb=" O GLU C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 231 Processing helix chain 'C' and resid 254 through 261 Proline residue: C 258 - end of helix removed outlier: 4.623A pdb=" N LEU C 261 " --> pdb=" O CYS C 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 254 through 261' Processing helix chain 'C' and resid 274 through 283 removed outlier: 3.672A pdb=" N THR C 278 " --> pdb=" O ILE C 274 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TYR C 279 " --> pdb=" O HIS C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 296 removed outlier: 3.530A pdb=" N TYR C 294 " --> pdb=" O ARG C 290 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 319 removed outlier: 3.732A pdb=" N THR C 318 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA C 319 " --> pdb=" O LYS C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 346 removed outlier: 4.070A pdb=" N GLY C 343 " --> pdb=" O VAL C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 355 No H-bonds generated for 'chain 'C' and resid 353 through 355' Processing helix chain 'C' and resid 359 through 364 Processing helix chain 'C' and resid 367 through 370 Processing helix chain 'A' and resid 55 through 60 Processing helix chain 'A' and resid 80 through 90 removed outlier: 3.670A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TRP A 86 " --> pdb=" O MET A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 122 removed outlier: 3.633A pdb=" N MET A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N THR A 120 " --> pdb=" O ARG A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 145 Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 182 through 193 removed outlier: 3.552A pdb=" N TYR A 188 " --> pdb=" O ASP A 184 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 215 removed outlier: 4.213A pdb=" N ARG A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 231 Processing helix chain 'A' and resid 254 through 261 Proline residue: A 258 - end of helix removed outlier: 4.623A pdb=" N LEU A 261 " --> pdb=" O CYS A 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 254 through 261' Processing helix chain 'A' and resid 274 through 283 removed outlier: 3.671A pdb=" N THR A 278 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TYR A 279 " --> pdb=" O HIS A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 296 removed outlier: 3.529A pdb=" N TYR A 294 " --> pdb=" O ARG A 290 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 319 removed outlier: 3.732A pdb=" N THR A 318 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA A 319 " --> pdb=" O LYS A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 346 removed outlier: 4.069A pdb=" N GLY A 343 " --> pdb=" O VAL A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 355 No H-bonds generated for 'chain 'A' and resid 353 through 355' Processing helix chain 'A' and resid 359 through 364 Processing helix chain 'A' and resid 367 through 370 Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'B' and resid 80 through 90 removed outlier: 3.670A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TRP B 86 " --> pdb=" O MET B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 122 removed outlier: 3.633A pdb=" N MET B 119 " --> pdb=" O ASN B 115 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N THR B 120 " --> pdb=" O ARG B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 145 Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 182 through 193 removed outlier: 3.552A pdb=" N TYR B 188 " --> pdb=" O ASP B 184 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU B 189 " --> pdb=" O LEU B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 215 removed outlier: 4.213A pdb=" N ARG B 210 " --> pdb=" O GLU B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 231 Processing helix chain 'B' and resid 254 through 261 Proline residue: B 258 - end of helix removed outlier: 4.623A pdb=" N LEU B 261 " --> pdb=" O CYS B 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 254 through 261' Processing helix chain 'B' and resid 274 through 283 removed outlier: 3.672A pdb=" N THR B 278 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TYR B 279 " --> pdb=" O HIS B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 296 removed outlier: 3.530A pdb=" N TYR B 294 " --> pdb=" O ARG B 290 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 319 removed outlier: 3.733A pdb=" N THR B 318 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA B 319 " --> pdb=" O LYS B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 346 removed outlier: 4.070A pdb=" N GLY B 343 " --> pdb=" O VAL B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 355 No H-bonds generated for 'chain 'B' and resid 353 through 355' Processing helix chain 'B' and resid 359 through 364 Processing helix chain 'B' and resid 367 through 370 Processing sheet with id= A, first strand: chain 'C' and resid 103 through 105 removed outlier: 6.926A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS C 18 " --> pdb=" O ASP C 11 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 52 through 54 Processing sheet with id= C, first strand: chain 'C' and resid 160 through 162 Processing sheet with id= D, first strand: chain 'C' and resid 240 through 242 removed outlier: 3.631A pdb=" N LEU C 242 " --> pdb=" O GLN C 246 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN C 246 " --> pdb=" O LEU C 242 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 103 through 105 removed outlier: 6.927A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS A 18 " --> pdb=" O ASP A 11 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 52 through 54 Processing sheet with id= G, first strand: chain 'A' and resid 160 through 162 Processing sheet with id= H, first strand: chain 'A' and resid 240 through 242 removed outlier: 3.630A pdb=" N LEU A 242 " --> pdb=" O GLN A 246 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 103 through 105 removed outlier: 6.927A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS B 18 " --> pdb=" O ASP B 11 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 52 through 54 Processing sheet with id= K, first strand: chain 'B' and resid 160 through 162 Processing sheet with id= L, first strand: chain 'B' and resid 240 through 242 removed outlier: 3.632A pdb=" N LEU B 242 " --> pdb=" O GLN B 246 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLN B 246 " --> pdb=" O LEU B 242 " (cutoff:3.500A) 189 hydrogen bonds defined for protein. 450 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.08 Time building geometry restraints manager: 3.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1452 1.30 - 1.42: 2208 1.42 - 1.55: 5086 1.55 - 1.68: 11 1.68 - 1.81: 108 Bond restraints: 8865 Sorted by residual: bond pdb=" CG HIC C 73 " pdb=" CD2 HIC C 73 " ideal model delta sigma weight residual 1.369 1.307 0.062 2.00e-02 2.50e+03 9.66e+00 bond pdb=" CG HIC A 73 " pdb=" CD2 HIC A 73 " ideal model delta sigma weight residual 1.369 1.307 0.062 2.00e-02 2.50e+03 9.64e+00 bond pdb=" CG HIC B 73 " pdb=" CD2 HIC B 73 " ideal model delta sigma weight residual 1.369 1.307 0.062 2.00e-02 2.50e+03 9.55e+00 bond pdb=" C HIC B 73 " pdb=" O HIC B 73 " ideal model delta sigma weight residual 1.231 1.169 0.062 2.00e-02 2.50e+03 9.54e+00 bond pdb=" C HIC C 73 " pdb=" O HIC C 73 " ideal model delta sigma weight residual 1.231 1.169 0.062 2.00e-02 2.50e+03 9.54e+00 ... (remaining 8860 not shown) Histogram of bond angle deviations from ideal: 97.94 - 105.44: 276 105.44 - 112.94: 4825 112.94 - 120.45: 3668 120.45 - 127.95: 3183 127.95 - 135.45: 90 Bond angle restraints: 12042 Sorted by residual: angle pdb=" C CYS C 217 " pdb=" N TYR C 218 " pdb=" CA TYR C 218 " ideal model delta sigma weight residual 121.76 130.12 -8.36 2.19e+00 2.09e-01 1.46e+01 angle pdb=" C CYS A 217 " pdb=" N TYR A 218 " pdb=" CA TYR A 218 " ideal model delta sigma weight residual 121.76 130.11 -8.35 2.19e+00 2.09e-01 1.45e+01 angle pdb=" C CYS B 217 " pdb=" N TYR B 218 " pdb=" CA TYR B 218 " ideal model delta sigma weight residual 121.76 130.11 -8.35 2.19e+00 2.09e-01 1.45e+01 angle pdb=" N GLU A 224 " pdb=" CA GLU A 224 " pdb=" C GLU A 224 " ideal model delta sigma weight residual 110.80 103.60 7.20 2.13e+00 2.20e-01 1.14e+01 angle pdb=" N GLU C 224 " pdb=" CA GLU C 224 " pdb=" C GLU C 224 " ideal model delta sigma weight residual 110.80 103.65 7.15 2.13e+00 2.20e-01 1.13e+01 ... (remaining 12037 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.21: 4929 16.21 - 32.42: 309 32.42 - 48.63: 60 48.63 - 64.84: 9 64.84 - 81.04: 9 Dihedral angle restraints: 5316 sinusoidal: 2136 harmonic: 3180 Sorted by residual: dihedral pdb=" CA ARG B 116 " pdb=" C ARG B 116 " pdb=" N GLU B 117 " pdb=" CA GLU B 117 " ideal model delta harmonic sigma weight residual 180.00 150.29 29.71 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA ARG C 116 " pdb=" C ARG C 116 " pdb=" N GLU C 117 " pdb=" CA GLU C 117 " ideal model delta harmonic sigma weight residual 180.00 150.33 29.67 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA ARG A 116 " pdb=" C ARG A 116 " pdb=" N GLU A 117 " pdb=" CA GLU A 117 " ideal model delta harmonic sigma weight