Starting phenix.real_space_refine on Wed Feb 14 06:58:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fx5_29524/02_2024/8fx5_29524_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fx5_29524/02_2024/8fx5_29524.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fx5_29524/02_2024/8fx5_29524_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fx5_29524/02_2024/8fx5_29524_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fx5_29524/02_2024/8fx5_29524_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fx5_29524/02_2024/8fx5_29524.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fx5_29524/02_2024/8fx5_29524.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fx5_29524/02_2024/8fx5_29524_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fx5_29524/02_2024/8fx5_29524_updated.pdb" } resolution = 2.45 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 5595 2.51 5 N 1487 2.21 5 O 1670 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8818 Number of models: 1 Model: "" Number of chains: 9 Chain: "R" Number of atoms: 2139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2139 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 260} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2602 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 434 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 1790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1790 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 224} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1768 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "R" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'XNO': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 44 Classifications: {'water': 44} Link IDs: {None: 43} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 5.32, per 1000 atoms: 0.60 Number of scatterers: 8818 At special positions: 0 Unit cell: (92.13, 122.01, 124.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 1670 8.00 N 1487 7.00 C 5595 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 105 " - pdb=" SG CYS R 185 " distance=2.02 Simple disulfide: pdb=" SG CYS R 426 " - pdb=" SG CYS R 429 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " distance=2.04 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: 3.34 Conformation dependent library (CDL) restraints added in 1.8 seconds 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2114 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 31 helices and 12 sheets defined 35.1% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'R' and resid 33 through 59 removed outlier: 3.738A pdb=" N ASN R 50 " --> pdb=" O THR R 46 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 95 removed outlier: 4.307A pdb=" N PHE R 70 " --> pdb=" O VAL R 66 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU R 71 " --> pdb=" O ASN R 67 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N MET R 86 " --> pdb=" O GLY R 82 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ASN R 87 " --> pdb=" O ALA R 83 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU R 88 " --> pdb=" O PHE R 84 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 135 removed outlier: 3.551A pdb=" N SER R 119 " --> pdb=" O VAL R 115 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 143 No H-bonds generated for 'chain 'R' and resid 140 through 143' Processing helix chain 'R' and resid 146 through 169 Proline residue: R 166 - end of helix Processing helix chain 'R' and resid 171 through 175 Processing helix chain 'R' and resid 188 through 190 No H-bonds generated for 'chain 'R' and resid 188 through 190' Processing helix chain 'R' and resid 193 through 203 Processing helix chain 'R' and resid 205 through 221 removed outlier: 3.667A pdb=" N VAL R 209 " --> pdb=" O TYR R 205 " (cutoff:3.500A) Processing helix chain 'R' and resid 393 through 425 Proline residue: R 415 - end of helix removed outlier: 3.960A pdb=" N LEU R 421 " --> pdb=" O ASN R 417 " (cutoff:3.500A) Processing helix chain 'R' and resid 432 through 453 removed outlier: 3.833A pdb=" N ASN R 445 " --> pdb=" O LEU R 441 