Starting phenix.real_space_refine on Fri Jan 19 02:05:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dw9_30877/01_2024/7dw9_30877_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dw9_30877/01_2024/7dw9_30877.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dw9_30877/01_2024/7dw9_30877.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dw9_30877/01_2024/7dw9_30877.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dw9_30877/01_2024/7dw9_30877_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dw9_30877/01_2024/7dw9_30877_updated.pdb" } resolution = 2.6 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= 0.003 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 67 5.16 5 C 6423 2.51 5 N 1757 2.21 5 O 1858 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 10105 Number of models: 1 Model: "" Number of chains: 8 Chain: "R" Number of atoms: 2177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2177 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 263} Chain breaks: 2 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: "A" Number of atoms: 1971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1971 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 231} Chain breaks: 2 Chain: "B" Number of atoms: 2605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2605 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 335} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "Y" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "S" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1787 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Chain: "C" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Unusual residues: {'NH2': 1} Classifications: {'peptide': 9, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'PTRANS': 1, 'TRANS': 7} Chain: "R" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {'CLR': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.68, per 1000 atoms: 0.56 Number of scatterers: 10105 At special positions: 0 Unit cell: (131.88, 89.04, 118.44, 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 67 16.00 O 1858 8.00 N 1757 7.00 C 6423 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS R 112 " - pdb=" SG CYS R 192 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 Simple disulfide: pdb=" SG CYS C 1 " - pdb=" SG CYS C 6 " distance=2.03 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: 4.12 Conformation dependent library (CDL) restraints added in 1.9 seconds 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2396 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 32 helices and 15 sheets defined 32.2% alpha, 23.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.92 Creating SS restraints... Processing helix chain 'R' and resid 34 through 66 removed outlier: 4.586A pdb=" N ALA R 39 " --> pdb=" O LEU R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 73 through 91 Processing helix chain 'R' and resid 93 through 101 Processing helix chain 'R' and resid 109 through 142 removed outlier: 4.242A pdb=" N ALA R 114 " --> pdb=" O ALA R 110 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N MET R 120 " --> pdb=" O LYS R 116 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLY R 122 " --> pdb=" O LEU R 118 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N MET R 123 " --> pdb=" O GLN R 119 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR R 124 " --> pdb=" O MET R 120 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE R 130 " --> pdb=" O SER R 126 " (cutoff:3.500A) Processing helix chain 'R' and resid 158 through 177 removed outlier: 3.591A pdb=" N SER R 171 " --> pdb=" O SER R 167 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU R 172 " --> pdb=" O LEU R 168 " (cutoff:3.500A) Proline residue: R 173 - end of helix removed outlier: 4.229A pdb=" N PHE R 176 " --> pdb=" O LEU R 172 " (cutoff:3.500A) Processing helix chain 'R' and resid 201 through 213 removed outlier: 3.948A pdb=" N TYR R 205 " --> pdb=" O GLY R 201 " (cutoff:3.500A) Processing helix chain 'R' and resid 215 through 234 Processing helix chain 'R' and resid 264 through 296 Proline residue: R 286 - end of helix Processing helix chain 'R' and resid 305 through 328 removed outlier: 3.913A pdb=" N LEU R 312 " --> pdb=" O VAL R 308 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU R 313 " --> pdb=" O LEU R 309 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ALA R 314 " --> pdb=" O LEU R 310 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N SER R 315 " --> pdb=" O MET R 311 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU R 316 " --> pdb=" O LEU R 312 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ASN R 317 " --> pdb=" O LEU R 313 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N SER R 318 " --> pdb=" O ALA R 314 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N CYS R 319 " --> pdb=" O SER R 315 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR R 320 " --> pdb=" O LEU R 316 " (cutoff:3.500A) Proline residue: R 322 - end of helix Processing helix chain 'R' and resid 330 through 337 removed outlier: 3.762A pdb=" N GLU R 335 " --> pdb=" O SER R 