Starting phenix.real_space_refine on Wed Feb 14 02:02:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rmg_24569/02_2024/7rmg_24569_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rmg_24569/02_2024/7rmg_24569.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rmg_24569/02_2024/7rmg_24569.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rmg_24569/02_2024/7rmg_24569.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rmg_24569/02_2024/7rmg_24569_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rmg_24569/02_2024/7rmg_24569_updated.pdb" } resolution = 3.0 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= 0.004 sd= 0.412 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1082 atoms to isotropic. 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 53 5.16 5 C 4737 2.51 5 N 1226 2.21 5 O 1300 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7316 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1510 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 4, 'TRANS': 188} Chain breaks: 3 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 7, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 71 Chain: "R" Number of atoms: 2306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2306 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 14, 'TRANS': 274} Chain breaks: 1 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 43 Chain: "S" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 85 Unusual residues: {'NH2': 1} Classifications: {'peptide': 11, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'NH2_CTERM': 1, 'PTRANS': 2, 'TRANS': 8} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2319 Classifications: {'peptide': 322} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 5, 'TRANS': 316} Chain breaks: 1 Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 2, 'ARG:plan': 7, 'ASN:plan1': 5, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 113 Chain: "G" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 245 Classifications: {'peptide': 38} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 1, 'TRANS': 36} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "N" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 851 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Time building chain proxies: 5.06, per 1000 atoms: 0.69 Number of scatterers: 7316 At special positions: 0 Unit cell: (70.14, 96.86, 131.93, 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 53 16.00 O 1300 8.00 N 1226 7.00 C 4737 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 105 " - pdb=" SG CYS R 180 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " 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: 3.20 Conformation dependent library (CDL) restraints added in 1.4 seconds 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1838 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 21 helices and 11 sheets defined 36.1% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'A' and resid 26 through 37 removed outlier: 3.515A pdb=" N GLN A 31 " --> pdb=" O GLU A 27 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP A 33 " --> pdb=" O GLN A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 238 Processing helix chain 'A' and resid 266 through 277 Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 333 through 351 removed outlier: 3.587A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 removed outlier: 3.553A pdb=" N ARG A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) Processing helix chain 'R' and resid 29 through 59 removed outlier: 3.988A pdb=" N ILE R 42 " --> pdb=" O ALA R 38 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 94 removed outlier: 3.573A pdb=" N TYR R 69 " --> pdb=" O VAL R 66 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N PHE R 70 " --> pdb=" O THR R 67 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER R 80 " --> pdb=" O ALA R 77 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA R 83 " --> pdb=" O SER R 80 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE R 84 " --> pdb=" O MET R 81 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASN R 85 " --> pdb=" O ALA R 82 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR R 86 " --> pdb=" O ALA R 83 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL R 87 " --> pdb=" O PHE R 84 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL R 88 " --> pdb=" O ASN R 85 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN R 89 " --> pdb=" O THR R 86 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL R 94 " --> pdb=" O THR R 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 135 Proline residue: R 112 - end of helix Processing helix chain 'R' and resid 144 through 167 Proline residue: R 164 - end of helix Processing helix chain 'R' and