Starting phenix.real_space_refine on Tue Feb 13 19:34:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hti_35010/02_2024/8hti_35010_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hti_35010/02_2024/8hti_35010.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hti_35010/02_2024/8hti_35010.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hti_35010/02_2024/8hti_35010.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hti_35010/02_2024/8hti_35010_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hti_35010/02_2024/8hti_35010_neut_updated.pdb" } resolution = 2.97 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= 0.024 sd= 0.080 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 51 5.16 5 C 4757 2.51 5 N 1274 2.21 5 O 1308 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 27": "OE1" <-> "OE2" Residue "R GLU 113": "OE1" <-> "OE2" 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: 7390 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1311 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 1, 'TRANS': 155} Chain breaks: 4 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "B" Number of atoms: 2454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2454 Classifications: {'peptide': 328} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 5, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 49 Chain: "G" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 364 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "N" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 848 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 3, 'ARG:plan': 3, 'PHE:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 58 Chain: "R" Number of atoms: 2403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2403 Classifications: {'peptide': 303} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 285} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1 OCA R 401 " occ=0.00 ... (8 atoms not shown) pdb=" O2 OCA R 401 " occ=0.00 Time building chain proxies: 4.48, per 1000 atoms: 0.61 Number of scatterers: 7390 At special positions: 0 Unit cell: (82.547, 95.312, 133.607, 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 51 16.00 O 1308 8.00 N 1274 7.00 C 4757 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 99 " - pdb=" SG CYS R 181 " distance=2.03 Simple disulfide: pdb=" SG CYS R 171 " - pdb=" SG CYS R 191 " 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: 2.74 Conformation dependent library (CDL) restraints added in 1.3 seconds 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1810 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 23 helices and 11 sheets defined 35.9% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'A' and resid 14 through 38 removed outlier: 3.539A pdb=" N LYS A 25 " --> pdb=" O GLU A 21 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP A 33 " --> pdb=" O GLN A 29 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 224 No H-bonds generated for 'chain 'A' and resid 222 through 224' Processing helix chain 'A' and resid 252 through 263 Processing helix chain 'A' and resid 325 through 335 removed outlier: 3.590A pdb=" N ILE A 334 " --> pdb=" O GLU A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 376 Processing helix chain 'B' and resid 10 through 25 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'G' and resid 11 through 23 Processing helix chain 'G' and resid 31 through 43 removed outlier: 3.558A pdb=" N ALA G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASP G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (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 helix chain 'R' and resid 23 through 25 No H-bonds generated for 'chain 'R' and resid 23 through 25' Processing helix chain 'R' and resid 30 through 53 removed outlier: 3.819A pdb=" N ALA R 35 " --> pdb=" O ILE R 31 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASN R 44 " --> pdb=" O ALA R 40 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N SER R 45 " --> pdb=" O LEU R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 77 removed outlier: 3.530A pdb=" N THR R 77 " --> pdb=" O LEU R 73 " (cutoff:3.500A) Processing helix chain 'R' and resid 80 through 89 Processing helix chain 'R' and resid 96 through 129 Processing helix chain 'R' and resid 131 through 137 removed outlier: 5.290A pdb=" N THR R 135 " --> pdb=" O LEU R 132 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE R 137 " --> pdb=" O TYR R 134 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 165 Proline residue: R 160 - end of helix removed outlier: 4.567A pdb=" N PHE R 163 " --> pdb=" O ILE R 159 " (cutoff:3.500A) Processing helix chain 'R' and resid 183 through 189 removed outlier: 4.546A pdb=" N LEU R 189 " --> pdb=" O GLY R 185 " (cutoff:3.500A) Processing helix chain 'R' and resid 195 through 227 removed outlier: 3.607A pdb=" N GLY R 210 " --> pdb=" O LEU R 206 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LEU R 211 " --> pdb=" O LEU R 207 " (cutoff:3.500A) Processing helix chain 'R' and resid 235 through 266 removed outlier: 4.070A pdb=" N LEU R 240 " --> pdb=" O ARG R 236 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N SER R 245 " --> pdb=" O SER R 241 " (cutoff:3.500A) Proline residue: R 256 - end of helix removed outlier: 4.397A pdb=" N ARG R 265 " --> pdb=" O PHE R 261 " (cutoff:3.500A) Processing helix chain 'R' and resid 272 through 280 Processing helix chain 'R' and resid 285 through 294 Proline residue: R 291 - end of helix Processing helix chain 'R' and resid 299 through 309 removed outlier: 3.899A pdb=" N GLU R 303 " --> pdb=" O LYS R 299 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ARG R 304 " --> pdb=" O GLN R 300 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE R 308 " --> pdb=" O ARG R 304 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE R 309 " --> pdb=" O VAL R 305 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 345 through 349 removed outlier: 7.223A pdb=" N VAL A 273 " --> pdb=" O TYR A 346 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N HIS A 348 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU A 275 " --> pdb=" O HIS A 348 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA A 229 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A 44 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A 233 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ASN A 204 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N LEU A 43 " --> pdb=" O ASN A 204 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N HIS A 206 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N LEU A 45 " --> pdb=" O HIS A 206 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N PHE A 208 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 62 removed outlier: 7.080A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.742A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.783A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.205A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.668A 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: 5.677A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.786A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.607A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.858A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 3 through 8 Processing sheet with id= J, first strand: chain 'N' and resid 122 through 124 removed outlier: 5.970A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'R' and resid 13 through 15 325 hydrogen bonds defined for protein. 939 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: 2.20 Time building geometry restraints manager: 2.