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 7 through 38 removed outlier: 4.068A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 63 Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 308 through 310 No H-bonds generated for 'chain 'A' and resid 308 through 310' Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 332 through 351 removed outlier: 3.598A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 390 removed outlier: 3.889A pdb=" N ALA A 372 " --> pdb=" O THR A 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 25 Processing helix chain 'B' and resid 30 through 35 removed outlier: 3.555A pdb=" N ASN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing helix chain 'Y' and resid 7 through 24 Processing helix chain 'Y' and resid 30 through 43 Processing helix chain 'Y' and resid 45 through 47 No H-bonds generated for 'chain 'Y' and resid 45 through 47' Processing helix chain 'Y' and resid 56 through 58 No H-bonds generated for 'chain 'Y' and resid 56 through 58' Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 62 through 64 No H-bonds generated for 'chain 'N' and resid 62 through 64' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 53 through 55 No H-bonds generated for 'chain 'S' and resid 53 through 55' Processing helix chain 'S' and resid 88 through 90 No H-bonds generated for 'chain 'S' and resid 88 through 90' Processing helix chain 'S' and resid 221 through 223 No H-bonds generated for 'chain 'S' and resid 221 through 223' Processing sheet with id= A, first strand: chain 'R' and resid 178 through 181 Processing sheet with id= B, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.294A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N GLY A 47 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N VAL A 224 " --> pdb=" O GLY A 47 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.068A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.973A 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: 6.882A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.181A 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: 6.781A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.773A 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: 6.856A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.431A 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: 6.679A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.071A 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: 6.546A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.236A 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 52 removed outlier: 6.678A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.607A pdb=" N THR N 78 " --> pdb=" O ASP N 73 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'N' and resid 122 through 124 removed outlier: 6.154A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'S' and resid 3 through 7 Processing sheet with id= M, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.148A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'S' and resid 140 through 142 Processing sheet with id= O, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.597A pdb=" N LYS S 244 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) 445 hydrogen bonds defined for protein. 1137 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: 2.91 Time building geometry restraints manager: 4.50 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: 3287 1.34 - 1.46: 2513 1.46 - 1.58: 4436 1.58 - 1.70: 0 1.70 - 1.82: 96 Bond restraints: 10332 Sorted by residual: bond pdb=" C GLY C 9 " pdb=" N NH2 C 10 " ideal model delta sigma weight residual 2.329 1.329 1.000 1.40e-02 5.10e+03 5.11e+03 bond pdb=" N GLU B 3 " pdb=" CA GLU B 3 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.99e+00 bond pdb=" N THR Y 6 " pdb=" CA THR Y 6 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.99e+00 bond pdb=" N CYS A 3 " pdb=" CA CYS A 3 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 bond pdb=" N THR R 31 " pdb=" CA THR R 31 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.74e+00 ... (remaining 10327 not shown) Histogram of bond angle deviations from ideal: 98.74 - 105.80: 220 105.80 - 112.86: 5403 112.86 - 119.91: 3574 119.91 - 126.97: 4691 126.97 - 134.03: 138 Bond angle restraints: 14026 Sorted by residual: angle pdb=" C14 CLR R 601 " pdb=" C8 CLR R 601 " pdb=" C7 CLR R 601 " ideal model delta sigma weight residual 110.19 122.27 -12.08 3.00e+00 1.11e-01 1.62e+01 angle pdb=" C14 CLR R 602 " pdb=" C8 CLR R 602 " pdb=" C7 CLR R 602 " ideal model delta sigma weight residual 110.19 122.20 -12.01 3.00e+00 1.11e-01 1.60e+01 angle pdb=" C14 CLR R 603 " pdb=" C8 CLR R 603 " pdb=" C7 CLR R 603 " ideal model delta sigma weight residual 110.19 121.54 -11.35 3.00e+00 1.11e-01 1.43e+01 angle pdb=" C7 CLR R 603 " pdb=" C8 CLR R 603 " pdb=" C9 CLR R 603 " ideal model delta sigma weight residual 110.39 119.43 -9.04 3.00e+00 1.11e-01 9.07e+00 angle pdb=" N MET S 192 " pdb=" CA MET S 192 " pdb=" C MET S 192 " ideal model delta sigma weight residual 110.80 117.14 -6.34 2.13e+00 2.20e-01 8.87e+00 ... (remaining 14021 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 