resid 191 through 224 removed outlier: 5.024A pdb=" N LEU R 207 " --> pdb=" O LEU R 203 " (cutoff:3.500A) Proline residue: R 208 - end of helix Processing helix chain 'R' and resid 240 through 272 Proline residue: R 263 - end of helix Proline residue: R 271 - end of helix Processing helix chain 'R' and resid 275 through 279 removed outlier: 4.246A pdb=" N TYR R 278 " --> pdb=" O PRO R 275 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU R 279 " --> pdb=" O ASP R 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 275 through 279' Processing helix chain 'R' and resid 282 through 308 removed outlier: 4.231A pdb=" N SER R 297 " --> pdb=" O LEU R 293 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N THR R 298 " --> pdb=" O ALA R 294 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N MET R 299 " --> pdb=" O MET R 295 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N TYR R 300 " --> pdb=" O SER R 296 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N ASN R 301 " --> pdb=" O SER R 297 " (cutoff:3.500A) Proline residue: R 302 - end of helix Processing helix chain 'R' and resid 310 through 319 Processing helix chain 'B' and resid 15 through 24 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 14 through 23 Processing helix chain 'G' and resid 30 through 44 removed outlier: 3.577A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.290A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N GLY A 47 " --> pdb=" O PHE A 222 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'R' and resid 169 through 174 Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.016A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.109A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.887A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.754A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.953A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.589A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.779A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= K, first strand: chain 'N' and resid 122 through 124 removed outlier: 5.783A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) 347 hydrogen bonds defined for protein. 954 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: 2.32 Time building geometry restraints manager: 3.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1362 1.33 - 1.45: 2059 1.45 - 1.58: 3997 1.58 - 1.71: 0 1.71 - 1.83: 75 Bond restraints: 7493 Sorted by residual: bond pdb=" C ILE A 382 " pdb=" O ILE A 382 " ideal model delta sigma weight residual 1.237 1.202 0.035 1.19e-02 7.06e+03 8.43e+00 bond pdb=" N ILE B 58 " pdb=" CA ILE B 58 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.24e-02 6.50e+03 7.66e+00 bond pdb=" C ASP A 381 " pdb=" O ASP A 381 " ideal model delta sigma weight residual 1.236 1.202 0.034 1.26e-02 6.30e+03 7.24e+00 bond pdb=" N ILE A 382 " pdb=" CA ILE A 382 " ideal model delta sigma weight residual 1.460 1.492 -0.032 1.21e-02 6.83e+03 7.09e+00 bond pdb=" C ILE B 58 " pdb=" O ILE B 58 " ideal model delta sigma weight residual 1.237 1.206 0.031 1.20e-02 6.94e+03 6.84e+00 ... (remaining 7488 not shown) Histogram of bond angle deviations from ideal: 99.51 - 106.42: 185 106.42 - 113.33: 4020 113.33 - 120.24: 2700 120.24 - 127.15: 3229 127.15 - 134.06: 94 Bond angle restraints: 10228 Sorted by residual: angle pdb=" CA ILE A 382 " pdb=" C ILE A 382 " pdb=" O ILE A 382 " ideal model delta sigma weight residual 120.85 116.82 4.03 1.06e+00 8.90e-01 1.45e+01 angle pdb=" O ILE A 382 " pdb=" C ILE A 382 " pdb=" N ILE A 383 " ideal model delta sigma weight residual 121.83 125.41 -3.58 1.03e+00 9.43e-01 1.21e+01 angle pdb=" O LYS A 380 " pdb=" C LYS A 380 " pdb=" N ASP A 381 " ideal model delta sigma weight residual 122.12 118.52 3.60 1.06e+00 8.90e-01 1.15e+01 angle pdb=" N PHE R 111 " pdb=" CA PHE R 111 " pdb=" C PHE R 111 " ideal model delta sigma weight residual 109.81 117.17 -7.36 2.21e+00 2.05e-01 1.11e+01 angle pdb=" CA LYS A 380 " pdb=" C LYS A 380 " pdb=" N ASP A 381 " ideal model delta sigma weight residual 117.30 121.10 -3.80 1.16e+00 7.43e-01 1.08e+01 ... (remaining 10223 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.21: 3968 16.21 - 32.41: 294 32.41 - 48.61: 50 48.61 - 64.82: 11 64.82 - 81.02: 9 Dihedral angle restraints: 4332 sinusoidal: 1495 harmonic: 2837 Sorted by residual: dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual -180.00 -154.28 -25.72 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA CYS N 99 " pdb=" C CYS N 99 " pdb=" N PRO N 100 " pdb=" CA PRO N 100 " ideal model delta harmonic sigma weight residual -180.00 -156.50 -23.50 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA TYR R 205 " pdb=" C TYR R 205 " pdb=" N PHE R 206 " pdb=" CA PHE R 206 " ideal model delta harmonic