residual 180.00 150.33 29.67 0 5.00e+00 4.00e-02 3.52e+01 ... (remaining 5313 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 743 0.044 - 0.088: 406 0.088 - 0.132: 139 0.132 - 0.176: 44 0.176 - 0.220: 9 Chirality restraints: 1341 Sorted by residual: chirality pdb=" CA SME A 47 " pdb=" N SME A 47 " pdb=" C SME A 47 " pdb=" CB SME A 47 " both_signs ideal model delta sigma weight residual False 2.40 2.18 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA SME B 47 " pdb=" N SME B 47 " pdb=" C SME B 47 " pdb=" CB SME B 47 " both_signs ideal model delta sigma weight residual False 2.40 2.18 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA SME C 47 " pdb=" N SME C 47 " pdb=" C SME C 47 " pdb=" CB SME C 47 " both_signs ideal model delta sigma weight residual False 2.40 2.19 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 1338 not shown) Planarity restraints: 1536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 101 " -0.041 5.00e-02 4.00e+02 6.11e-02 5.97e+00 pdb=" N PRO A 102 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO A 102 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 102 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 101 " -0.040 5.00e-02 4.00e+02 6.10e-02 5.94e+00 pdb=" N PRO B 102 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO B 102 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 102 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 101 " 0.040 5.00e-02 4.00e+02 6.09e-02 5.93e+00 pdb=" N PRO C 102 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO C 102 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 102 " 0.034 5.00e-02 4.00e+02 ... (remaining 1533 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 295 2.64 - 3.20: 9724 3.20 - 3.77: 13968 3.77 - 4.33: 19668 4.33 - 4.90: 29721 Nonbonded interactions: 73376 Sorted by model distance: nonbonded pdb=" OG1 THR B 358 " pdb=" OE1 GLU B 361 " model vdw 2.072 2.440 nonbonded pdb=" OG1 THR C 358 " pdb=" OE1 GLU C 361 " model vdw 2.072 2.440 nonbonded pdb=" OG1 THR A 358 " pdb=" OE1 GLU A 361 " model vdw 2.072 2.440 nonbonded pdb=" OG SER C 155 " pdb=" OG1 THR C 303 " model vdw 2.073 2.440 nonbonded pdb=" OG SER A 155 " pdb=" OG1 THR A 303 " model vdw 2.073 2.440 ... (remaining 73371 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.94 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.370 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 26.640 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 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 : 0.009 0.062 8865 Z= 0.571 Angle : 1.130 9.701 12042 Z= 0.573 Chirality : 0.061 0.220 1341 Planarity : 0.006 0.061 1536 Dihedral : 11.850 81.044 3282 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 27.43 Ramachandran Plot: Outliers : 0.28 % Allowed : 12.92 % Favored : 86.80 % Rotamer: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.00 (0.19), residues: 1068 helix: -4.19 (0.14), residues: 330 sheet: -1.74 (0.34), residues: 210 loop : -3.41 (0.20), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP C 86 HIS 0.009 0.003 HIS A 87 PHE 0.031 0.003 PHE B 262 TYR 0.028 0.003 TYR A 218 ARG 0.009 0.001 ARG C 254 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 252 time to evaluate : 0.974 Fit side-chains revert: symmetry clash REVERT: C 118 LYS cc_start: 0.8422 (mtpp) cc_final: 0.7923 (tptp) REVERT: C 148 THR cc_start: 0.8234 (t) cc_final: 0.7978 (m) REVERT: C 153 LEU cc_start: 0.8606 (tt) cc_final: 0.8351 (tp) REVERT: C 159 VAL cc_start: 0.8680 (p) cc_final: 0.8404 (m) REVERT: C 325 MET cc_start: 0.8267 (ttp) cc_final: 0.8023 (mtt) REVERT: C 356 TRP cc_start: 0.7797 (m100) cc_final: 0.7330 (m100) REVERT: A 118 LYS cc_start: 0.8403 (mtpp) cc_final: 0.7903 (mtpt) REVERT: A 159 VAL cc_start: 0.8816 (p) cc_final: 0.8510 (m) REVERT: A 299 MET cc_start: 0.8180 (ptm) cc_final: 0.7877 (ppp) REVERT: A 315 LYS cc_start: 0.8382 (tttm) cc_final: 0.8171 (tppt) REVERT: A 356 TRP cc_start: 0.7819 (m100) cc_final: 0.7493 (m100) REVERT: B 79 TRP cc_start: 0.8017 (m100) cc_final: 0.6528 (m-90) REVERT: B 123 MET cc_start: 0.9098 (mmt) cc_final: 0.8870 (mmt) REVERT: B 159 VAL cc_start: 0.8789 (p) cc_final: 0.8457 (m) REVERT: B 299 MET cc_start: 0.8018 (ptm) cc_final: 0.7754 (ppp) REVERT: B 325 MET cc_start: 0.8277 (ttp) cc_final: 0.8072 (mtt) REVERT: B 354 GLN cc_start: 0.8559 (pm20) cc_final: 0.8074 (pm20) outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.2483 time to fit residues: 82.4633 Evaluate side-chains 152 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 84 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN C 314 GLN ** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN A 314 GLN ** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8865 Z= 0.286 Angle : 0.911 8.232 12042 Z= 0.442 Chirality : 0.051 0.177 1341 Planarity : 0.005 0.052 1536 Dihedral : 9.231 59.966 1245 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 19.