5869 17.86 - 35.72: 340 35.72 - 53.58: 44 53.58 - 71.44: 14 71.44 - 89.30: 9 Dihedral angle restraints: 6276 sinusoidal: 2562 harmonic: 3714 Sorted by residual: dihedral pdb=" CA TRP B 169 " pdb=" C TRP B 169 " pdb=" N ASP B 170 " pdb=" CA ASP B 170 " ideal model delta harmonic sigma weight residual 180.00 150.93 29.07 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA PHE B 292 " pdb=" C PHE B 292 " pdb=" N ASN B 293 " pdb=" CA ASN B 293 " ideal model delta harmonic sigma weight residual 180.00 150.97 29.03 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA CYS C 1 " pdb=" C CYS C 1 " pdb=" N TYR C 2 " pdb=" CA TYR C 2 " ideal model delta harmonic sigma weight residual -180.00 -151.42 -28.58 0 5.00e+00 4.00e-02 3.27e+01 ... (remaining 6273 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.389: 1571 0.389 - 0.778: 0 0.778 - 1.167: 0 1.167 - 1.556: 0 1.556 - 1.945: 3 Chirality restraints: 1574 Sorted by residual: chirality pdb=" C8 CLR R 602 " pdb=" C14 CLR R 602 " pdb=" C7 CLR R 602 " pdb=" C9 CLR R 602 " both_signs ideal model delta sigma weight residual False 2.69 0.75 1.95 2.00e-01 2.50e+01 9.46e+01 chirality pdb=" C8 CLR R 603 " pdb=" C14 CLR R 603 " pdb=" C7 CLR R 603 " pdb=" C9 CLR R 603 " both_signs ideal model delta sigma weight residual False 2.69 0.77 1.93 2.00e-01 2.50e+01 9.26e+01 chirality pdb=" C8 CLR R 601 " pdb=" C14 CLR R 601 " pdb=" C7 CLR R 601 " pdb=" C9 CLR R 601 " both_signs ideal model delta sigma weight residual False 2.69 0.80 1.89 2.00e-01 2.50e+01 8.93e+01 ... (remaining 1571 not shown) Planarity restraints: 1772 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 137 " 0.268 9.50e-02 1.11e+02 1.21e-01 1.06e+01 pdb=" NE ARG B 137 " -0.024 2.00e-02 2.50e+03 pdb=" CZ ARG B 137 " 0.020 2.00e-02 2.50e+03 pdb=" NH1 ARG B 137 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG B 137 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 150 " 0.257 9.50e-02 1.11e+02 1.15e-01 8.47e+00 pdb=" NE ARG B 150 " -0.019 2.00e-02 2.50e+03 pdb=" CZ ARG B 150 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG B 150 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 150 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP S 47 " -0.002 2.00e-02 2.50e+03 1.70e-02 7.25e+00 pdb=" CG TRP S 47 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 TRP S 47 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP S 47 " 0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP S 47 " -0.042 2.00e-02 2.50e+03 pdb=" CE2 TRP S 47 " 0.012 2.00e-02 2.50e+03 pdb=" CE3 TRP S 47 " -0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP S 47 " 0.014 2.00e-02 2.50e+03 pdb=" CZ3 TRP S 47 " -0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP S 47 " 0.006 2.00e-02 2.50e+03 ... (remaining 1769 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2993 2.83 - 3.34: 9589 3.34 - 3.86: 16058 3.86 - 4.38: 19629 4.38 - 4.90: 33736 Nonbonded interactions: 82005 Sorted by model distance: nonbonded pdb=" O GLY S 9 " pdb=" NH1 ARG S 18 " model vdw 2.306 2.520 nonbonded pdb=" OE1 GLU R 40 " pdb=" NZ LYS R 100 " model vdw 2.322 2.520 nonbonded pdb=" OG1 THR N 28 " pdb=" OD1 ASN N 31 " model vdw 2.354 2.440 nonbonded pdb=" O ASP B 333 " pdb=" OG SER B 334 " model vdw 2.356 2.440 nonbonded pdb=" O THR B 86 " pdb=" OG1 THR B 87 " model vdw 2.362 2.440 ... (remaining 82000 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: 0.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.880 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 30.200 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 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:12.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 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 : 0.012 1.000 10332 Z= 0.837 Angle : 0.771 12.081 14026 Z= 0.428 Chirality : 0.097 1.945 1574 Planarity : 0.009 0.121 1772 Dihedral : 12.291 89.296 3865 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 1.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.09 % Allowed : 0.84 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -0.01 (0.22), residues: 1259 helix: -0.18 (0.24), residues: 395 sheet: 0.67 (0.26), residues: 340 loop : -0.15 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.005 TRP S 47 HIS 0.013 0.003 HIS A 357 PHE 0.018 0.002 PHE B 235 TYR 0.027 0.005 TYR A 253 ARG 0.023 0.003 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 181 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 116 LYS cc_start: 0.7483 (mmmt) cc_final: 0.7200 (mmmt) REVERT: R 136 ASP cc_start: 0.8439 (t0) cc_final: 0.8176 (t0) REVERT: R 200 TRP cc_start: 0.7592 (m-10) cc_final: 0.7381 (m-10) REVERT: R 297 ASP cc_start: 0.7950 (t0) cc_final: 0.6876 (t0) REVERT: R 316 LEU cc_start: 0.8894 (tp) cc_final: 0.8517 (pt) REVERT: Y 58 GLU cc_start: 0.8159 (pm20) cc_final: 0.7646 (pm20) REVERT: Y 63 GLU cc_start: 0.7154 (tt0) cc_final: 0.6581 (tp30) REVERT: N 73 ASP cc_start: 0.8318 (t0) cc_final: 0.7942 (t0) REVERT: N 76 LYS cc_start: 0.9217 (ttmm) cc_final: 0.9004 (ttmm) REVERT: S 18 ARG cc_start: 0.8826 (tpp80) cc_final: 0.8583 (tpt-90) REVERT: S 73 ASP cc_start: 0.7282 (t70) cc_final: 0.7052 (t70) REVERT: S 83 MET cc_start: 0.9188 (mtm) cc_final: 0.8979 (mtp) REVERT: S 223 ASP cc_start: 0.8189 (m-30) cc_final: 0.7828 (m-30) outliers start: 1 outliers final: 1 residues processed: 182 average time/residue: 1.6424 time to fit residues: 314.9875 Evaluate side-chains 136 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 135 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 89 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 6.9990 chunk 94 optimal weight: 9.9990 chunk 52 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 50 optimal weight: 30.0000 chunk 97 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 72 optimal weight: 9.9990 chunk 113 optimal weight: 4.