sigma weight residual 180.00 -160.45 -19.55 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 4329 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 786 0.041 - 0.082: 272 0.082 - 0.123: 99 0.123 - 0.165: 31 0.165 - 0.206: 6 Chirality restraints: 1194 Sorted by residual: chirality pdb=" CB ILE B 58 " pdb=" CA ILE B 58 " pdb=" CG1 ILE B 58 " pdb=" CG2 ILE B 58 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CB ILE A 382 " pdb=" CA ILE A 382 " pdb=" CG1 ILE A 382 " pdb=" CG2 ILE A 382 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CB ILE A 383 " pdb=" CA ILE A 383 " pdb=" CG1 ILE A 383 " pdb=" CG2 ILE A 383 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 1191 not shown) Planarity restraints: 1276 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.044 5.00e-02 4.00e+02 6.70e-02 7.17e+00 pdb=" N PRO B 236 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA R 82 " 0.013 2.00e-02 2.50e+03 2.62e-02 6.85e+00 pdb=" C ALA R 82 " -0.045 2.00e-02 2.50e+03 pdb=" O ALA R 82 " 0.017 2.00e-02 2.50e+03 pdb=" N ALA R 83 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 241 " 0.013 2.00e-02 2.50e+03 1.95e-02 6.62e+00 pdb=" CG PHE B 241 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE B 241 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE B 241 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE B 241 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 241 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE B 241 " -0.001 2.00e-02 2.50e+03 ... (remaining 1273 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2024 2.81 - 3.33: 6140 3.33 - 3.86: 12130 3.86 - 4.38: 14067 4.38 - 4.90: 25035 Nonbonded interactions: 59396 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.290 2.440 nonbonded pdb=" O ALA R 36 " pdb=" OG1 THR R 40 " model vdw 2.290 2.440 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.315 2.440 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.322 2.440 nonbonded pdb=" O GLN B 75 " pdb=" OG SER B 98 " model vdw 2.349 2.440 ... (remaining 59391 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: 1.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 5.490 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 25.600 Find NCS groups from input model: 0.200 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:13.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 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 : 0.004 0.062 7493 Z= 0.255 Angle : 0.758 8.659 10228 Z= 0.433 Chirality : 0.051 0.206 1194 Planarity : 0.006 0.067 1276 Dihedral : 12.654 81.023 2485 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.14 % Allowed : 0.41 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.25), residues: 942 helix: -0.67 (0.24), residues: 352 sheet: 0.38 (0.34), residues: 211 loop : -0.97 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 99 HIS 0.015 0.002 HIS B 54 PHE 0.044 0.002 PHE B 241 TYR 0.020 0.002 TYR R 92 ARG 0.004 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 148 time to evaluate : 0.918 Fit side-chains REVERT: A 272 ASP cc_start: 0.6554 (m-30) cc_final: 0.5659 (m-30) outliers start: 1 outliers final: 0 residues processed: 149 average time/residue: 0.8880 time to fit residues: 142.1242 Evaluate side-chains 108 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 79 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 73 optimal weight: 8.9990 chunk 28 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN R 27 GLN R 73 ASN R 318 HIS B 75 GLN B 340 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7493 Z= 0.177 Angle : 0.501 8.852 10228 Z= 0.272 Chirality : 0.042 0.194 1194 Planarity : 0.004 0.052 1276 Dihedral : 4.172 21.839 1034 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.06 % Allowed : 10.03 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.26), residues: 942 helix: 0.60 (0.26), residues: 358 sheet: 0.55 (0.33), residues: 208 loop : -0.70 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.004 0.001 HIS A 220 PHE 0.013 0.001 PHE R 264 TYR 0.011 0.001 TYR G 40 ARG 0.006 0.000 ARG R 313 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 113 time to evaluate : 0.942 Fit side-chains REVERT: R 186 GLU cc_start: 0.6937 (OUTLIER) cc_final: 0.6308 (tm-30) REVERT: B 101 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.7310 (mmm) REVERT: N 50 ASP cc_start: 0.7610 (p0) cc_final: 0.7262 (p0) outliers start: 15 outliers final: 5 residues processed: 119 average time/residue: 0.9893 time to fit residues: 126.2454 Evaluate side-chains 105 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 98 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain R residue 186 GLU Chi-restraints excluded: chain R residue 251 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 245 