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.14 % Favored : 88.86 % Rotamer: Outliers : 4.89 % Allowed : 9.45 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -3.67 (0.22), residues: 1068 helix: -2.56 (0.22), residues: 351 sheet: -1.51 (0.34), residues: 210 loop : -2.71 (0.24), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP A 79 HIS 0.008 0.002 HIS A 88 PHE 0.019 0.002 PHE C 352 TYR 0.019 0.002 TYR B 218 ARG 0.004 0.001 ARG A 183 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 214 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 159 VAL cc_start: 0.8833 (p) cc_final: 0.8592 (m) REVERT: C 283 MET cc_start: 0.8731 (mmm) cc_final: 0.8512 (mmp) REVERT: C 356 TRP cc_start: 0.7946 (m100) cc_final: 0.7350 (m100) REVERT: A 159 VAL cc_start: 0.8952 (p) cc_final: 0.8711 (m) REVERT: A 356 TRP cc_start: 0.7874 (m100) cc_final: 0.7409 (m100) REVERT: B 133 TYR cc_start: 0.8045 (t80) cc_final: 0.7436 (t80) REVERT: B 159 VAL cc_start: 0.8846 (p) cc_final: 0.8569 (m) REVERT: B 299 MET cc_start: 0.8023 (ptm) cc_final: 0.7774 (ppp) REVERT: B 315 LYS cc_start: 0.8244 (tppt) cc_final: 0.7634 (ttmt) REVERT: B 325 MET cc_start: 0.8157 (ttp) cc_final: 0.7944 (mtt) REVERT: B 355 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7718 (mpp) outliers start: 45 outliers final: 27 residues processed: 234 average time/residue: 0.1716 time to fit residues: 58.3099 Evaluate side-chains 181 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 153 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 355 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 81 optimal weight: 0.0030 chunk 66 optimal weight: 5.9990 chunk 27 optimal weight: 0.0060 chunk 98 optimal weight: 9.9990 chunk 106 optimal weight: 0.0770 chunk 87 optimal weight: 8.9990 chunk 97 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 78 optimal weight: 0.8980 overall best weight: 1.1966 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 GLN ** C 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8865 Z= 0.176 Angle : 0.806 8.996 12042 Z= 0.383 Chirality : 0.047 0.159 1341 Planarity : 0.004 0.046 1536 Dihedral : 7.935 58.125 1245 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.21 % Favored : 89.79 % Rotamer: Outliers : 4.02 % Allowed : 14.77 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.23), residues: 1068 helix: -1.46 (0.26), residues: 348 sheet: -1.37 (0.34), residues: 210 loop : -2.45 (0.24), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 79 HIS 0.003 0.001 HIS C 87 PHE 0.013 0.002 PHE A 223 TYR 0.014 0.001 TYR C 218 ARG 0.003 0.001 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 211 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 159 VAL cc_start: 0.8737 (p) cc_final: 0.8511 (m) REVERT: C 315 LYS cc_start: 0.8229 (tppt) cc_final: 0.7664 (ttmm) REVERT: C 355 MET cc_start: 0.8277 (mtp) cc_final: 0.7971 (mtp) REVERT: A 75 ILE cc_start: 0.8417 (OUTLIER) cc_final: 0.8017 (tt) REVERT: A 159 VAL cc_start: 0.8884 (p) cc_final: 0.8641 (m) REVERT: A 297 ASN cc_start: 0.7891 (p0) cc_final: 0.7664 (p0) REVERT: A 356 TRP cc_start: 0.7632 (m100) cc_final: 0.7118 (m100) REVERT: B 107 GLU cc_start: 0.8771 (tm-30) cc_final: 0.8529 (tm-30) REVERT: B 159 VAL cc_start: 0.8761 (p) cc_final: 0.8479 (m) REVERT: B 315 LYS cc_start: 0.8248 (tppt) cc_final: 0.7527 (ttmm) REVERT: B 325 MET cc_start: 0.8128 (ttp) cc_final: 0.7914 (mtt) REVERT: B 349 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8142 (pp) REVERT: B 355 MET cc_start: 0.8072 (OUTLIER) cc_final: 0.7801 (mtp) outliers start: 37 outliers final: 20 residues processed: 232 average time/residue: 0.1733 time to fit residues: 58.5664 Evaluate side-chains 185 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 162 time to evaluate : 1.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 246 GLN Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 355 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 5.9990 chunk 73 optimal weight: 20.0000 chunk 50 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 46 optimal weight: 20.0000 chunk 65 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 chunk 104 optimal weight: 5.9990 chunk 51 optimal weight: 20.0000 chunk 93 optimal weight: 0.7980 chunk 28 optimal weight: 10.0000 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 87 HIS ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 HIS B 87 HIS ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8865 Z= 0.253 Angle : 0.838 8.922 12042 Z= 0.395 Chirality : 0.048 0.189 1341 Planarity : 0.004 0.047 1536 Dihedral : 7.897 58.807 1245 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 18.