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS B 293 ASN N 3 GLN S 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10332 Z= 0.292 Angle : 0.636 6.909 14026 Z= 0.340 Chirality : 0.045 0.203 1574 Planarity : 0.005 0.033 1772 Dihedral : 5.703 47.861 1602 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.40 % Allowed : 7.26 % Favored : 91.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.01 (0.23), residues: 1259 helix: 1.37 (0.26), residues: 400 sheet: 0.86 (0.27), residues: 328 loop : 0.13 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 169 HIS 0.008 0.001 HIS A 357 PHE 0.024 0.002 PHE B 292 TYR 0.019 0.002 TYR C 2 ARG 0.006 0.000 ARG S 160 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 149 time to evaluate : 1.183 Fit side-chains revert: symmetry clash REVERT: R 136 ASP cc_start: 0.8463 (t0) cc_final: 0.8131 (t0) REVERT: R 157 ASN cc_start: 0.7701 (OUTLIER) cc_final: 0.7324 (p0) REVERT: R 297 ASP cc_start: 0.7717 (t0) cc_final: 0.7203 (t0) REVERT: B 172 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7446 (pp20) REVERT: Y 21 MET cc_start: 0.7798 (mmm) cc_final: 0.7501 (mmm) REVERT: Y 32 LYS cc_start: 0.8344 (mptm) cc_final: 0.7987 (mtpp) REVERT: Y 36 ASP cc_start: 0.8472 (m-30) cc_final: 0.8179 (m-30) REVERT: Y 58 GLU cc_start: 0.8162 (pm20) cc_final: 0.7726 (pm20) REVERT: Y 63 GLU cc_start: 0.7213 (tt0) cc_final: 0.5991 (tm-30) REVERT: N 73 ASP cc_start: 0.8310 (t0) cc_final: 0.7871 (t0) REVERT: N 76 LYS cc_start: 0.9325 (ttmm) cc_final: 0.9003 (ttmm) REVERT: S 223 ASP cc_start: 0.8460 (m-30) cc_final: 0.8191 (m-30) outliers start: 15 outliers final: 3 residues processed: 153 average time/residue: 1.5860 time to fit residues: 256.8572 Evaluate side-chains 138 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 133 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 157 ASN Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain S residue 137 ASP Chi-restraints excluded: chain S residue 144 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 63 optimal weight: 4.9990 chunk 35 optimal weight: 0.5980 chunk 94 optimal weight: 9.9990 chunk 77 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 113 optimal weight: 8.9990 chunk 122 optimal weight: 0.9990 chunk 101 optimal weight: 20.0000 chunk 112 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 91 optimal weight: 9.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 317 ASN A 59 GLN N 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10332 Z= 0.202 Angle : 0.564 8.093 14026 Z= 0.296 Chirality : 0.042 0.165 1574 Planarity : 0.004 0.037 1772 Dihedral : 5.194 58.780 1599 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.51 % Allowed : 9.21 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.29 (0.24), residues: 1259 helix: 1.91 (0.27), residues: 387 sheet: 0.89 (0.27), residues: 326 loop : 0.16 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 169 HIS 0.006 0.001 HIS A 357 PHE 0.019 0.001 PHE B 292 TYR 0.014 0.001 TYR R 148 ARG 0.007 0.000 ARG S 218 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 138 time to evaluate : 1.243 Fit side-chains REVERT: R 136 ASP cc_start: 0.8484 (t0) cc_final: 0.8178 (t0) REVERT: R 212 MET cc_start: 0.8549 (mmp) cc_final: 0.8132 (mmp) REVERT: R 297 ASP cc_start: 0.7815 (t0) cc_final: 0.7261 (t0) REVERT: A 231 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.8623 (ptp-170) REVERT: A 299 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8071 (mp0) REVERT: B 172 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7476 (pp20) REVERT: Y 21 MET cc_start: 0.7772 (mmm) cc_final: 0.7478 (mmm) REVERT: Y 32 LYS cc_start: 0.8360 (mptm) cc_final: 0.8117 (mptm) REVERT: Y 36 ASP cc_start: 0.8504 (m-30) cc_final: 0.8196 (m-30) REVERT: Y 63 GLU cc_start: 0.7260 (tt0) cc_final: 0.6035 (tm-30) REVERT: N 43 LYS cc_start: 0.7374 (ptmm) cc_final: 0.7137 (pptt) REVERT: N 73 ASP cc_start: 0.8306 (t0) cc_final: 0.7783 (t0) REVERT: N 76 LYS cc_start: 0.9375 (ttmm) cc_final: 0.9038 (ttmm) REVERT: S 43 LYS cc_start: 0.9206 (mppt) cc_final: 0.8049 (mppt) REVERT: S 73 ASP cc_start: 0.7264 (t70) cc_final: 0.6935 (t70) REVERT: S 76 LYS cc_start: 0.9374 (mtmm) cc_final: 0.9126 (mttp) REVERT: S 218 ARG cc_start: 0.8182 (ttp-110) cc_final: 0.7664 (ttp-110) REVERT: S 223 ASP cc_start: 0.8499 (m-30) cc_final: 0.7427 (m-30) outliers start: 27 outliers final: 4 residues processed: 148 average time/residue: 1.5993 time to