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 47 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 85 optimal weight: 8.9990 chunk 92 optimal weight: 7.9990 chunk 76 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN R 318 HIS B 175 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 7493 Z= 0.364 Angle : 0.601 11.784 10228 Z= 0.325 Chirality : 0.046 0.189 1194 Planarity : 0.004 0.041 1276 Dihedral : 4.599 24.771 1034 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.88 % Allowed : 11.81 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.26), residues: 942 helix: 0.95 (0.27), residues: 361 sheet: 0.65 (0.34), residues: 198 loop : -0.68 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.006 0.001 HIS R 197 PHE 0.017 0.002 PHE R 264 TYR 0.011 0.001 TYR N 95 ARG 0.005 0.001 ARG R 313 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 95 time to evaluate : 0.796 Fit side-chains revert: symmetry clash REVERT: R 139 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7571 (mp10) REVERT: R 186 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6320 (tm-30) REVERT: N 50 ASP cc_start: 0.7928 (p0) cc_final: 0.7508 (p0) outliers start: 21 outliers final: 7 residues processed: 106 average time/residue: 1.0613 time to fit residues: 119.8876 Evaluate side-chains 100 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 91 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain R residue 139 GLN Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 186 GLU Chi-restraints excluded: chain R residue 251 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain N residue 7 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 84 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 75 optimal weight: 7.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN R 50 ASN R 284 GLN R 318 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7493 Z= 0.187 Angle : 0.499 10.063 10228 Z= 0.269 Chirality : 0.042 0.149 1194 Planarity : 0.003 0.038 1276 Dihedral : 4.132 20.894 1034 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.47 % Allowed : 14.01 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.27), residues: 942 helix: 1.36 (0.27), residues: 355 sheet: 0.65 (0.34), residues: 199 loop : -0.50 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.005 0.001 HIS R 318 PHE 0.015 0.001 PHE R 264 TYR 0.012 0.001 TYR A 339 ARG 0.003 0.000 ARG R 313 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 103 time to evaluate : 0.823 Fit side-chains revert: symmetry clash REVERT: R 63 MET cc_start: 0.6911 (OUTLIER) cc_final: 0.6419 (mmt) REVERT: R 139 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7622 (mp10) REVERT: R 186 GLU cc_start: 0.7077 (OUTLIER) cc_final: 0.6182 (tm-30) REVERT: N 50 ASP cc_start: 0.7839 (p0) cc_final: 0.7442 (p0) outliers start: 18 outliers final: 7 residues processed: 114 average time/residue: 0.9564 time to fit residues: 116.9786 Evaluate side-chains 107 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 97 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain R residue 63 MET Chi-restraints excluded: chain R residue 139 GLN Chi-restraints excluded: chain R residue 186 GLU Chi-restraints excluded: chain R residue 308 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain N residue 7 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 51 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 0.8980 chunk 81 optimal weight: 0.0000 chunk 22 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN ** R 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 318 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7493 Z= 0.246 Angle : 0.532 10.346 10228 Z= 0.285 Chirality : 0.043 0.164 1194 Planarity : 0.003 0.037 1276 Dihedral : 4.160 20.481 1034 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.30 % Allowed : 14.84 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.27), residues: 942 helix: 1.47 (0.28), residues: 355 sheet: 0.71 (0.34), residues: 198 loop : -0.45 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.005 0.001 HIS R 197 PHE 0.016 0.001 PHE R 264 TYR 0.013 0.001 TYR A 339 ARG 0.003 0.000 ARG R 313 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 99 time to evaluate : 0.794 Fit side-chains revert: symmetry clash REVERT: A 272 ASP cc_start: 0.6847 (m-30) cc_final: 0.6508 (m-30) REVERT: R 139 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7664 (mp10) REVERT: R 186 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6099 (tm-30) REVERT: N 50 ASP cc_start: 0.7935 (p0) cc_final: 0.7529 (p0) outliers start: 24 outliers final: 14 residues processed: 112 average time/residue: 0.9260 time to fit residues: 111.3963 Evaluate side-chains 106 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 90 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain R residue 139 GLN Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 186 GLU Chi-restraints excluded: chain R residue 251 ILE Chi-restraints excluded: chain R residue 273 ILE Chi-restraints excluded: chain R residue 306 CYS Chi-restraints excluded: chain R residue 308 LEU Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 99 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 81 optimal weight: 0.0170 chunk 17 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 90 optimal weight: 10.0000 chunk 75 optimal weight: 7.9990 chunk 42 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 0.0050 chunk 87 optimal weight: 9.9990 overall best weight: 0.7434 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 227 GLN R 284 GLN R 318 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7493 Z= 0.163 Angle : 0.492 8.046 10228 Z= 0.263 Chirality : 0.042 0.157 1194 Planarity : 0.003 0.037 1276 Dihedral : 3.954 20.025 1034 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.88 % Allowed : 15.38 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.27), residues: 942 helix: 1.64 (0.28), residues: 353 sheet: 0.67 (0.34), residues: 199 loop : -0.42 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.004 0.001 HIS R 318 PHE 0.013 0.001 PHE R 264 TYR 0.011 0.001 TYR R 278 ARG 0.003 0.000 ARG R 313 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 99 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 139 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7690 (mp10) REVERT: R 181 MET cc_start: 0.7596 (OUTLIER) cc_final: 0.7160 (ptt) REVERT: R 186 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6159 (tm-30) REVERT: N 50 ASP cc_start: 0.7826 (p0) cc_final: 0.7433 (p0) outliers start: 21 outliers final: 9 residues processed: 112 average time/residue: 0.9513 time to fit residues: 114.3799 Evaluate side-chains 111 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 99 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain R residue 139 GLN Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 181 MET Chi-restraints excluded: chain R residue 186 GLU Chi-restraints excluded: chain R residue 306 CYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 99 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 10 optimal weight: 0.9990 chunk 51 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 76 optimal weight: 8.9990 chunk 50 optimal weight: 0.4980 chunk 90 optimal weight: 0.4980 chunk 56 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 318 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7493 Z= 0.167 Angle : 0.491 7.630 10228 Z= 0.262 Chirality : 0.042 0.190 1194 Planarity : 0.003 0.036 1276 Dihedral : 3.848 19.815 1034 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.16 % Allowed : 15.66 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.27), residues: 942 helix: 1.70 (0.28), residues: 359 sheet: 0.68 (0.33), residues: 207 loop : -0.43 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.003 0.001 HIS R 197 PHE 0.013 0.001 PHE R 264 TYR 0.013 0.001 TYR R 278 ARG 0.002 0.000 ARG R 313 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 103 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 139 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7687 (mp10) REVERT: R 186 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6141 (tm-30) REVERT: B 138 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.6922 (mt-10) REVERT: N 50 ASP cc_start: 0.7824 (p0) cc_final: 0.7423 (p0) outliers start: 23 outliers final: 11 residues processed: 116 average time/residue: 0.9466 time to fit residues: 118.5285 Evaluate side-chains 110 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 96 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain R residue 139 GLN Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 186 GLU Chi-restraints excluded: chain R residue 251 ILE Chi-restraints excluded: chain R residue 273 ILE Chi-restraints excluded: chain R residue 306 CYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 99 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 27 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 71 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 79 optimal weight: 7.9990 chunk 84 optimal weight: 6.