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2367 1.34 - 1.46: 1821 1.46 - 1.58: 3291 1.58 - 1.70: 0 1.70 - 1.82: 72 Bond restraints: 7551 Sorted by residual: bond pdb=" N ASP B 312 " pdb=" CA ASP B 312 " ideal model delta sigma weight residual 1.456 1.489 -0.034 1.35e-02 5.49e+03 6.24e+00 bond pdb=" N HIS R 183 " pdb=" CA HIS R 183 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.24e-02 6.50e+03 5.42e+00 bond pdb=" CE1 HIS R 183 " pdb=" NE2 HIS R 183 " ideal model delta sigma weight residual 1.321 1.338 -0.017 1.00e-02 1.00e+04 2.86e+00 bond pdb=" C HIS R 183 " pdb=" O HIS R 183 " ideal model delta sigma weight residual 1.236 1.247 -0.012 1.19e-02 7.06e+03 9.35e-01 bond pdb=" CA ILE R 159 " pdb=" C ILE R 159 " ideal model delta sigma weight residual 1.524 1.534 -0.010 1.05e-02 9.07e+03 8.68e-01 ... (remaining 7546 not shown) Histogram of bond angle deviations from ideal: 98.07 - 105.26: 113 105.26 - 112.45: 3893 112.45 - 119.65: 2500 119.65 - 126.84: 3646 126.84 - 134.03: 100 Bond angle restraints: 10252 Sorted by residual: angle pdb=" N ILE R 159 " pdb=" CA ILE R 159 " pdb=" C ILE R 159 " ideal model delta sigma weight residual 108.88 114.86 -5.98 2.16e+00 2.14e-01 7.66e+00 angle pdb=" C HIS R 10 " pdb=" N PRO R 11 " pdb=" CA PRO R 11 " ideal model delta sigma weight residual 120.03 122.72 -2.69 9.90e-01 1.02e+00 7.38e+00 angle pdb=" N ASP B 312 " pdb=" CA ASP B 312 " pdb=" C ASP B 312 " ideal model delta sigma weight residual 113.38 110.28 3.10 1.23e+00 6.61e-01 6.34e+00 angle pdb=" N GLY B 306 " pdb=" CA GLY B 306 " pdb=" C GLY B 306 " ideal model delta sigma weight residual 110.38 114.03 -3.65 1.48e+00 4.57e-01 6.09e+00 angle pdb=" CA HIS R 183 " pdb=" C HIS R 183 " pdb=" O HIS R 183 " ideal model delta sigma weight residual 120.55 117.99 2.56 1.07e+00 8.73e-01 5.73e+00 ... (remaining 10247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 3913 17.74 - 35.49: 418 35.49 - 53.23: 96 53.23 - 70.98: 18 70.98 - 88.72: 7 Dihedral angle restraints: 4452 sinusoidal: 1657 harmonic: 2795 Sorted by residual: dihedral pdb=" CB CYS R 171 " pdb=" SG CYS R 171 " pdb=" SG CYS R 191 " pdb=" CB CYS R 191 " ideal model delta sinusoidal sigma weight residual -86.00 -134.25 48.25 1 1.00e+01 1.00e-02 3.21e+01 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 -157.96 -22.04 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA ASP R 123 " pdb=" CB ASP R 123 " pdb=" CG ASP R 123 " pdb=" OD1 ASP R 123 " ideal model delta sinusoidal sigma weight residual -30.00 -89.16 59.16 1 2.00e+01 2.50e-03 1.17e+01 ... (remaining 4449 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 774 0.036 - 0.073: 309 0.073 - 0.109: 76 0.109 - 0.146: 28 0.146 - 0.182: 1 Chirality restraints: 1188 Sorted by residual: chirality pdb=" CB ILE R 159 " pdb=" CA ILE R 159 " pdb=" CG1 ILE R 159 " pdb=" CG2 ILE R 159 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.28e-01 chirality pdb=" CA PHE R 109 " pdb=" N PHE R 109 " pdb=" C PHE R 109 " pdb=" CB PHE R 109 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.84e-01 chirality pdb=" CA PRO B 236 " pdb=" N PRO B 236 " pdb=" C PRO B 236 " pdb=" CB PRO B 236 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.68e-01 ... (remaining 1185 not shown) Planarity restraints: 1288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE R 159 " 0.042 5.00e-02 4.00e+02 6.39e-02 6.53e+00 pdb=" N PRO R 160 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO R 160 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO R 160 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO R 286 " 0.042 5.00e-02 4.00e+02 6.26e-02 6.27e+00 pdb=" N PRO R 287 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO R 287 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO R 287 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.037 5.00e-02 4.00e+02 5.65e-02 5.12e+00 pdb=" N PRO B 236 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.031 5.00e-02 4.00e+02 ... (remaining 1285 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1875 2.80 - 3.33: 6292 3.33 - 3.85: 11531 3.85 - 4.38: 13137 4.38 - 4.90: 24253 Nonbonded interactions: 57088 Sorted by model distance: nonbonded pdb=" O ASN N 77 " pdb=" OD1 ASN N 77 " model vdw 2.277 3.040 nonbonded pdb=" OG SER R 114 " pdb=" OD2 ASP R 212 " model vdw 2.305 2.440 nonbonded pdb=" NE2 GLN G 18 " pdb=" OE2 GLU G 22 " model vdw 2.306 2.520 nonbonded pdb=" O ILE R 276 " pdb=" ND2 ASN R 280 " model vdw 2.322 2.520 nonbonded pdb=" O SER R 8 " pdb=" OG SER R 8 " model vdw 2.342 2.440 ... (remaining 57083 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=0.00 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: 4.300 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: 13.290 