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.21 % Favored : 89.79 % Rotamer: Outliers : 6.08 % Allowed : 15.64 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.24), residues: 1068 helix: -1.26 (0.26), residues: 360 sheet: -1.24 (0.35), residues: 210 loop : -2.44 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 79 HIS 0.003 0.001 HIS B 87 PHE 0.018 0.002 PHE B 31 TYR 0.019 0.002 TYR C 218 ARG 0.005 0.001 ARG C 290 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 175 time to evaluate : 1.066 Fit side-chains revert: symmetry clash REVERT: C 118 LYS cc_start: 0.8482 (mtmm) cc_final: 0.8000 (tptt) REVERT: C 159 VAL cc_start: 0.8823 (p) cc_final: 0.8610 (m) REVERT: C 221 LEU cc_start: 0.7935 (tp) cc_final: 0.7649 (tp) REVERT: C 315 LYS cc_start: 0.8244 (tppt) cc_final: 0.7626 (ttmm) REVERT: C 355 MET cc_start: 0.8150 (mtp) cc_final: 0.7949 (mtp) REVERT: A 75 ILE cc_start: 0.8507 (OUTLIER) cc_final: 0.8031 (tt) REVERT: A 159 VAL cc_start: 0.8906 (p) cc_final: 0.8674 (m) REVERT: A 221 LEU cc_start: 0.7993 (tp) cc_final: 0.7650 (tp) REVERT: A 297 ASN cc_start: 0.7915 (p0) cc_final: 0.7652 (p0) REVERT: A 349 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8131 (pp) REVERT: A 356 TRP cc_start: 0.7690 (m100) cc_final: 0.7099 (m100) REVERT: B 12 ASN cc_start: 0.6784 (m-40) cc_final: 0.6554 (m-40) REVERT: B 159 VAL cc_start: 0.8776 (p) cc_final: 0.8521 (m) REVERT: B 254 ARG cc_start: 0.8504 (mtp-110) cc_final: 0.8281 (mtp-110) REVERT: B 315 LYS cc_start: 0.8340 (tppt) cc_final: 0.7527 (ttmm) REVERT: B 349 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8107 (pp) outliers start: 56 outliers final: 34 residues processed: 210 average time/residue: 0.1570 time to fit residues: 48.8298 Evaluate side-chains 194 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 157 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 246 GLN Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 349 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 1 optimal weight: 20.0000 chunk 77 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 89 optimal weight: 20.0000 chunk 72 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 93 optimal weight: 0.4980 chunk 26 optimal weight: 7.9990 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.4565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8865 Z= 0.256 Angle : 0.827 9.155 12042 Z= 0.391 Chirality : 0.048 0.182 1341 Planarity : 0.005 0.047 1536 Dihedral : 7.906 59.946 1245 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.33 % Favored : 88.67 % Rotamer: Outliers : 7.17 % Allowed : 16.07 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.24), residues: 1068 helix: -1.30 (0.26), residues: 366 sheet: -1.09 (0.36), residues: 210 loop : -2.43 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 79 HIS 0.005 0.001 HIS B 87 PHE 0.013 0.002 PHE B 200 TYR 0.018 0.002 TYR C 218 ARG 0.003 0.001 ARG A 312 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 168 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 159 VAL cc_start: 0.8839 (p) cc_final: 0.8592 (m) REVERT: C 221 LEU cc_start: 0.8102 (tp) cc_final: 0.7817 (tp) REVERT: C 356 TRP cc_start: 0.7878 (m100) cc_final: 0.7382 (m100) REVERT: A 75 ILE cc_start: 0.8552 (OUTLIER) cc_final: 0.8106 (tt) REVERT: A 159 VAL cc_start: 0.8920 (p) cc_final: 0.8691 (m) REVERT: A 221 LEU cc_start: 0.8001 (tp) cc_final: 0.7734 (tp) REVERT: A 297 ASN cc_start: 0.8018 (p0) cc_final: 0.7721 (p0) REVERT: A 349 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8137 (pp) REVERT: A 356 TRP cc_start: 0.7747 (m100) cc_final: 0.7309 (m100) REVERT: B 12 ASN cc_start: 0.6873 (m-40) cc_final: 0.6571 (m-40) REVERT: B 159 VAL cc_start: 0.8894 (p) cc_final: 0.8643 (m) REVERT: B 315 LYS cc_start: 0.8359 (tppt) cc_final: 0.7540 (ttmm) REVERT: B 349 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8113 (pp) REVERT: B 355 MET cc_start: 0.8098 (mtp) cc_final: 0.7833 (mpp) outliers start: 66 outliers final: 40 residues processed: 211 average time/residue: 0.1599 time to fit residues: 49.7317 Evaluate side-chains 198 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 155 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 246 GLN Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 349 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 20.0000 chunk 94 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 chunk 61 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 104 optimal weight: 7.9990 chunk 86 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 34 optimal weight: 8.9990 chunk 54 optimal weight: 6.