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N SER R 446 " --> pdb=" O CYS R 442 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N THR R 447 " --> pdb=" O TYR R 443 " (cutoff:3.500A) Proline residue: R 450 - end of helix Processing helix chain 'R' and resid 458 through 465 Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'G' and resid 9 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'H' and resid 53 through 55 No H-bonds generated for 'chain 'H' and resid 53 through 55' Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing helix chain 'H' and resid 221 through 223 No H-bonds generated for 'chain 'H' and resid 221 through 223' Processing helix chain 'A' and resid 7 through 31 Processing helix chain 'A' and resid 46 through 54 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 227 through 230 Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 280 removed outlier: 3.847A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 310 removed outlier: 4.373A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 350 Processing sheet with id= A, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.962A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.800A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.712A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.957A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.720A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.522A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 317 through 320 removed outlier: 3.524A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'H' and resid 3 through 7 Processing sheet with id= I, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.873A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'H' and resid 146 through 148 removed outlier: 6.454A pdb=" N LYS H 244 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LEU H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N LEU H 187 " --> pdb=" O LEU H 178 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'H' and resid 155 through 160 removed outlier: 3.838A pdb=" N ALA H 211 " --> pdb=" O SER H 208 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.731A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) 410 hydrogen bonds defined for protein. 1167 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: 2.75 Time building geometry restraints manager: 3.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2791 1.34 - 1.46: 2202 1.46 - 1.58: 3867 1.58 - 1.70: 4 1.70 - 1.82: 93 Bond restraints: 8957 Sorted by residual: bond pdb=" C8 XNO R 501 " pdb=" C9 XNO R 501 " ideal model delta sigma weight residual 1.549 1.329 0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" C8 XNO R 502 " pdb=" C9 XNO R 502 " ideal model delta sigma weight residual 1.549 1.332 0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C6 XNO R 501 " pdb=" C7 XNO R 501 " ideal model delta sigma weight residual 1.587 1.429 0.158 2.00e-02 2.50e+03 6.20e+01 bond pdb=" C6 XNO R 502 " pdb=" C7 XNO R 502 " ideal model delta sigma weight residual 1.587 1.431 0.156 2.00e-02 2.50e+03 6.06e+01 bond pdb=" C11 XNO R 502 " pdb=" N2 XNO R 502 " ideal model delta sigma weight residual 1.308 1.462 -0.154 2.00e-02 2.50e+03 5.90e+01 ... (remaining 8952 not shown) Histogram of bond angle deviations from ideal: 98.43 - 105.59: 143 105.59 - 112.75: 4689 112.75 - 119.91: 3196 119.91 - 127.07: 4018 127.07 - 134.23: 104 Bond angle restraints: 12150 Sorted by residual: angle pdb=" N XNO R 502 " pdb=" C6 XNO R 502 " pdb=" O XNO R 502 " ideal model delta sigma weight residual 91.30 123.54 -32.24 3.00e+00 1.11e-01 1.16e+02 angle pdb=" N XNO R 501 " pdb=" C6 XNO R 501 " pdb=" O XNO R 501 " ideal model delta sigma weight residual 91.30 123.39 -32.09 3.00e+00 1.11e-01 1.14e+02 angle pdb=" O XNO R 502 " pdb=" C6 XNO R 502 " pdb=" C7 XNO R 502 " ideal model delta sigma weight residual 151.31 121.73 29.58 3.00e+00 1.11e-01 9.72e+01 angle pdb=" O XNO R 501 " pdb=" C6 XNO R 501 " pdb=" C7 XNO R 501 " ideal model delta sigma weight residual 151.31 121.82 29.49 3.00e+00 1.11e-01 9.66e+01 angle pdb=" C ARG H 191 " pdb=" N