Starting phenix.real_space_refine on Thu Mar 14 20:31:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rx0_24721/03_2024/7rx0_24721_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rx0_24721/03_2024/7rx0_24721.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rx0_24721/03_2024/7rx0_24721.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rx0_24721/03_2024/7rx0_24721.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rx0_24721/03_2024/7rx0_24721_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rx0_24721/03_2024/7rx0_24721_updated.pdb" } resolution = 3.89 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= 0.002 sd= 0.010 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: 6 Type Number sf(0) Gaussians P 9 5.49 5 Mg 1 5.21 5 S 55 5.16 5 C 6047 2.51 5 N 1679 2.21 5 O 1882 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 152": "OE1" <-> "OE2" Residue "C GLU 187": "OE1" <-> "OE2" Residue "C ARG 302": "NH1" <-> "NH2" Residue "A GLU 77": "OE1" <-> "OE2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A GLU 254": "OE1" <-> "OE2" Residue "A GLU 290": "OE1" <-> "OE2" Residue "A GLU 415": "OE1" <-> "OE2" Residue "A GLU 423": "OE1" <-> "OE2" Residue "A GLU 429": "OE1" <-> "OE2" Residue "A GLU 434": "OE1" <-> "OE2" Residue "B GLU 3": "OE1" <-> "OE2" Residue "B GLU 27": "OE1" <-> "OE2" Residue "B GLU 55": "OE1" <-> "OE2" Residue "B GLU 71": "OE1" <-> "OE2" Residue "B GLU 127": "OE1" <-> "OE2" Residue "B GLU 159": "OE1" <-> "OE2" Residue "B GLU 327": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9673 Number of models: 1 Model: "" Number of chains: 7 Chain: "C" Number of atoms: 2482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2482 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 317} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 32 Chain: "G" Number of atoms: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 395 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'TRANS': 78} Chain breaks: 2 Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 79 Planarities with less than four sites: {'UNK:plan-1': 79} Unresolved non-hydrogen planarities: 79 Chain: "A" Number of atoms: 3349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3349 Classifications: {'peptide': 428} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3351 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" N VAL C 47 " occ=0.71 ... (5 atoms not shown) pdb=" CG2 VAL C 47 " occ=0.71 residue: pdb=" N PHE C 86 " occ=0.51 ... (9 atoms not shown) pdb=" CZ PHE C 86 " occ=0.51 residue: pdb=" N PHE C 91 " occ=0.63 ... (9 atoms not shown) pdb=" CZ PHE C 91 " occ=0.63 residue: pdb=" N LEU C 168 " occ=0.62 ... (6 atoms not shown) pdb=" CD2 LEU C 168 " occ=0.62 residue: pdb=" N SER C 304 " occ=0.51 ... (4 atoms not shown) pdb=" OG SER C 304 " occ=0.51 Time building chain proxies: 5.51, per 1000 atoms: 0.57 Number of scatterers: 9673 At special positions: 0 Unit cell: (81.9, 111.8, 118.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 55 16.00 P 9 15.00 Mg 1 11.99 O 1882 8.00 N 1679 7.00 C 6047 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.48 Conformation dependent library (CDL) restraints added in 1.7 seconds 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2336 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 51 helices and 9 sheets defined 46.1% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.96 Creating SS restraints... Processing helix chain 'C' and resid 27 through 32 removed outlier: 4.841A pdb=" N HIS C 32 " --> pdb=" O LYS C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 83 removed outlier: 4.949A pdb=" N GLN C 76 " --> pdb=" O GLN C 72 " (cutoff:3.500A) Proline residue: C 77 - end of helix removed outlier: 4.830A pdb=" N PHE C 83 " --> pdb=" O LEU C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 103 No H-bonds generated for 'chain 'C' and resid 100 through 103' Processing helix chain 'C' and resid 119 through 131 Processing helix chain 'C' and resid 189 through 202 Processing helix chain 'C' and resid 259 through 261 No H-bonds generated for 'chain 'C' and resid 259 through 261' Processing helix chain 'C' and resid 267 through 288 removed outlier: 3.934A pdb=" N GLN C 274 " --> pdb=" O LYS C 270 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ILE C 275 " --> pdb=" O GLU C 271 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA C 288 " --> pdb=" O ASN C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 313 removed outlier: 4.367A pdb=" N ASP C 312 " --> pdb=" O ARG C 308 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N SER C 313 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 346 removed outlier: 3.549A pdb=" N ARG C 345 " --> pdb=" O ASN C 341 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA C 346 " --> pdb=" O TYR C 342 " (cutoff:3.500A) Processing helix chain 'G' and resid 15 through 25 Processing helix chain 'G' and resid 51 through 61 Processing helix chain 'G' and resid 81 through 91 Processing helix chain 'A' and resid 11 through 27 Processing helix chain 'A' and resid 72 through 80 Processing helix chain 'A' and resid 82 through 86 removed outlier: 4.374A pdb=" N GLN A 85 " --> pdb=" O THR A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 107 Processing helix chain 'A' and resid 111 through 113 No H-bonds generated for 'chain 'A' and resid 111 through 113' Processing helix chain 'A' and resid 115 through 128 Processing helix chain 'A' and resid 148 through 160 Processing helix chain 'A' and resid 183 through 197 removed outlier: 3.880A pdb=" N THR A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 215 Processing helix chain 'A' and resid 224 through 243 removed outlier: 4.276A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 258 Processing helix chain 'A' and resid 278 through 281 No H-bonds generated for 'chain 'A' and resid 278 through 281' Processing helix chain 'A' and resid 288 through 296 removed outlier: 4.234A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 325 through 338 Processing helix chain 'A' and resid 382 through 401 Processing helix chain 'A' and resid 405 through 411 Processing helix chain 