fit residues: 250.3758 Evaluate side-chains 136 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 129 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain Y residue 57 SER Chi-restraints excluded: chain S residue 137 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 10.0000 chunk 85 optimal weight: 9.9990 chunk 59 optimal weight: 8.9990 chunk 12 optimal weight: 9.9990 chunk 54 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 114 optimal weight: 0.6980 chunk 120 optimal weight: 20.0000 chunk 108 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 100 optimal weight: 0.0070 overall best weight: 3.9404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10332 Z= 0.263 Angle : 0.573 7.753 14026 Z= 0.301 Chirality : 0.043 0.174 1574 Planarity : 0.004 0.032 1772 Dihedral : 5.166 59.147 1599 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.14 % Allowed : 10.42 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.18 (0.23), residues: 1259 helix: 1.82 (0.27), residues: 395 sheet: 0.86 (0.27), residues: 331 loop : 0.02 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 234 HIS 0.006 0.001 HIS A 357 PHE 0.020 0.002 PHE B 292 TYR 0.016 0.002 TYR B 105 ARG 0.005 0.000 ARG S 160 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 134 time to evaluate : 1.285 Fit side-chains REVERT: R 136 ASP cc_start: 0.8539 (t0) cc_final: 0.8238 (t0) REVERT: R 212 MET cc_start: 0.8685 (mmp) cc_final: 0.8237 (mmp) REVERT: R 297 ASP cc_start: 0.7906 (t0) cc_final: 0.7288 (t0) REVERT: A 231 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.8546 (ptp-170) REVERT: A 299 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8083 (mp0) REVERT: B 172 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7468 (pp20) REVERT: Y 21 MET cc_start: 0.7766 (mmm) cc_final: 0.7485 (mmm) REVERT: Y 32 LYS cc_start: 0.8430 (mptm) cc_final: 0.8018 (mtpm) REVERT: Y 36 ASP cc_start: 0.8459 (m-30) cc_final: 0.8170 (m-30) REVERT: Y 58 GLU cc_start: 0.8363 (pm20) cc_final: 0.7869 (pm20) REVERT: Y 63 GLU cc_start: 0.7322 (tt0) cc_final: 0.6056 (tm-30) REVERT: N 43 LYS cc_start: 0.7392 (ptmm) cc_final: 0.7157 (pptt) REVERT: N 73 ASP cc_start: 0.8344 (t0) cc_final: 0.7806 (t0) REVERT: N 76 LYS cc_start: 0.9416 (ttmm) cc_final: 0.9076 (ttmm) outliers start: 23 outliers final: 9 residues processed: 148 average time/residue: 1.6123 time to fit residues: 252.0947 Evaluate side-chains 140 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 128 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 157 ASN Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain Y residue 47 GLU Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain S residue 137 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 68 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 89 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 chunk 0 optimal weight: 50.0000 chunk 61 optimal weight: 6.9990 chunk 108 optimal weight: 8.9990 chunk 30 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 55 ASN R 96 GLN A 294 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10332 Z= 0.309 Angle : 0.587 8.111 14026 Z= 0.309 Chirality : 0.043 0.176 1574 Planarity : 0.004 0.031 1772 Dihedral : 5.156 56.972 1599 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.70 % Allowed : 11.63 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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 (0.23), residues: 1259 helix: 1.81 (0.27), residues: 395 sheet: 0.80 (0.27), residues: 335 loop : -0.11 (0.26), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 234 HIS 0.006 0.001 HIS A 357 PHE 0.020 0.002 PHE B 292 TYR 0.016 0.002 TYR B 105 ARG 0.006 0.000 ARG S 160 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 129 time to evaluate : 1.273 Fit side-chains REVERT: R 136 ASP cc_start: 0.8562 (t0) cc_final: 0.8251 (t0) REVERT: R 212 MET cc_start: 0.8716 (mmp) cc_final: 0.8283 (mmp) REVERT: R 297 ASP cc_start: 0.7926 (t0) cc_final: 0.7401 (t0) REVERT: A 231 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.8554 (ptp-170) REVERT: A 299 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8085 (mp0) REVERT: B 23 LYS cc_start: 0.9060 (tppt) cc_final: 0.8643 (tppt) REVERT: B 172 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7438 (pp20) REVERT: Y 21 MET cc_start: 0.7775 (mmm) cc_final: 0.7479 (mmm) REVERT: Y 32 LYS cc_start: 0.8432 (mptm) cc_final: 0.8009 (mtpm) REVERT: Y 36 ASP cc_start: 0.8501 (m-30) cc_final: 0.8181 (m-30) REVERT: Y 58 GLU cc_start: 0.8338 (pm20) cc_final: 0.7840 (pm20) REVERT: Y 63 GLU cc_start: 0.7297 (tt0) cc_final: 0.6123 (tm-30) REVERT: N 73 ASP cc_start: 0.8360 (t0) cc_final: 0.7799 (t0) REVERT: N 76 LYS cc_start: 0.9432 (ttmm) cc_final: 0.9097 (ttmm) REVERT: S 43 LYS cc_start: 0.9182 (mppt) cc_final: 0.8888 (mmtm) REVERT: S 73 ASP cc_start: 0.7261 (t70) cc_final: 0.6948 (t70) REVERT: S 76 LYS cc_start: 0.9384 (mtmm) cc_final: 0.9176 (mttp) outliers start: 29 outliers final: 12 residues processed: 146 average time/residue: 1.5799 time to fit residues: 244.1974 Evaluate side-chains 142 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 127 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 157 ASN Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain Y residue 57 SER Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain S residue 137 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 29 optimal weight: 0.6980 chunk 120 optimal weight: 7.9990 chunk 100 optimal weight: 7.9990 chunk 55 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 116 optimal weight: 8.