MET H 192 " pdb=" CA MET H 192 " ideal model delta sigma weight residual 121.54 129.52 -7.98 1.91e+00 2.74e-01 1.74e+01 ... (remaining 12145 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.95: 5117 23.95 - 47.89: 157 47.89 - 71.84: 22 71.84 - 95.79: 4 95.79 - 119.74: 2 Dihedral angle restraints: 5302 sinusoidal: 2027 harmonic: 3275 Sorted by residual: dihedral pdb=" C10 XNO R 501 " pdb=" C11 XNO R 501 " pdb=" N2 XNO R 501 " pdb=" C12 XNO R 501 " ideal model delta sinusoidal sigma weight residual 56.95 -62.79 119.74 1 3.00e+01 1.11e-03 1.60e+01 dihedral pdb=" C11 XNO R 501 " pdb=" C12 XNO R 501 " pdb=" N2 XNO R 501 " pdb=" C8 XNO R 501 " ideal model delta sinusoidal sigma weight residual 52.12 -60.02 112.14 1 3.00e+01 1.11e-03 1.47e+01 dihedral pdb=" CA ASP B 153 " pdb=" CB ASP B 153 " pdb=" CG ASP B 153 " pdb=" OD1 ASP B 153 " ideal model delta sinusoidal sigma weight residual -30.00 -89.82 59.82 1 2.00e+01 2.50e-03 1.19e+01 ... (remaining 5299 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 883 0.043 - 0.085: 336 0.085 - 0.128: 120 0.128 - 0.170: 40 0.170 - 0.213: 12 Chirality restraints: 1391 Sorted by residual: chirality pdb=" CA THR B 196 " pdb=" N THR B 196 " pdb=" C THR B 196 " pdb=" CB THR B 196 " both_signs ideal model delta sigma weight residual False 2.53 2.31 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CG LEU B 286 " pdb=" CB LEU B 286 " pdb=" CD1 LEU B 286 " pdb=" CD2 LEU B 286 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CB THR B 164 " pdb=" CA THR B 164 " pdb=" OG1 THR B 164 " pdb=" CG2 THR B 164 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.97e-01 ... (remaining 1388 not shown) Planarity restraints: 1524 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR R 90 " 0.018 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C THR R 90 " -0.062 2.00e-02 2.50e+03 pdb=" O THR R 90 " 0.023 2.00e-02 2.50e+03 pdb=" N VAL R 91 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR R 399 " 0.013 2.00e-02 2.50e+03 2.70e-02 7.30e+00 pdb=" C THR R 399 " -0.047 2.00e-02 2.50e+03 pdb=" O THR R 399 " 0.017 2.00e-02 2.50e+03 pdb=" N ARG R 400 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.042 5.00e-02 4.00e+02 6.29e-02 6.33e+00 pdb=" N PRO B 236 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.035 5.00e-02 4.00e+02 ... (remaining 1521 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2520 2.82 - 3.34: 7773 3.34 - 3.86: 15092 3.86 - 4.38: 18086 4.38 - 4.90: 31048 Nonbonded interactions: 74519 Sorted by model distance: nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.299 2.440 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.318 2.440 nonbonded pdb=" O SER R 116 " pdb=" OG SER R 119 " model vdw 2.332 2.440 nonbonded pdb=" OH TYR H 175 " pdb=" OE2 GLU A 8 " model vdw 2.335 2.440 nonbonded pdb=" OH TYR A 290 " pdb=" O SER A 293 " model vdw 2.384 2.440 ... (remaining 74514 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.430 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: 0.000 Extract box with map and model: 4.140 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 27.560 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 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:14.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.220 8957 Z= 0.467 Angle : 1.016 32.242 12150 Z= 0.506 Chirality : 0.055 0.213 1391 Planarity : 0.007 0.063 1524 Dihedral : 12.348 119.736 3176 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.11 % Allowed : 0.95 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.73 (0.23), residues: 1111 helix: -0.62 (0.23), residues: 396 sheet: 0.42 (0.29), residues: 298 loop : -0.83 (0.27), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 82 HIS 0.008 0.001 HIS A 188 PHE 0.033 0.002 PHE B 234 TYR 0.023 0.002 TYR H 190 ARG 0.004 0.000 ARG R 396 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 152 time to evaluate : 1.062 Fit side-chains revert: symmetry clash REVERT: R 148 MET cc_start: 0.7422 (mtp) cc_final: 0.7211 (ttt) REVERT: R 432 ASP cc_start: 0.8224 (m-30) cc_final: 0.8022 (m-30) REVERT: R 465 ARG cc_start: 