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 23.580 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 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 0.045 7551 Z= 0.239 Angle : 0.603 7.257 10252 Z= 0.341 Chirality : 0.043 0.182 1188 Planarity : 0.005 0.064 1288 Dihedral : 15.486 88.721 2633 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.00 % Allowed : 17.04 % Favored : 82.96 % 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: 0.28 (0.28), residues: 940 helix: 1.81 (0.30), residues: 345 sheet: 0.26 (0.37), residues: 201 loop : -1.35 (0.28), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 339 HIS 0.006 0.001 HIS R 178 PHE 0.021 0.001 PHE A 259 TYR 0.016 0.002 TYR N 117 ARG 0.003 0.000 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 0.792 Fit side-chains REVERT: B 294 CYS cc_start: 0.8392 (p) cc_final: 0.8171 (m) REVERT: G 19 LEU cc_start: 0.8130 (mt) cc_final: 0.7906 (mm) REVERT: R 9 PHE cc_start: 0.8071 (t80) cc_final: 0.7786 (t80) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 1.2793 time to fit residues: 144.3313 Evaluate side-chains 91 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.892 ------------------------------------------------------------------------------- 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: 0.9980 chunk 71 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 73 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 HIS R 107 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.0698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 7551 Z= 0.210 Angle : 0.529 6.983 10252 Z= 0.277 Chirality : 0.042 0.142 1188 Planarity : 0.004 0.062 1288 Dihedral : 4.141 29.283 1042 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.15 % Allowed : 18.61 % Favored : 78.24 % 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: 0.50 (0.28), residues: 940 helix: 1.94 (0.29), residues: 347 sheet: 0.36 (0.37), residues: 200 loop : -1.19 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 220 HIS 0.006 0.001 HIS R 178 PHE 0.016 0.001 PHE R 109 TYR 0.011 0.001 TYR N 117 ARG 0.004 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 94 time to evaluate : 0.891 Fit side-chains REVERT: A 29 GLN cc_start: 0.8784 (tp-100) cc_final: 0.8419 (tp-100) REVERT: A 342 ARG cc_start: 0.6995 (mmm160) cc_final: 0.6618 (tpt90) REVERT: B 96 ARG cc_start: 0.7205 (OUTLIER) cc_final: 0.6793 (ttt-90) REVERT: B 101 MET cc_start: 0.8837 (OUTLIER) cc_final: 0.8507 (ptm) REVERT: B 294 CYS cc_start: 0.8456 (p) cc_final: 0.8096 (p) REVERT: G 19 LEU cc_start: 0.8064 (mt) cc_final: 0.7842 (mm) REVERT: R 93 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7107 (tm-30) REVERT: R 304 ARG cc_start: 0.7052 (OUTLIER) cc_final: 0.5784 (mpp80) outliers start: 24 outliers final: 7 residues processed: 107 average time/residue: 1.1389 time to fit residues: 129.4918 Evaluate side-chains 105 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 94 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 93 GLU Chi-restraints excluded: chain R residue 176 ILE Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 304 ARG 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: 0.9980 chunk 71 optimal weight: 0.0970 chunk 58 optimal weight: 2.9990 chunk 23 optimal weight: 0.0010 chunk 85 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 76 optimal weight: 0.0050 chunk 84 optimal weight: 0.6980 chunk 29 optimal weight: 0.3980 chunk 68 optimal weight: 0.5980 overall best weight: 0.2198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 ASN B 176 GLN N 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 7551 Z= 0.127 Angle : 0.453 6.990 10252 Z= 0.238 Chirality : 0.040 0.132 1188 Planarity : 0.004 0.056 1288 Dihedral : 3.751 27.861 1042 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.23 % Allowed : 21.10 % Favored : 76.67 % 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: 0.70 (0.28), residues: 940 helix: 2.32 (0.30), residues: 347 sheet: 0.28 (0.37), residues: 213 loop : -1.23 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 220 HIS 0.002 0.000 HIS A 343 PHE 0.014 0.001 PHE R 109 TYR 0.007 0.001 TYR R 282 ARG 