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10332 Z= 0.221 Angle : 0.548 8.877 14026 Z= 0.287 Chirality : 0.041 0.161 1574 Planarity : 0.004 0.029 1772 Dihedral : 4.918 52.109 1599 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.23 % Allowed : 13.02 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.13 (0.23), residues: 1259 helix: 1.94 (0.27), residues: 393 sheet: 0.83 (0.27), residues: 331 loop : -0.14 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.005 0.001 HIS A 357 PHE 0.017 0.001 PHE B 292 TYR 0.012 0.001 TYR A 63 ARG 0.007 0.000 ARG S 218 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 136 time to evaluate : 1.234 Fit side-chains REVERT: R 136 ASP cc_start: 0.8533 (t70) cc_final: 0.8228 (t0) REVERT: R 212 MET cc_start: 0.8717 (mmp) cc_final: 0.8308 (mmp) REVERT: R 297 ASP cc_start: 0.7967 (t0) cc_final: 0.7351 (t0) REVERT: A 231 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.8522 (ptp-170) REVERT: A 299 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8089 (mp0) REVERT: B 23 LYS cc_start: 0.9084 (tppt) cc_final: 0.8661 (tppt) REVERT: B 172 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7437 (pp20) REVERT: B 303 ASP cc_start: 0.8165 (m-30) cc_final: 0.7960 (m-30) REVERT: Y 21 MET cc_start: 0.7753 (mmm) cc_final: 0.7470 (mmm) REVERT: Y 29 LYS cc_start: 0.8633 (ttmm) cc_final: 0.8311 (mmmm) REVERT: Y 32 LYS cc_start: 0.8446 (mptm) cc_final: 0.8214 (mptm) REVERT: Y 36 ASP cc_start: 0.8489 (m-30) cc_final: 0.8173 (m-30) REVERT: Y 58 GLU cc_start: 0.8352 (pm20) cc_final: 0.7861 (pm20) REVERT: Y 63 GLU cc_start: 0.7324 (tt0) cc_final: 0.6148 (tm-30) REVERT: N 73 ASP cc_start: 0.8344 (t0) cc_final: 0.7819 (t0) REVERT: N 76 LYS cc_start: 0.9451 (ttmm) cc_final: 0.9105 (ttmm) REVERT: S 73 ASP cc_start: 0.7219 (t70) cc_final: 0.7010 (t70) REVERT: S 218 ARG cc_start: 0.8057 (ttp-110) cc_final: 0.7655 (tmm-80) outliers start: 24 outliers final: 14 residues processed: 148 average time/residue: 1.7647 time to fit residues: 276.1309 Evaluate side-chains 149 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 132 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 157 ASN Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain Y residue 47 GLU Chi-restraints excluded: chain Y residue 57 SER Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain S residue 137 ASP Chi-restraints excluded: chain S residue 192 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 13 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 chunk 88 optimal weight: 3.9990 chunk 101 optimal weight: 20.0000 chunk 67 optimal weight: 7.9990 chunk 120 optimal weight: 0.1980 chunk 75 optimal weight: 2.9990 chunk 73 optimal weight: 0.0980 chunk 55 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 48 optimal weight: 6.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 138 HIS A 220 HIS N 84 ASN S 194 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10332 Z= 0.156 Angle : 0.526 9.379 14026 Z= 0.272 Chirality : 0.040 0.158 1574 Planarity : 0.004 0.029 1772 Dihedral : 4.528 47.028 1599 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.95 % Allowed : 14.23 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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 (0.24), residues: 1259 helix: 2.07 (0.27), residues: 393 sheet: 0.97 (0.27), residues: 324 loop : -0.16 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.003 0.001 HIS A 357 PHE 0.014 0.001 PHE B 292 TYR 0.010 0.001 TYR R 148 ARG 0.006 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 145 time to evaluate : 1.293 Fit side-chains revert: symmetry clash REVERT: R 136 ASP cc_start: 0.8547 (t70) cc_final: 0.8196 (t0) REVERT: R 212 MET cc_start: 0.8705 (mmp) cc_final: 0.8277 (mmp) REVERT: R 297 ASP cc_start: 0.8028 (t0) cc_final: 0.7469 (t0) REVERT: R 316 LEU cc_start: 0.8958 (tp) cc_final: 0.8747 (mt) REVERT: A 231 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.8569 (ptp-170) REVERT: A 299 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8087 (mp0) REVERT: B 172 GLU cc_start: 0.7906 (tm-30) cc_final: 0.7421 (pp20) REVERT: B 262 MET cc_start: 0.8120 (ttm) cc_final: 0.7867 (ttm) REVERT: B 303 ASP cc_start: 0.8110 (m-30) cc_final: 0.7870 (m-30) REVERT: Y 21 MET cc_start: 0.7738 (mmm) cc_final: 0.7448 (mmm) REVERT: Y 29 LYS cc_start: 0.8580 (ttmm) cc_final: 0.8200 (mmmm) REVERT: Y 32 LYS cc_start: 0.8375 (mptm) cc_final: 0.8151 (mptm) REVERT: Y 36 ASP cc_start: 0.8471 (m-30) cc_final: 0.8131 (m-30) REVERT: Y 58 GLU cc_start: 0.8350 (pm20) cc_final: 0.8100 (pm20) REVERT: Y 63 GLU cc_start: 0.7306 (tt0) cc_final: 0.6091 (tm-30) REVERT: N 73 ASP cc_start: 0.8285 (t0) cc_final: 0.7768 (t0) REVERT: N 76 LYS cc_start: 0.9444 (ttmm) cc_final: 0.9098 (ttmm) REVERT: S 