0.8878 (mtt-85) cc_final: 0.7820 (ppt170) REVERT: G 17 GLU cc_start: 0.8694 (tp30) cc_final: 0.8181 (tp30) REVERT: H 13 GLN cc_start: 0.8922 (mm110) cc_final: 0.8642 (mp-120) REVERT: H 73 ASP cc_start: 0.8829 (t0) cc_final: 0.8533 (t0) REVERT: H 244 LYS cc_start: 0.9015 (tttt) cc_final: 0.8686 (tttp) REVERT: A 287 TYR cc_start: 0.9087 (m-80) cc_final: 0.8640 (m-80) outliers start: 1 outliers final: 1 residues processed: 152 average time/residue: 1.8127 time to fit residues: 287.9063 Evaluate side-chains 125 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 124 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 270 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 10.0000 chunk 99 optimal weight: 7.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 188 GLN B 36 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8957 Z= 0.209 Angle : 0.523 7.225 12150 Z= 0.276 Chirality : 0.042 0.135 1391 Planarity : 0.004 0.048 1524 Dihedral : 6.112 88.090 1244 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 0.95 % Allowed : 8.59 % Favored : 90.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 (0.24), residues: 1111 helix: 1.27 (0.26), residues: 392 sheet: 0.61 (0.29), residues: 288 loop : -0.56 (0.27), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.004 0.001 HIS A 188 PHE 0.014 0.001 PHE A 189 TYR 0.014 0.001 TYR H 190 ARG 0.005 0.000 ARG R 400 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 129 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 178 ARG cc_start: 0.7851 (ttm170) cc_final: 0.7629 (ttm170) REVERT: R 396 ARG cc_start: 0.8009 (mpt-90) cc_final: 0.7805 (mmt90) REVERT: R 432 ASP cc_start: 0.8123 (m-30) cc_final: 0.7904 (m-30) REVERT: R 465 ARG cc_start: 0.8835 (mtt-85) cc_final: 0.7806 (ppt170) REVERT: B 197 ARG cc_start: 0.8512 (mtp-110) cc_final: 0.8283 (mmm160) REVERT: B 215 GLU cc_start: 0.8682 (mp0) cc_final: 0.8114 (mp0) REVERT: B 217 MET cc_start: 0.8905 (ptm) cc_final: 0.8568 (pmm) REVERT: G 17 GLU cc_start: 0.8739 (tp30) cc_final: 0.8032 (tp30) REVERT: G 21 MET cc_start: 0.9057 (mmm) cc_final: 0.8666 (mmm) REVERT: H 13 GLN cc_start: 0.8941 (mm110) cc_final: 0.8706 (mp-120) outliers start: 9 outliers final: 1 residues processed: 131 average time/residue: 1.9625 time to fit residues: 268.0904 Evaluate side-chains 125 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 124 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 83 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 chunk 100 optimal weight: 4.9990 chunk 108 optimal weight: 0.2980 chunk 89 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 80 optimal weight: 7.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8957 Z= 0.212 Angle : 0.514 7.224 12150 Z= 0.269 Chirality : 0.041 0.136 1391 Planarity : 0.003 0.045 1524 Dihedral : 5.565 78.748 1242 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.38 % Allowed : 9.54 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.07 (0.25), residues: 1111 helix: 1.88 (0.27), residues: 393 sheet: 0.69 (0.29), residues: 286 loop : -0.31 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.004 0.001 HIS B 54 PHE 0.014 0.001 PHE R 84 TYR 0.014 0.001 TYR H 190 ARG 0.008 0.000 ARG R 143 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 127 time to evaluate : 0.948 Fit side-chains revert: symmetry clash REVERT: R 223 ARG cc_start: 0.8198 (mpp80) cc_final: 0.7673 (mpt-90) REVERT: R 395 GLU cc_start: 0.7683 (tt0) cc_final: 0.7277 (tt0) REVERT: R 432 ASP cc_start: 0.8151 (m-30) cc_final: 0.7915 (m-30) REVERT: R 465 ARG cc_start: 0.8846 (mtt-85) cc_final: 0.7787 (ppt170) REVERT: B 215 GLU cc_start: 0.8666 (mp0) cc_final: 0.8000 (mp0) REVERT: B 217 MET cc_start: 0.8961 (ptm) cc_final: 0.8612 (pmm) REVERT: G 17 GLU cc_start: 0.8755 (tp30) cc_final: 0.8112 (tp30) REVERT: G 21 MET cc_start: 0.9083 (mmm) cc_final: 0.8699 (mmm) REVERT: H 13 GLN cc_start: 0.8917 (mm110) cc_final: 0.8706 (mp-120) REVERT: A 242 ARG cc_start: 0.8893 (mtp85) cc_final: 0.8685 (mtp85) outliers start: 13 outliers final: 2 residues processed: 132 average time/residue: 1.9562 time to fit residues: 269.1274 Evaluate side-chains 128 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 126 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain H residue 149 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 9.9990 chunk 75 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 95 optimal weight: 0.3980 chunk 28 optimal weight: 6.