0.004 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 101 time to evaluate : 0.879 Fit side-chains REVERT: A 29 GLN cc_start: 0.8742 (tp-100) cc_final: 0.8461 (tp-100) REVERT: B 96 ARG cc_start: 0.7188 (OUTLIER) cc_final: 0.6764 (ttt-90) REVERT: B 101 MET cc_start: 0.8790 (OUTLIER) cc_final: 0.8420 (ptm) REVERT: B 294 CYS cc_start: 0.8381 (p) cc_final: 0.7988 (p) REVERT: G 19 LEU cc_start: 0.8070 (mt) cc_final: 0.7861 (mm) REVERT: N 104 THR cc_start: 0.8284 (m) cc_final: 0.8016 (p) outliers start: 17 outliers final: 5 residues processed: 110 average time/residue: 1.2178 time to fit residues: 141.9838 Evaluate side-chains 102 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 95 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 176 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 84 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 90 optimal weight: 0.0980 chunk 81 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN N 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7551 Z= 0.185 Angle : 0.503 7.178 10252 Z= 0.260 Chirality : 0.041 0.132 1188 Planarity : 0.004 0.059 1288 Dihedral : 3.885 26.713 1042 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.54 % Allowed : 20.71 % Favored : 75.75 % 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: 0.72 (0.28), residues: 940 helix: 2.41 (0.30), residues: 341 sheet: 0.26 (0.36), residues: 211 loop : -1.20 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 339 HIS 0.004 0.001 HIS R 178 PHE 0.019 0.001 PHE R 89 TYR 0.010 0.001 TYR A 344 ARG 0.006 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 96 time to evaluate : 0.876 Fit side-chains REVERT: A 29 GLN cc_start: 0.8775 (tp-100) cc_final: 0.8443 (tp-100) REVERT: A 342 ARG cc_start: 0.6959 (mmm160) cc_final: 0.6671 (tpt90) REVERT: B 52 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.7304 (ptp90) REVERT: B 96 ARG cc_start: 0.7191 (OUTLIER) cc_final: 0.6694 (ttt-90) REVERT: B 101 MET cc_start: 0.8834 (OUTLIER) cc_final: 0.8528 (ptm) REVERT: B 294 CYS cc_start: 0.8382 (p) cc_final: 0.7977 (p) REVERT: G 19 LEU cc_start: 0.8070 (mt) cc_final: 0.7847 (mm) REVERT: R 26 HIS cc_start: 0.8083 (OUTLIER) cc_final: 0.7687 (m170) REVERT: R 304 ARG cc_start: 0.7118 (OUTLIER) cc_final: 0.5767 (mpp80) outliers start: 27 outliers final: 8 residues processed: 112 average time/residue: 1.1545 time to fit residues: 137.2453 Evaluate side-chains 107 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 94 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 26 HIS Chi-restraints excluded: chain R residue 176 ILE Chi-restraints excluded: chain R residue 304 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 51 optimal weight: 0.0570 chunk 1 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 77 optimal weight: 0.4980 chunk 62 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 81 optimal weight: 0.2980 chunk 22 optimal weight: 1.9990 chunk 30 optimal weight: 0.3980 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN G 59 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7551 Z= 0.144 Angle : 0.468 6.806 10252 Z= 0.244 Chirality : 0.041 0.131 1188 Planarity : 0.004 0.056 1288 Dihedral : 3.769 26.061 1042 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.28 % Allowed : 21.10 % Favored : 75.62 % 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: 0.85 (0.28), residues: 940 helix: 2.53 (0.30), residues: 343 sheet: 0.28 (0.36), residues: 211 loop : -1.13 (0.29), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 220 HIS 0.003 0.001 HIS R 178 PHE 0.013 0.001 PHE R 109 TYR 0.011 0.001 TYR A 344 ARG 0.003 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 98 time to evaluate : 0.885 Fit side-chains REVERT: A 29 GLN cc_start: 0.8755 (tp-100) cc_final: 0.8443 (tp-100) REVERT: A 342 ARG cc_start: 0.6914 (mmm160) cc_final: 0.6627 (tpt90) REVERT: B 96 ARG cc_start: 0.7183 (OUTLIER) cc_final: 0.6751 (ttt-90) REVERT: B 101 MET cc_start: 0.8832 (OUTLIER) cc_final: 0.8465 (ptm) REVERT: B 294 CYS cc_start: 0.8369 (p) cc_final: 0.7975 (p) REVERT: G 19 LEU cc_start: 0.8069 (mt) cc_final: 0.7853 (mm) REVERT: R 26 HIS cc_start: 