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.4785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8865 Z= 0.266 Angle : 0.834 8.807 12042 Z= 0.395 Chirality : 0.048 0.192 1341 Planarity : 0.005 0.047 1536 Dihedral : 7.871 58.382 1245 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 18.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.14 % Favored : 88.86 % Rotamer: Outliers : 6.08 % Allowed : 19.00 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.24), residues: 1068 helix: -1.25 (0.26), residues: 363 sheet: -0.94 (0.36), residues: 210 loop : -2.45 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 79 HIS 0.005 0.001 HIS C 87 PHE 0.018 0.002 PHE B 31 TYR 0.020 0.002 TYR C 218 ARG 0.003 0.000 ARG B 290 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 161 time to evaluate : 1.021 Fit side-chains revert: symmetry clash REVERT: C 159 VAL cc_start: 0.8829 (p) cc_final: 0.8600 (m) REVERT: C 221 LEU cc_start: 0.7950 (tp) cc_final: 0.7682 (tp) REVERT: C 356 TRP cc_start: 0.7798 (m100) cc_final: 0.7348 (m100) REVERT: A 75 ILE cc_start: 0.8551 (OUTLIER) cc_final: 0.8194 (tt) REVERT: A 88 HIS cc_start: 0.8141 (m-70) cc_final: 0.7728 (t-90) REVERT: A 159 VAL cc_start: 0.8940 (p) cc_final: 0.8706 (m) REVERT: A 221 LEU cc_start: 0.8044 (tp) cc_final: 0.7731 (tp) REVERT: A 297 ASN cc_start: 0.8117 (p0) cc_final: 0.7895 (p0) REVERT: A 349 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8292 (pp) REVERT: A 356 TRP cc_start: 0.7773 (m100) cc_final: 0.7344 (m100) REVERT: B 104 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.7329 (tp) REVERT: B 159 VAL cc_start: 0.8937 (p) cc_final: 0.8667 (m) REVERT: B 315 LYS cc_start: 0.8347 (tppt) cc_final: 0.7505 (ttmm) REVERT: B 349 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.7989 (pp) outliers start: 56 outliers final: 44 residues processed: 194 average time/residue: 0.1596 time to fit residues: 46.5531 Evaluate side-chains 199 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 151 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 352 PHE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 246 GLN Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 349 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 chunk 59 optimal weight: 0.2980 chunk 76 optimal weight: 20.0000 chunk 87 optimal weight: 9.9990 chunk 58 optimal weight: 10.0000 chunk 104 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 overall best weight: 3.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.4967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8865 Z= 0.241 Angle : 0.818 8.114 12042 Z= 0.385 Chirality : 0.047 0.182 1341 Planarity : 0.005 0.046 1536 Dihedral : 7.731 58.226 1245 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 18.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.24 % Favored : 88.76 % Rotamer: Outliers : 6.62 % Allowed : 18.68 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.24), residues: 1068 helix: -1.12 (0.27), residues: 360 sheet: -0.95 (0.36), residues: 210 loop : -2.51 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 79 HIS 0.004 0.001 HIS C 87 PHE 0.013 0.002 PHE C 200 TYR 0.017 0.002 TYR C 218 ARG 0.005 0.000 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 162 time to evaluate : 1.018 Fit side-chains revert: symmetry clash REVERT: C 159 VAL cc_start: 0.8816 (p) cc_final: 0.8592 (m) REVERT: C 221 LEU cc_start: 0.8109 (tp) cc_final: 0.7844 (tp) REVERT: C 356 TRP cc_start: 0.7808 (m100) cc_final: 0.7510 (m-90) REVERT: A 75 ILE cc_start: 0.8554 (OUTLIER) cc_final: 0.8187 (tt) REVERT: A 159 VAL cc_start: 0.8931 (p) cc_final: 0.8694 (m) REVERT: A 216 LEU cc_start: 0.8718 (pt) cc_final: 0.8436 (pt) REVERT: A 221 LEU cc_start: 0.7961 (tp) cc_final: 0.7656 (tp) REVERT: A 349 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8343 (pp) REVERT: A 356 TRP cc_start: 0.7788 (m100) cc_final: 0.7340 (m100) REVERT: A 360 GLN cc_start: 0.8381 (tp40) cc_final: 0.8153 (mp10) REVERT: B 104 LEU cc_start: 0.7429 (tp) cc_final: 0.7129 (tp) REVERT: B 159 VAL cc_start: 0.8907 (p) cc_final: 0.8660 (m) REVERT: B 315 LYS cc_start: 0.8341 (tppt) cc_final: 0.7499 (ttmm) REVERT: B 349 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.7999 (pp) outliers start: 61 outliers final: 42 residues processed: 200 average time/residue: 0.1613 time to fit residues: 48.1714 Evaluate side-chains 194 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 149 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 246 GLN Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 349 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 20.0000 chunk 62 optimal weight: 0.9990 chunk 31 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 70 optimal weight: 20.0000 chunk 51 optimal weight: 5.9990 chunk 9 optimal weight: 20.0000 chunk 81 optimal weight: 9.9990 chunk 94 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.5113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8865 Z= 0.237 Angle : 0.821 9.032 12042 Z= 0.388 Chirality : 0.047 0.184 1341 Planarity : 0.005 0.055 1536 Dihedral : 7.684 57.684 1245 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.24 % Favored : 88.76 % Rotamer: Outliers : 5.97 % Allowed : 20.96 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.25), residues: 1068 helix: -1.02 (0.27), residues: 357 sheet: -0.93 (0.36), residues: 210 loop : -2.48 (0.25), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 79 HIS 0.006 0.001 HIS B 88 PHE 0.019 0.002 PHE B 31 TYR 0.021 0.002 TYR B 218 ARG 0.004 0.000 ARG B 254 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 163 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 159 VAL cc_start: 0.8825 (p) cc_final: 0.8613 (m) REVERT: C 221 LEU cc_start: 0.8038 (tp) cc_final: 0.7782 (tp) REVERT: C 356 TRP cc_start: 0.7672 (m100) cc_final: 0.7378 (m-90) REVERT: A 88 HIS cc_start: 0.8133 (m-70) cc_final: 0.7510 (t-90) REVERT: A 159 VAL cc_start: 0.8933 (p) cc_final: 0.8707 (m) REVERT: A 216 LEU cc_start: 0.8742 (pt) cc_final: 0.8475 (pt) REVERT: A 221 LEU cc_start: 0.7956 (tp) cc_final: 0.7677 (tp) REVERT: A 349 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8300 (pp) REVERT: A 356 TRP cc_start: 0.7846 (m100) cc_final: 0.7336 (m100) REVERT: A 360 GLN cc_start: 0.8376 (tp40) cc_final: 0.8160 (mp10) REVERT: B 101 HIS cc_start: 0.5330 (OUTLIER) cc_final: 0.5033 (t-90) REVERT: B 104 LEU cc_start: 0.7439 (OUTLIER) cc_final: 0.7185 (tp) REVERT: B 159 VAL cc_start: 0.8901 (p) cc_final: 0.8664 (m) REVERT: B 315 LYS cc_start: 0.8366 (tppt) cc_final: 0.7531 (ttmm) REVERT: B 349 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8013 (pp) outliers start: 55 outliers final: 42 residues processed: 196 average time/residue: 0.1565 time to fit residues: 45.8932 Evaluate side-chains 199 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 153 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 246 GLN Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 349 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 10.0000 chunk 97 optimal weight: 0.3980 chunk 99 optimal weight: 0.2980 chunk 58 optimal weight: 9.9990 chunk 42 optimal weight: 0.9980 chunk 76 optimal weight: 30.0000 chunk 29 optimal weight: 9.9990 chunk 87 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 chunk 96 optimal weight: 20.0000 chunk 63 optimal weight: 8.9990 overall best weight: 2.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.5305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8865 Z= 0.208 Angle : 0.812 9.010 12042 Z= 0.380 Chirality : 0.047 0.176 1341 Planarity : 0.005 0.045 1536 Dihedral : 7.469 58.777 1245 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.77 % Favored : 89.23 % Rotamer: Outliers : 5.43 % Allowed : 22.48 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.25), residues: 1068 helix: -0.89 (0.28), residues: 342 sheet: -0.89 (0.36), residues: 210 loop : -2.28 (0.25), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 79 HIS 0.005 0.001 HIS B 88 PHE 0.016 0.002 PHE C 223 TYR 0.017 0.001 TYR B 218 ARG 0.006 0.000 ARG B 254 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 166 time to evaluate : 0.851 Fit side-chains REVERT: C 221 LEU cc_start: 0.8115 (tp) cc_final: 0.7873 (tp) REVERT: C 356 TRP cc_start: 0.7543 (m100) cc_final: 0.7169 (m100) REVERT: A 133 TYR cc_start: 0.8176 (t80) cc_final: 0.7773 (t80) REVERT: A 159 VAL cc_start: 0.8930 (p) cc_final: 0.8702 (m) REVERT: A 216 LEU cc_start: 0.8745 (pt) cc_final: 0.8437 (pt) REVERT: A 221 LEU cc_start: 0.7858 (tp) cc_final: 0.7612 (tp) REVERT: A 314 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.7990 (mp10) REVERT: A 349 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8246 (pp) REVERT: A 356 TRP cc_start: 0.7753 (m100) cc_final: 0.7182 (m100) REVERT: A 360 GLN cc_start: 0.8374 (tp40) cc_final: 