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 318 HIS B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7493 Z= 0.295 Angle : 0.570 9.771 10228 Z= 0.306 Chirality : 0.044 0.156 1194 Planarity : 0.003 0.035 1276 Dihedral : 4.253 23.276 1034 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.88 % Allowed : 16.62 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.27), residues: 942 helix: 1.59 (0.28), residues: 354 sheet: 0.96 (0.34), residues: 193 loop : -0.50 (0.31), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.005 0.001 HIS R 197 PHE 0.017 0.001 PHE R 264 TYR 0.015 0.001 TYR R 278 ARG 0.002 0.000 ARG R 313 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 94 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 139 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.7644 (mp10) REVERT: R 186 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6049 (tm-30) REVERT: N 50 ASP cc_start: 0.7973 (p0) cc_final: 0.7558 (p0) outliers start: 21 outliers final: 12 residues processed: 108 average time/residue: 0.9917 time to fit residues: 114.7147 Evaluate side-chains 107 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 93 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain R residue 139 GLN Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 186 GLU Chi-restraints excluded: chain R residue 251 ILE Chi-restraints excluded: chain R residue 273 ILE Chi-restraints excluded: chain R residue 306 CYS Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 99 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 86 optimal weight: 4.9990 chunk 50 optimal weight: 0.0370 chunk 36 optimal weight: 0.2980 chunk 66 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 76 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 55 optimal weight: 0.0000 chunk 89 optimal weight: 9.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.3662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 284 GLN R 318 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7493 Z= 0.146 Angle : 0.501 9.409 10228 Z= 0.266 Chirality : 0.041 0.157 1194 Planarity : 0.003 0.035 1276 Dihedral : 3.800 19.287 1034 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.79 % Allowed : 17.99 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.27), residues: 942 helix: 1.75 (0.28), residues: 355 sheet: 0.66 (0.33), residues: 205 loop : -0.39 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 297 HIS 0.005 0.001 HIS R 318 PHE 0.013 0.001 PHE A 212 TYR 0.017 0.001 TYR R 278 ARG 0.002 0.000 ARG R 313 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 103 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 50 ASP cc_start: 0.7794 (p0) cc_final: 0.7403 (p0) outliers start: 13 outliers final: 8 residues processed: 112 average time/residue: 0.9747 time to fit residues: 117.3868 Evaluate side-chains 106 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 98 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain R residue 306 CYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 99 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 42 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 86 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 318 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7493 Z= 0.186 Angle : 0.531 10.935 10228 Z= 0.281 Chirality : 0.043 0.205 1194 Planarity : 0.003 0.035 1276 Dihedral : 3.859 19.802 1034 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.37 % Allowed : 18.27 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.27), residues: 942 helix: 1.67 (0.28), residues: 356 sheet: 0.72 (0.33), residues: 207 loop : -0.39 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.004 0.001 HIS R 197 PHE 0.017 0.001 PHE R 282 TYR 0.015 0.001 TYR R 278 ARG 0.002 0.000 ARG R 313 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 99 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 50 ASP cc_start: 0.7871 (p0) cc_final: 0.7473 (p0) outliers start: 10 outliers final: 9 residues processed: 107 average time/residue: 0.9833 time to fit residues: 112.5632 Evaluate side-chains 107 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 98 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 306 CYS Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 99 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 68 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 318 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.105600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.093470 restraints weight = 15881.973| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.36 r_work: 0.3285 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7493 Z= 0.174 Angle : 0.524 10.405 10228 Z= 0.277 Chirality : 0.043 0.189 1194 Planarity : 0.003 0.035 1276 Dihedral : 3.823 19.858 1034 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.65 % Allowed : 18.13 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.27), residues: 942 helix: 1.68 (0.28), residues: 356 sheet: 0.72 (0.33), residues: 207 loop : -0.35 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.003 0.001 HIS R 197 PHE 0.015 0.001 PHE A 212 TYR 0.017 0.001 TYR R 278 ARG 0.002 0.000 ARG R 313 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2692.27 seconds wall clock time: 48 minutes 44.14 seconds (2924.14 seconds total)