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8957 Z= 0.275 Angle : 0.528 8.006 12150 Z= 0.277 Chirality : 0.042 0.131 1391 Planarity : 0.003 0.044 1524 Dihedral : 5.640 85.928 1242 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.27 % Allowed : 11.03 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.24 (0.25), residues: 1111 helix: 2.01 (0.27), residues: 399 sheet: 0.69 (0.29), residues: 287 loop : -0.16 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS B 62 PHE 0.016 0.001 PHE R 84 TYR 0.013 0.001 TYR H 190 ARG 0.009 0.000 ARG R 143 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 129 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 148 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.8056 (mpp) REVERT: R 184 GLN cc_start: 0.8075 (mm-40) cc_final: 0.7834 (mm-40) REVERT: R 223 ARG cc_start: 0.8264 (mpp80) cc_final: 0.7778 (mpt-90) REVERT: R 395 GLU cc_start: 0.7744 (tt0) cc_final: 0.7303 (tt0) REVERT: R 432 ASP cc_start: 0.8124 (m-30) cc_final: 0.7917 (m-30) REVERT: R 465 ARG cc_start: 0.8860 (mtt-85) cc_final: 0.7804 (ppt170) REVERT: B 197 ARG cc_start: 0.8661 (mmm160) cc_final: 0.8301 (mmm-85) REVERT: B 214 ARG cc_start: 0.8696 (mmt-90) cc_final: 0.8495 (mmt90) REVERT: B 215 GLU cc_start: 0.8702 (mp0) cc_final: 0.8088 (mp0) REVERT: B 217 MET cc_start: 0.8965 (ptm) cc_final: 0.8634 (pmm) REVERT: G 17 GLU cc_start: 0.8767 (tp30) cc_final: 0.8301 (tp30) REVERT: G 58 GLU cc_start: 0.8657 (pm20) cc_final: 0.8312 (pm20) REVERT: H 13 GLN cc_start: 0.8928 (mm110) cc_final: 0.8680 (mp-120) REVERT: A 242 ARG cc_start: 0.8912 (mtp85) cc_final: 0.8709 (mtp85) outliers start: 12 outliers final: 4 residues processed: 132 average time/residue: 1.9520 time to fit residues: 268.5945 Evaluate side-chains 132 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 127 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 148 MET Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain A residue 325 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.9980 chunk 60 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 0.2980 chunk 95 optimal weight: 0.0370 chunk 26 optimal weight: 5.9990 overall best weight: 1.6662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 188 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8957 Z= 0.214 Angle : 0.518 8.914 12150 Z= 0.268 Chirality : 0.041 0.131 1391 Planarity : 0.003 0.043 1524 Dihedral : 5.474 88.345 1242 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.70 % Allowed : 11.13 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.36 (0.25), residues: 1111 helix: 2.12 (0.27), residues: 399 sheet: 0.74 (0.29), residues: 286 loop : -0.09 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS A 188 PHE 0.016 0.001 PHE R 84 TYR 0.013 0.001 TYR H 190 ARG 0.009 0.000 ARG R 143 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 130 time to evaluate : 0.999 Fit side-chains revert: symmetry clash REVERT: R 61 ARG cc_start: 0.8482 (ttm110) cc_final: 0.8012 (tpp80) REVERT: R 78 ASP cc_start: 0.8629 (m-30) cc_final: 0.8095 (t0) REVERT: R 184 GLN cc_start: 0.8192 (mm-40) cc_final: 0.7898 (mm-40) REVERT: R 223 ARG cc_start: 0.8265 (mpp80) cc_final: 0.7813 (mpt-90) REVERT: R 395 GLU cc_start: 0.7678 (tt0) cc_final: 0.7306 (tt0) REVERT: R 432 ASP cc_start: 0.8147 (m-30) cc_final: 0.7852 (m-30) REVERT: R 465 ARG cc_start: 0.8858 (mtt-85) cc_final: 0.7829 (ppt170) REVERT: B 217 MET cc_start: 0.8977 (ptm) cc_final: 0.8662 (pmm) REVERT: G 17 GLU cc_start: 0.8742 (tp30) cc_final: 0.8298 (tp30) REVERT: G 58 GLU cc_start: 0.8634 (pm20) cc_final: 0.8224 (pm20) REVERT: H 13 GLN cc_start: 0.8946 (mm110) cc_final: 0.8701 (mp-120) REVERT: H 65 LYS cc_start: 0.9188 (OUTLIER) cc_final: 0.8848 (tptp) REVERT: H 220 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8283 (mt-10) REVERT: A 242 ARG cc_start: 0.8919 (mtp85) cc_final: 0.8718 (mtp85) outliers start: 16 outliers final: 4 residues processed: 135 average time/residue: 2.0070 time to fit residues: 282.1797 Evaluate side-chains 132 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 127 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 188 GLN Chi-restraints excluded: chain H residue 65 LYS Chi-restraints excluded: chain H residue 149 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.3980 chunk 95 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 102 optimal weight: 7.