0.8047 (OUTLIER) cc_final: 0.7717 (m170) REVERT: R 304 ARG cc_start: 0.7107 (OUTLIER) cc_final: 0.5774 (mpp80) REVERT: R 307 LYS cc_start: 0.7803 (ttmt) cc_final: 0.7412 (ttmm) outliers start: 25 outliers final: 12 residues processed: 110 average time/residue: 1.1410 time to fit residues: 133.2268 Evaluate side-chains 114 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 98 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 343 HIS Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 26 HIS Chi-restraints excluded: chain R residue 176 ILE Chi-restraints excluded: chain R residue 304 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 81 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 42 optimal weight: 0.4980 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN N 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7551 Z= 0.258 Angle : 0.548 7.085 10252 Z= 0.287 Chirality : 0.043 0.148 1188 Planarity : 0.004 0.059 1288 Dihedral : 4.175 27.364 1042 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.67 % Allowed : 21.36 % Favored : 74.97 % 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: 0.65 (0.28), residues: 940 helix: 2.19 (0.29), residues: 344 sheet: 0.49 (0.37), residues: 197 loop : -1.22 (0.28), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 63 HIS 0.006 0.001 HIS R 275 PHE 0.018 0.002 PHE R 89 TYR 0.012 0.002 TYR N 95 ARG 0.003 0.000 ARG R 265 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 101 time to evaluate : 0.897 Fit side-chains REVERT: A 29 GLN cc_start: 0.8814 (tp-100) cc_final: 0.8428 (tp-100) REVERT: B 52 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.7326 (ptp90) REVERT: B 96 ARG cc_start: 0.7230 (OUTLIER) cc_final: 0.6728 (ttt-90) REVERT: B 101 MET cc_start: 0.8890 (OUTLIER) cc_final: 0.8651 (ptm) REVERT: B 294 CYS cc_start: 0.8369 (p) cc_final: 0.8102 (m) REVERT: B 336 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8847 (mp) REVERT: G 19 LEU cc_start: 0.8086 (mt) cc_final: 0.7877 (mm) REVERT: R 25 VAL cc_start: 0.7923 (m) cc_final: 0.7373 (p) REVERT: R 26 HIS cc_start: 0.8113 (OUTLIER) cc_final: 0.7811 (m170) REVERT: R 304 ARG cc_start: 0.7127 (OUTLIER) cc_final: 0.5763 (mpp80) outliers start: 28 outliers final: 13 residues processed: 116 average time/residue: 1.1251 time to fit residues: 138.4946 Evaluate side-chains 117 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 98 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 343 HIS Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 26 HIS Chi-restraints excluded: chain R residue 93 GLU Chi-restraints excluded: chain R residue 176 ILE Chi-restraints excluded: chain R residue 304 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 10 optimal weight: 3.9990 chunk 51 optimal weight: 0.0040 chunk 66 optimal weight: 1.9990 chunk 76 optimal weight: 0.1980 chunk 50 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7551 Z= 0.170 Angle : 0.491 6.889 10252 Z= 0.257 Chirality : 0.041 0.131 1188 Planarity : 0.004 0.058 1288 Dihedral : 3.984 27.791 1042 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.88 % Allowed : 22.28 % Favored : 74.84 % 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: 0.79 (0.28), residues: 940 helix: 2.39 (0.29), residues: 345 sheet: 0.37 (0.36), residues: 205 loop : -1.16 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 220 HIS 0.003 0.001 HIS R 178 PHE 0.014 0.001 PHE R 109 TYR 0.009 0.001 TYR N 80 ARG 0.006 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 100 time to evaluate : 1.008 Fit side-chains REVERT: A 29 GLN cc_start: 0.8777 (tp-100) cc_final: 0.8449 (tp-100) REVERT: B 52 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.7293 (ptp90) REVERT: B 96 ARG cc_start: 0.7210 (OUTLIER) cc_final: 0.6712 (ttt-90) REVERT: B 101 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.8505 (ptm) REVERT: B 251 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.7970 (mtt-85) REVERT: B 294 CYS cc_start: 0.8394 (p) cc_final: 0.8148 (m) REVERT: B 336 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8822 (mp) REVERT: G 19 LEU cc_start: 0.8087 (mt) cc_final: 0.7885 (mm) REVERT: R 