43 LYS cc_start: 0.9054 (mppt) cc_final: 0.8596 (mmmt) REVERT: S 73 ASP cc_start: 0.6853 (t70) cc_final: 0.6549 (t0) REVERT: S 76 LYS cc_start: 0.9383 (mttp) cc_final: 0.9167 (mmtm) REVERT: S 220 GLU cc_start: 0.7774 (mp0) cc_final: 0.7438 (mp0) REVERT: S 223 ASP cc_start: 0.8658 (m-30) cc_final: 0.8420 (m-30) outliers start: 21 outliers final: 9 residues processed: 154 average time/residue: 1.5500 time to fit residues: 252.8116 Evaluate side-chains 142 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 131 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 157 ASN Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain Y residue 47 GLU Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain S residue 137 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 71 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 chunk 76 optimal weight: 0.8980 chunk 82 optimal weight: 10.0000 chunk 59 optimal weight: 8.9990 chunk 11 optimal weight: 0.9990 chunk 94 optimal weight: 9.9990 chunk 109 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 chunk 105 optimal weight: 8.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10332 Z= 0.230 Angle : 0.569 9.069 14026 Z= 0.297 Chirality : 0.041 0.157 1574 Planarity : 0.004 0.031 1772 Dihedral : 4.659 46.791 1599 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.95 % Allowed : 14.60 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.20 (0.24), residues: 1259 helix: 2.05 (0.27), residues: 394 sheet: 0.88 (0.27), residues: 331 loop : -0.17 (0.26), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 234 HIS 0.005 0.001 HIS A 357 PHE 0.016 0.001 PHE B 292 TYR 0.012 0.001 TYR A 339 ARG 0.008 0.000 ARG S 160 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 134 time to evaluate : 1.200 Fit side-chains revert: symmetry clash REVERT: R 136 ASP cc_start: 0.8555 (t70) cc_final: 0.8247 (t0) REVERT: R 212 MET cc_start: 0.8742 (mmp) cc_final: 0.8314 (mmp) REVERT: R 297 ASP cc_start: 0.8024 (t0) cc_final: 0.7478 (t0) REVERT: R 316 LEU cc_start: 0.8979 (tp) cc_final: 0.8766 (mt) REVERT: A 231 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.8503 (ptp-170) REVERT: A 299 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8099 (mp0) REVERT: B 172 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7389 (pp20) REVERT: B 262 MET cc_start: 0.8108 (ttm) cc_final: 0.7832 (ttm) REVERT: B 303 ASP cc_start: 0.8163 (m-30) cc_final: 0.7941 (m-30) REVERT: Y 21 MET cc_start: 0.7713 (mmm) cc_final: 0.7435 (mmm) REVERT: Y 29 LYS cc_start: 0.8591 (ttmm) cc_final: 0.8224 (mmmm) REVERT: Y 32 LYS cc_start: 0.8390 (mptm) cc_final: 0.8163 (mptm) REVERT: Y 36 ASP cc_start: 0.8474 (m-30) cc_final: 0.8142 (m-30) REVERT: Y 58 GLU cc_start: 0.8569 (pm20) cc_final: 0.8096 (pm20) REVERT: Y 63 GLU cc_start: 0.7414 (tt0) cc_final: 0.6191 (tm-30) REVERT: N 73 ASP cc_start: 0.8352 (t0) cc_final: 0.7816 (t0) REVERT: N 76 LYS cc_start: 0.9430 (ttmm) cc_final: 0.9085 (ttmm) REVERT: S 220 GLU cc_start: 0.7735 (mp0) cc_final: 0.7478 (mp0) outliers start: 21 outliers final: 11 residues processed: 147 average time/residue: 1.5983 time to fit residues: 248.4454 Evaluate side-chains 142 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 129 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 157 ASN Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain Y residue 47 GLU Chi-restraints excluded: chain N residue 33 LYS Chi-restraints excluded: chain S residue 137 ASP Chi-restraints excluded: chain S residue 219 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 20.0000 chunk 115 optimal weight: 10.0000 chunk 67 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 88 optimal weight: 0.0050 chunk 34 optimal weight: 8.9990 chunk 101 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 chunk 111 optimal weight: 7.9990 chunk 73 optimal weight: 4.9990 chunk 118 optimal weight: 6.9990 overall best weight: 3.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 84 ASN S 113 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10332 Z= 0.254 Angle : 0.594 9.354 14026 Z= 0.309 Chirality : 0.042 0.160 1574 Planarity : 0.004 0.031 1772 Dihedral : 4.726 45.022 1599 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.58 % Allowed : 15.07 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.15 (0.23), residues: 1259 helix: 2.01 (0.27), residues: 395 sheet: 0.83 (0.27), residues: 331 loop : -0.18 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.005 0.001 HIS A 357 PHE 0.017 0.001 PHE B 292 TYR 0.018 0.001 TYR A 63 ARG 0.008 0.000 ARG S 160 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 132 time to evaluate : 1.319 Fit side-chains revert: symmetry clash REVERT: R 136 ASP cc_start: 0.8534 (t70) cc_final: 0.8188 (t0) REVERT: R 212 MET cc_start: 0.8741 (mmp) cc_final: 0.8305 (mmp) REVERT: R 297 ASP cc_start: 0.8035 (t0) cc_final: 0.7485 (t0) REVERT: R 316 LEU cc_start: 0.8981 (tp) cc_final: 0.8769 (mt) REVERT: A 231 ARG cc_start: 0.8891 (OUTLIER) cc_final: 0.8520 (ptp-170) REVERT: A 299 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8093 (mp0) REVERT: B 23 LYS cc_start: 0.9169 (tppt) cc_final: 0.8728 (tppt) REVERT: B 172 GLU