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 188 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8957 Z= 0.218 Angle : 0.522 9.988 12150 Z= 0.271 Chirality : 0.041 0.132 1391 Planarity : 0.003 0.045 1524 Dihedral : 5.431 88.487 1242 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.48 % Allowed : 11.66 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.39 (0.25), residues: 1111 helix: 2.14 (0.27), residues: 399 sheet: 0.75 (0.29), residues: 287 loop : -0.05 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS A 188 PHE 0.019 0.001 PHE R 84 TYR 0.013 0.001 TYR H 190 ARG 0.011 0.001 ARG R 143 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 132 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 61 ARG cc_start: 0.8487 (ttm110) cc_final: 0.7981 (tpp80) REVERT: R 78 ASP cc_start: 0.8638 (m-30) cc_final: 0.8398 (m-30) REVERT: R 223 ARG cc_start: 0.8275 (mpp80) cc_final: 0.7850 (mpt-90) REVERT: R 395 GLU cc_start: 0.7689 (tt0) cc_final: 0.7298 (tt0) REVERT: R 432 ASP cc_start: 0.8158 (m-30) cc_final: 0.7886 (m-30) REVERT: R 465 ARG cc_start: 0.8857 (mtt-85) cc_final: 0.7836 (ppt170) REVERT: B 217 MET cc_start: 0.8985 (ptm) cc_final: 0.8663 (pmm) REVERT: G 17 GLU cc_start: 0.8754 (tp30) cc_final: 0.8327 (tp30) REVERT: G 58 GLU cc_start: 0.8594 (pm20) cc_final: 0.8177 (pm20) REVERT: H 13 GLN cc_start: 0.8946 (mm110) cc_final: 0.8701 (mp-120) REVERT: H 65 LYS cc_start: 0.9186 (OUTLIER) cc_final: 0.8852 (tptp) REVERT: A 242 ARG cc_start: 0.8925 (mtp85) cc_final: 0.8705 (mtp85) outliers start: 14 outliers final: 6 residues processed: 135 average time/residue: 1.9510 time to fit residues: 274.5596 Evaluate side-chains 134 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 127 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 188 GLN Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain H residue 65 LYS Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain A residue 53 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 chunk 77 optimal weight: 8.9990 chunk 89 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 48 optimal weight: 0.1980 chunk 65 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 188 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8957 Z= 0.275 Angle : 0.555 10.709 12150 Z= 0.285 Chirality : 0.042 0.130 1391 Planarity : 0.003 0.050 1524 Dihedral : 5.485 87.601 1242 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.48 % Allowed : 12.51 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.42 (0.25), residues: 1111 helix: 2.19 (0.27), residues: 393 sheet: 0.71 (0.29), residues: 293 loop : -0.01 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS A 188 PHE 0.020 0.001 PHE R 84 TYR 0.012 0.001 TYR H 190 ARG 0.011 0.000 ARG R 400 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 124 time to evaluate : 1.047 Fit side-chains revert: symmetry clash REVERT: R 61 ARG cc_start: 0.8495 (ttm110) cc_final: 0.7985 (tpp80) REVERT: R 78 ASP cc_start: 0.8669 (m-30) cc_final: 0.8400 (m-30) REVERT: R 223 ARG cc_start: 0.8294 (mpp80) cc_final: 0.7865 (mpt-90) REVERT: R 395 GLU cc_start: 0.7726 (tt0) cc_final: 0.7331 (tt0) REVERT: R 432 ASP cc_start: 0.8177 (m-30) cc_final: 0.7909 (m-30) REVERT: R 465 ARG cc_start: 0.8847 (mtt-85) cc_final: 0.7882 (ppt170) REVERT: B 9 GLN cc_start: 0.8750 (mm-40) cc_final: 0.8411 (mm-40) REVERT: B 197 ARG cc_start: 0.8650 (mmm160) cc_final: 0.8317 (mmm-85) REVERT: B 217 MET cc_start: 0.8997 (ptm) cc_final: 0.8680 (pmm) REVERT: G 17 GLU cc_start: 0.8750 (tp30) cc_final: 0.8310 (tp30) REVERT: G 58 GLU cc_start: 0.8590 (pm20) cc_final: 0.8107 (pm20) REVERT: H 13 GLN cc_start: 0.8950 (mm110) cc_final: 0.8679 (mp-120) REVERT: H 65 LYS cc_start: 0.9195 (OUTLIER) cc_final: 0.8861 (tptp) REVERT: A 242 ARG cc_start: 0.8929 (mtp85) cc_final: 0.8714 (mtp85) outliers start: 14 outliers final: 5 residues processed: 128 average time/residue: 2.0264 time to fit residues: 270.2603 Evaluate side-chains 129 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 123 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 65 LYS Chi-restraints excluded: chain H residue 149 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 52 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 96 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 188 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8957 Z= 0.223 Angle : 0.547 11.441 12150 Z= 0.282 Chirality : 0.042 0.137 1391 Planarity : 0.004 0.052 1524 Dihedral : 5.402 88.837 1242 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.27 % Allowed : 12.51 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.36 (0.25), residues: 1111 helix: 2.06 (0.27), residues: 399 sheet: 0.72 (0.29), residues: 293 loop : -0.03 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS A 188 PHE 0.022 0.001 PHE R 84 TYR 0.013 0.001 TYR H 190 ARG 0.013 0.001 ARG R 143 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 127 time to evaluate : 1.142 Fit side-chains revert: symmetry clash REVERT: R 61 ARG cc_start: 0.8480 (ttm110) cc_final: 0.8001 (tpp80) REVERT: R 223 ARG cc_start: 0.8247 (mpp80) cc_final: 0.7833 (mpt-90) REVERT: R 395 GLU cc_start: 0.7699 (tt0) cc_final: 0.7356 (tt0) REVERT: R 432 ASP cc_start: 0.8159 (m-30) cc_final: 0.7888 (m-30) REVERT: R 465 ARG cc_start: 0.8843 (mtt-85) cc_final: 0.7894 (ppt170) REVERT: B 9 GLN cc_start: 0.8772 (mm-40) cc_final: 0.8437 (mm-40) REVERT: B 217 MET cc_start: 0.8970 (ptm) cc_final: 0.8725 (pmm) REVERT: G 17 GLU cc_start: 0.8747 (tp30) cc_final: 0.8302 (tp30) REVERT: G 58 GLU cc_start: 0.8569 (pm20) cc_final: 0.8168 (pm20) REVERT: H 13 GLN cc_start: 0.8965 (mm110) cc_final: 0.8691 (mp-120) REVERT: H 65 LYS cc_start: 0.9189 (OUTLIER) cc_final: 0.8858 (tptp) REVERT: H 89 GLU cc_start: 0.8623 (pm20) cc_final: 0.8398 (pp20) REVERT: H 220 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8261 (mt-10) REVERT: A 242 ARG cc_start: 0.8933 (mtp85) cc_final: 0.8720 (mtp85) REVERT: A 318 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.8059 (tp30) outliers start: 12 outliers final: 6 residues processed: 130 average time/residue: 1.9251 time to fit residues: 260.9159 Evaluate side-chains 132 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 124 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 188 GLN Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain H residue 65 LYS Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 318 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 8.9990 chunk 101 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 77 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 64 optimal weight: 0.2980 chunk 104 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 188 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8957 Z= 0.185 Angle : 0.548 12.008 12150 Z= 0.280 Chirality : 0.041 0.132 1391 Planarity : 0.004 0.057 1524 Dihedral : 5.287 89.686 1242 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.95 % Allowed : 13.57 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.40 (0.25), residues: 1111 helix: 2.12 (0.27), residues: 394 sheet: 0.74 (0.29), residues: 293 loop : 0.01 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS A 188 PHE 0.025 0.001 PHE R 84 TYR 0.013 0.001 TYR H 190 ARG 0.014 0.001 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 129 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 61 ARG cc_start: 0.8455 (ttm110) cc_final: 0.7942 (tpp80) REVERT: R 223 ARG cc_start: 0.8252 (mpp80) cc_final: 0.7841 (mpt-90) REVERT: R 395 GLU cc_start: 0.7734 (tt0) cc_final: 0.7376 (tt0) REVERT: R 432 ASP cc_start: 0.8142 (m-30) cc_final: 0.7873 (m-30) REVERT: R 465 ARG cc_start: 0.8857 (mtt-85) cc_final: 0.7851 (ppt170) REVERT: B 9 GLN cc_start: 0.8798 (mm-40) cc_final: 0.8477 (mm-40) REVERT: B 23 LYS cc_start: 0.9234 (tppp) cc_final: 0.8935 (tptp) REVERT: B 217 MET cc_start: 0.8933 (ptm) cc_final: 0.8714 (pmm) REVERT: G 17 GLU cc_start: 0.8752 (tp30) cc_final: 0.8310 (tp30) REVERT: G 58 GLU cc_start: 0.8536 (pm20) cc_final: 0.8146 (pm20) REVERT: H 13 GLN cc_start: 0.8954 (mm110) cc_final: 0.8700 (mp-120) REVERT: H 43 LYS cc_start: 0.8925 (mmmm) cc_final: 0.8695 (mmmt) REVERT: A 242 ARG cc_start: 0.8922 (mtp85) cc_final: 0.8705 (mtp85) REVERT: A 318 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.8058 (tp30) outliers start: 9 outliers final: 5 residues processed: 133 average time/residue: 1.9964 time to fit residues: 276.7277 Evaluate side-chains 129 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 123 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 188 GLN Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 318 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 188 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8957 Z= 0.198 Angle : 0.555 11.739 12150 Z= 0.285 Chirality : 0.041 0.132 1391 Planarity : 0.004 0.060 1524 Dihedral : 5.255 89.936 1242 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.74 % Allowed : 14.10 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.33 (0.25), residues: 1111 helix: 1.97 (0.27), residues: 400 sheet: 0.73 (0.29), residues: 293 loop : 0.01 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS A 188 PHE 0.026 0.001 PHE R 84 TYR 0.012 0.001 TYR H 190 ARG 0.014 0.001 ARG R 143 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 125 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 61 ARG cc_start: 0.8468 (ttm110) cc_final: 0.7952 (tpp80) REVERT: R 223 ARG cc_start: 0.8253 (mpp80) cc_final: 0.7683 (mpt-90) REVERT: R 432 ASP cc_start: 0.8127 (m-30) cc_final: 0.7883 (m-30) REVERT: R 465 ARG cc_start: 0.8837 (mtt-85) cc_final: 0.7884 (ppt170) REVERT: B 9 GLN cc_start: 0.8810 (mm-40) cc_final: 0.8424 (mm-40) REVERT: B 215 GLU cc_start: 0.8771 (mp0) cc_final: 0.8542 (mp0) REVERT: B 217 MET cc_start: 0.8925 (ptm) cc_final: 0.8713 (pmm) REVERT: G 17 GLU cc_start: 0.8753 (tp30) cc_final: 0.8300 (tp30) REVERT: G 58 GLU cc_start: 0.8527 (pm20) cc_final: 0.8140 (pm20) REVERT: H 13 GLN cc_start: 0.8939 (mm110) cc_final: 0.8699 (mp-120) REVERT: A 242 ARG cc_start: 0.8923 (mtp85) cc_final: 0.8705 (mtp85) REVERT: A 318 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8022 (tp30) outliers start: 7 outliers final: 6 residues processed: 128 average time/residue: 2.0101 time to fit residues: 268.1032 Evaluate side-chains 130 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 123 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 188 GLN Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 318 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 76 optimal weight: 8.9990 chunk 4 optimal weight: 6.9990 chunk 63 optimal weight: 0.9980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 188 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.085298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.052846 restraints weight = 16378.004| |-----------------------------------------------------------------------------| r_work (start): 0.2627 rms_B_bonded: 2.51 r_work: 0.2470 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2334 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8957 Z= 0.201 Angle : 0.558 10.743 12150 Z= 0.285 Chirality : 0.041 0.132 1391 Planarity : 0.004 0.062 1524 Dihedral : 5.226 89.770 1242 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.74 % Allowed : 14.32 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.38 (0.25), residues: 1111 helix: 2.05 (0.27), residues: 394 sheet: 0.73 (0.29), residues: 293 loop : 0.05 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS A 188 PHE 0.026 0.001 PHE R 84 TYR 0.013 0.001 TYR H 190 ARG 0.014 0.001 ARG R 400 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4658.65 seconds wall clock time: 82 minutes 57.77 seconds (4977.77 seconds total)