25 VAL cc_start: 0.7914 (m) cc_final: 0.7371 (p) REVERT: R 26 HIS cc_start: 0.8073 (OUTLIER) cc_final: 0.7747 (m170) REVERT: R 304 ARG cc_start: 0.7125 (OUTLIER) cc_final: 0.5831 (mpp80) REVERT: R 307 LYS cc_start: 0.7719 (ttmt) cc_final: 0.7349 (ttmm) outliers start: 22 outliers final: 13 residues processed: 112 average time/residue: 1.2380 time to fit residues: 146.7038 Evaluate side-chains 119 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 99 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 343 HIS Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 26 HIS Chi-restraints excluded: chain R residue 176 ILE Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 304 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 27 optimal weight: 0.6980 chunk 17 optimal weight: 0.0000 chunk 57 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 0.4980 chunk 8 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 82 optimal weight: 5.9990 chunk 86 optimal weight: 0.0070 chunk 79 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 overall best weight: 0.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7551 Z= 0.137 Angle : 0.470 6.843 10252 Z= 0.244 Chirality : 0.041 0.132 1188 Planarity : 0.004 0.058 1288 Dihedral : 3.818 26.314 1042 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.01 % Allowed : 22.80 % Favored : 74.18 % 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: 0.88 (0.28), residues: 940 helix: 2.58 (0.29), residues: 344 sheet: 0.27 (0.36), residues: 209 loop : -1.13 (0.29), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 220 HIS 0.002 0.001 HIS R 275 PHE 0.019 0.001 PHE R 89 TYR 0.011 0.001 TYR A 344 ARG 0.004 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 103 time to evaluate : 0.847 Fit side-chains REVERT: A 29 GLN cc_start: 0.8756 (tp-100) cc_final: 0.8446 (tp-100) REVERT: B 52 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.7278 (ptp90) REVERT: B 96 ARG cc_start: 0.7197 (OUTLIER) cc_final: 0.6695 (ttt-90) REVERT: B 101 MET cc_start: 0.8830 (OUTLIER) cc_final: 0.8454 (ptm) REVERT: B 251 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.8051 (mtt-85) REVERT: B 294 CYS cc_start: 0.8390 (p) cc_final: 0.8156 (m) REVERT: G 19 LEU cc_start: 0.8088 (mt) cc_final: 0.7876 (mm) REVERT: R 25 VAL cc_start: 0.7921 (m) cc_final: 0.7387 (p) REVERT: R 26 HIS cc_start: 0.8041 (OUTLIER) cc_final: 0.7701 (m170) REVERT: R 304 ARG cc_start: 0.7100 (OUTLIER) cc_final: 0.5816 (mpp80) REVERT: R 307 LYS cc_start: 0.7772 (ttmt) cc_final: 0.7434 (ttmm) outliers start: 23 outliers final: 11 residues processed: 114 average time/residue: 1.2092 time to fit residues: 146.0096 Evaluate side-chains 120 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 103 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 HIS Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 26 HIS Chi-restraints excluded: chain R residue 176 ILE Chi-restraints excluded: chain R residue 304 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 86 optimal weight: 0.9990 chunk 50 optimal weight: 0.3980 chunk 36 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 55 optimal weight: 8.9990 chunk 89 optimal weight: 0.9980 chunk 54 optimal weight: 0.0050 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7551 Z= 0.158 Angle : 0.485 6.790 10252 Z= 0.252 Chirality : 0.041 0.131 1188 Planarity : 0.004 0.058 1288 Dihedral : 3.821 25.480 1042 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.49 % Allowed : 23.46 % Favored : 74.05 % 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 (0.28), residues: 940 helix: 2.61 (0.29), residues: 343 sheet: 0.37 (0.36), residues: 208 loop : -1.13 (0.29), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 220 HIS 0.003 0.001 HIS R 178 PHE 0.014 0.001 PHE R 109 TYR 0.012 0.001 TYR N 80 ARG 0.007 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 102 time to evaluate : 0.926 Fit side-chains REVERT: A 29 GLN cc_start: 0.8766 (tp-100) cc_final: 0.8346 (tp-100) REVERT: B 52 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.7279 (ptp90) REVERT: B 96 ARG cc_start: 0.7200 (OUTLIER) cc_final: 0.6698 (ttt-90) REVERT: B 101 MET cc_start: 0.8845 (OUTLIER) cc_final: 0.8478 (ptm) REVERT: B 251 ARG cc_start: 0.8885 (OUTLIER) cc_final: 0.8056 (mtt-85) REVERT: B 294 CYS cc_start: 0.8375 (p) cc_final: 0.8167 (m) REVERT: G 19 LEU cc_start: 0.8092 (mt) cc_final: 0.7877 (mm) REVERT: R 25 VAL cc_start: 0.7929 (m) cc_final: 0.7397 (p) REVERT: R 26 HIS cc_start: 0.8045 (OUTLIER) cc_final: 0.7712 (m170) REVERT: R 304 ARG cc_start: 0.7078 (OUTLIER) cc_final: 0.5802 (mpp80) REVERT: R 307 LYS cc_start: 0.7775 (ttmt) cc_final: 0.7444 (ttmm) outliers start: 19 outliers final: 10 residues processed: 113 average time/residue: 1.2094 time to fit residues: 144.5457 Evaluate side-chains 117 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 101 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 HIS Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 26 HIS Chi-restraints excluded: chain R residue 176 ILE Chi-restraints excluded: chain R residue 304 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 42 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 93 optimal weight: 0.5980 chunk 86 optimal weight: 0.0670 chunk 74 optimal weight: 0.8980 chunk 7 optimal weight: 0.0870 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7551 Z= 0.146 Angle : 0.475 6.741 10252 Z= 0.246 Chirality : 0.041 0.132 1188 Planarity : 0.004 0.057 1288 Dihedral : 3.769 24.348 1042 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.49 % Allowed : 23.46 % Favored : 74.05 % 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 (0.28), residues: 940 helix: 2.64 (0.29), residues: 343 sheet: 0.27 (0.36), residues: 209 loop : -1.10 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 220 HIS 0.003 0.001 HIS R 178 PHE 0.021 0.001 PHE R 89 TYR 0.011 0.001 TYR A 344 ARG 0.007 0.000 ARG A 342 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 103 time to evaluate : 0.896 Fit side-chains REVERT: A 29 GLN cc_start: 0.8764 (tp-100) cc_final: 0.8450 (tp-100) REVERT: B 52 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.7281 (ptp90) REVERT: B 96 ARG cc_start: 0.7197 (OUTLIER) cc_final: 0.6696 (ttt-90) REVERT: B 101 MET cc_start: 0.8842 (OUTLIER) cc_final: 0.8470 (ptm) REVERT: B 251 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8044 (mtt-85) REVERT: B 294 CYS cc_start: 0.8372 (p) cc_final: 0.8162 (m) REVERT: G 19 LEU cc_start: 0.8092 (mt) cc_final: 0.7861 (mm) REVERT: R 25 VAL cc_start: 0.7932 (m) cc_final: 0.7401 (p) REVERT: R 26 HIS cc_start: 0.8037 (OUTLIER) cc_final: 0.7707 (m170) REVERT: R 304 ARG cc_start: 0.7066 (OUTLIER) cc_final: 0.5808 (mpp80) REVERT: R 307 LYS cc_start: 0.7767 (ttmt) cc_final: 0.7443 (ttmm) outliers start: 19 outliers final: 11 residues processed: 113 average time/residue: 1.2581 time to fit residues: 150.1436 Evaluate side-chains 120 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 103 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 HIS Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 26 HIS Chi-restraints excluded: chain R residue 176 ILE Chi-restraints excluded: chain R residue 304 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 68 optimal weight: 0.6980 chunk 11 optimal weight: 0.0970 chunk 20 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.112161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.095365 restraints weight = 12248.230| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.93 r_work: 0.3216 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7551 Z= 0.178 Angle : 0.502 6.794 10252 Z= 0.261 Chirality : 0.041 0.131 1188 Planarity : 0.004 0.057 1288 Dihedral : 3.858 23.875 1042 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.36 % Allowed : 24.12 % Favored : 73.53 % 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 (0.28), residues: 940 helix: 2.55 (0.29), residues: 343 sheet: 0.33 (0.36), residues: 207 loop : -1.15 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 339 HIS 0.004 0.001 HIS R 275 PHE 0.015 0.001 PHE R 109 TYR 0.013 0.001 TYR N 80 ARG 0.008 0.000 ARG A 342 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3262.29 seconds wall clock time: 58 minutes 24.35 seconds (3504.35 seconds total)