cc_start: 0.7916 (tm-30) cc_final: 0.7391 (pp20) REVERT: B 262 MET cc_start: 0.8130 (ttm) cc_final: 0.7821 (ttm) REVERT: B 303 ASP cc_start: 0.8175 (m-30) cc_final: 0.7959 (m-30) REVERT: Y 21 MET cc_start: 0.7708 (mmm) cc_final: 0.7430 (mmm) REVERT: Y 29 LYS cc_start: 0.8616 (ttmm) cc_final: 0.8255 (mmmm) REVERT: Y 32 LYS cc_start: 0.8408 (mptm) cc_final: 0.8173 (mptm) REVERT: Y 36 ASP cc_start: 0.8480 (m-30) cc_final: 0.8148 (m-30) REVERT: Y 58 GLU cc_start: 0.8578 (pm20) cc_final: 0.8105 (pm20) REVERT: Y 63 GLU cc_start: 0.7354 (tt0) cc_final: 0.6209 (tm-30) REVERT: N 73 ASP cc_start: 0.8371 (t0) cc_final: 0.7822 (t0) REVERT: N 76 LYS cc_start: 0.9436 (ttmm) cc_final: 0.9092 (ttmm) REVERT: S 73 ASP cc_start: 0.6995 (t70) cc_final: 0.6701 (t0) outliers start: 17 outliers final: 12 residues processed: 143 average time/residue: 1.6269 time to fit residues: 245.8859 Evaluate side-chains 144 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 130 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 157 ASN Chi-restraints excluded: chain R residue 272 MET Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain Y residue 47 GLU Chi-restraints excluded: chain N residue 33 LYS Chi-restraints excluded: chain S residue 137 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 72 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 124 optimal weight: 9.9990 chunk 114 optimal weight: 7.9990 chunk 99 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 60 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 105 optimal weight: 0.0970 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10332 Z= 0.186 Angle : 0.582 10.270 14026 Z= 0.299 Chirality : 0.041 0.156 1574 Planarity : 0.004 0.032 1772 Dihedral : 4.524 42.934 1599 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.40 % Allowed : 15.35 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.16 (0.24), residues: 1259 helix: 2.08 (0.27), residues: 394 sheet: 0.82 (0.27), residues: 328 loop : -0.21 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.005 0.001 HIS R 150 PHE 0.014 0.001 PHE B 292 TYR 0.010 0.001 TYR R 117 ARG 0.008 0.000 ARG N 105 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 133 time to evaluate : 1.138 Fit side-chains revert: symmetry clash REVERT: R 136 ASP cc_start: 0.8531 (t70) cc_final: 0.8180 (t0) REVERT: R 212 MET cc_start: 0.8765 (mmp) cc_final: 0.8338 (mmp) REVERT: R 297 ASP cc_start: 0.8031 (t0) cc_final: 0.7485 (t0) REVERT: R 316 LEU cc_start: 0.8954 (tp) cc_final: 0.8753 (mt) REVERT: A 231 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8566 (ptp-170) REVERT: A 299 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8110 (mp0) REVERT: B 172 GLU cc_start: 0.7903 (tm-30) cc_final: 0.7362 (pp20) REVERT: B 262 MET cc_start: 0.8104 (ttm) cc_final: 0.7760 (ttm) REVERT: B 303 ASP cc_start: 0.8124 (m-30) cc_final: 0.7889 (m-30) REVERT: Y 21 MET cc_start: 0.7687 (mmm) cc_final: 0.7372 (mmm) REVERT: Y 32 LYS cc_start: 0.8376 (mptm) cc_final: 0.8163 (mptm) REVERT: Y 36 ASP cc_start: 0.8444 (m-30) cc_final: 0.8105 (m-30) REVERT: Y 58 GLU cc_start: 0.8593 (pm20) cc_final: 0.8126 (pm20) REVERT: Y 63 GLU cc_start: 0.7356 (tt0) cc_final: 0.6160 (tm-30) REVERT: N 73 ASP cc_start: 0.8302 (t0) cc_final: 0.7778 (t0) REVERT: N 76 LYS cc_start: 0.9434 (ttmm) cc_final: 0.9104 (ttmm) outliers start: 15 outliers final: 8 residues processed: 143 average time/residue: 1.5637 time to fit residues: 236.7924 Evaluate side-chains 140 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 130 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 157 ASN Chi-restraints excluded: chain R residue 272 MET Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain S residue 137 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 30 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 chunk 14 optimal weight: 20.0000 chunk 27 optimal weight: 4.9990 chunk 99 optimal weight: 0.2980 chunk 41 optimal weight: 3.9990 chunk 101 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 18 optimal weight: 8.9990 chunk 87 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 overall best weight: 5.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 182 ASN N 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.094181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.060439 restraints weight = 19309.853| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 3.01 r_work: 0.2659 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10332 Z= 0.332 Angle : 0.640 9.441 14026 Z= 0.332 Chirality : 0.044 0.171 1574 Planarity : 0.004 0.033 1772 Dihedral : 4.880 42.701 1599 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.58 % Allowed : 15.63 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.03 (0.24), residues: 1259 helix: 1.97 (0.27), residues: 395 sheet: 0.67 (0.27), residues: 335 loop : -0.24 (0.26), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 234 HIS 0.006 0.001 HIS A 357 PHE 0.018 0.002 PHE B 292 TYR 0.015 0.002 TYR A 63 ARG 0.009 0.000 ARG S 160 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4490.12 seconds wall clock time: 80 minutes 14.80 seconds (4814.80 seconds total)