0.8167 (mp10) REVERT: B 104 LEU cc_start: 0.7336 (tp) cc_final: 0.7085 (tp) REVERT: B 116 ARG cc_start: 0.6778 (ptt180) cc_final: 0.6415 (ptt90) REVERT: B 159 VAL cc_start: 0.8899 (p) cc_final: 0.8663 (m) REVERT: B 315 LYS cc_start: 0.8360 (tppt) cc_final: 0.7513 (ttmm) REVERT: B 349 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.7949 (pp) outliers start: 50 outliers final: 41 residues processed: 196 average time/residue: 0.1560 time to fit residues: 45.7296 Evaluate side-chains 208 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 164 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 349 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 71 optimal weight: 7.9990 chunk 107 optimal weight: 6.9990 chunk 99 optimal weight: 5.9990 chunk 85 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 chunk 66 optimal weight: 8.9990 chunk 52 optimal weight: 10.0000 chunk 68 optimal weight: 0.0970 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.5363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8865 Z= 0.230 Angle : 0.827 9.743 12042 Z= 0.390 Chirality : 0.048 0.181 1341 Planarity : 0.005 0.044 1536 Dihedral : 7.475 59.395 1245 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 18.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.67 % Favored : 89.33 % Rotamer: Outliers : 5.32 % Allowed : 23.02 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.25), residues: 1068 helix: -0.89 (0.28), residues: 342 sheet: -0.87 (0.36), residues: 201 loop : -2.31 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP B 79 HIS 0.016 0.002 HIS B 101 PHE 0.026 0.002 PHE B 223 TYR 0.018 0.001 TYR B 218 ARG 0.005 0.000 ARG B 254 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 166 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 221 LEU cc_start: 0.8149 (tp) cc_final: 0.7907 (tp) REVERT: C 356 TRP cc_start: 0.7612 (m100) cc_final: 0.7263 (m100) REVERT: A 88 HIS cc_start: 0.8140 (m-70) cc_final: 0.7532 (t-90) REVERT: A 159 VAL cc_start: 0.8942 (p) cc_final: 0.8720 (m) REVERT: A 216 LEU cc_start: 0.8734 (pt) cc_final: 0.8454 (pt) REVERT: A 221 LEU cc_start: 0.7890 (tp) cc_final: 0.7647 (tp) REVERT: A 314 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.8011 (mp10) REVERT: A 349 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8230 (pp) REVERT: A 356 TRP cc_start: 0.7792 (m100) cc_final: 0.7242 (m100) REVERT: A 360 GLN cc_start: 0.8372 (tp40) cc_final: 0.8162 (mp10) REVERT: B 104 LEU cc_start: 0.7334 (tp) cc_final: 0.7086 (tp) REVERT: B 116 ARG cc_start: 0.6831 (ptt180) cc_final: 0.6421 (ptt90) REVERT: B 159 VAL cc_start: 0.8910 (p) cc_final: 0.8667 (m) REVERT: B 216 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8183 (pp) REVERT: B 315 LYS cc_start: 0.8367 (tppt) cc_final: 0.7526 (ttmm) REVERT: B 349 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.7940 (pp) outliers start: 49 outliers final: 41 residues processed: 195 average time/residue: 0.1590 time to fit residues: 45.8747 Evaluate side-chains 211 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 166 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 349 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 79 optimal weight: 0.0980 chunk 12 optimal weight: 9.9990 chunk 23 optimal weight: 0.9980 chunk 85 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 15 optimal weight: 8.9990 chunk 75 optimal weight: 1.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.094132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.084266 restraints weight = 24098.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.086349 restraints weight = 12232.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.087799 restraints weight = 7413.290| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.5514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8865 Z= 0.202 Angle : 0.821 9.833 12042 Z= 0.384 Chirality : 0.047 0.190 1341 Planarity : 0.005 0.043 1536 Dihedral : 7.285 59.253 1245 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.39 % Favored : 89.61 % Rotamer: Outliers : 4.78 % Allowed : 23.78 % Favored : 71.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.25), residues: 1068 helix: -0.87 (0.29), residues: 342 sheet: -1.05 (0.36), residues: 204 loop : -2.33 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP B 79 HIS 0.014 0.001 HIS B 101 PHE 0.027 0.002 PHE B 223 TYR 0.016 0.001 TYR B 218 ARG 0.005 0.000 ARG B 254 =============================================================================== Job complete usr+sys time: 1806.00 seconds wall clock time: 34 minutes 1.53 seconds (2041.53 seconds total)