'A' and resid 415 through 436 Processing helix chain 'B' and resid 10 through 27 Processing helix chain 'B' and resid 41 through 47 removed outlier: 3.742A pdb=" N GLU B 47 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 51 No H-bonds generated for 'chain 'B' and resid 49 through 51' Processing helix chain 'B' and resid 72 through 80 Processing helix chain 'B' and resid 89 through 91 No H-bonds generated for 'chain 'B' and resid 89 through 91' Processing helix chain 'B' and resid 103 through 107 Processing helix chain 'B' and resid 111 through 128 removed outlier: 3.855A pdb=" N SER B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 160 removed outlier: 3.625A pdb=" N GLY B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 197 Proline residue: B 184 - end of helix removed outlier: 4.178A pdb=" N VAL B 195 " --> pdb=" O HIS B 192 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN B 197 " --> pdb=" O LEU B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 215 Processing helix chain 'B' and resid 224 through 240 removed outlier: 4.002A pdb=" N THR B 239 " --> pdb=" O MET B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 259 Processing helix chain 'B' and resid 278 through 280 No H-bonds generated for 'chain 'B' and resid 278 through 280' Processing helix chain 'B' and resid 288 through 296 Processing helix chain 'B' and resid 298 through 300 No H-bonds generated for 'chain 'B' and resid 298 through 300' Processing helix chain 'B' and resid 307 through 309 No H-bonds generated for 'chain 'B' and resid 307 through 309' Processing helix chain 'B' and resid 325 through 338 Processing helix chain 'B' and resid 340 through 342 No H-bonds generated for 'chain 'B' and resid 340 through 342' Processing helix chain 'B' and resid 382 through 401 removed outlier: 4.656A pdb=" N GLU B 393 " --> pdb=" O ARG B 390 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N PHE B 399 " --> pdb=" O THR B 396 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ARG B 400 " --> pdb=" O ALA B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 removed outlier: 3.958A pdb=" N GLU B 411 " --> pdb=" O TRP B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 436 Processing sheet with id= A, first strand: chain 'C' and resid 20 through 22 removed outlier: 7.409A pdb=" N ARG C 21 " --> pdb=" O MET C 322 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N ALA C 324 " --> pdb=" O ARG C 21 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHE C 91 " --> pdb=" O VAL C 321 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE C 323 " --> pdb=" O PHE C 91 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N CYS C 325 " --> pdb=" O TYR C 93 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS C 249 " --> pdb=" O ALA C 88 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL C 90 " --> pdb=" O HIS C 249 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL C 251 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N SER C 246 " --> pdb=" O LEU C 225 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LEU C 225 " --> pdb=" O SER C 246 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 38 through 41 Processing sheet with id= C, first strand: chain 'C' and resid 167 through 170 Processing sheet with id= D, first strand: chain 'A' and resid 92 through 94 removed outlier: 8.203A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.715A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ILE A 5 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N PHE A 135 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ILE A 7 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N VAL A 137 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N VAL A 9 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N HIS A 139 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N SER A 165 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N VAL A 137 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU A 167 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N HIS A 139 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N PHE A 169 " --> pdb=" O HIS A 139 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 53 through 55 Processing sheet with id= F, first strand: chain 'A' and resid 269 through 273 Processing sheet with id= G, first strand: chain 'B' and resid 92 through 94 removed outlier: 8.194A pdb=" N VAL B 93 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N LEU B 67 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N ILE B 66 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N HIS B 6 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N VAL B 68 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N GLN B 8 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N VAL B 5 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N PHE B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ILE B 7 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU B 137 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N ALA B 9 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N HIS B 139 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE B 165 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N LEU B 137 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ASN B 167 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 9.050A pdb=" N HIS B 139 " --> pdb=" O ASN B 167 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N PHE B 169 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N TYR B 202 " --> pdb=" O SER B 170 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 53 through 56 Processing sheet with id= I, first strand: chain 'B' and resid 269 through 273 403 hydrogen bonds defined for protein. 1059 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: 3.26 Time building geometry restraints manager: 4.77 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: 3265 1.34 - 1.46: 2174 1.46 - 1.58: 4324 1.58 - 1.70: 13 1.70 - 1.81: 89 Bond restraints: 9865 Sorted by residual: bond pdb=" O3B G2P B 501 " pdb=" PG G2P B 501 " ideal model delta sigma weight residual 1.716 1.611 0.105 2.00e-02 2.50e+03 2.78e+01 bond pdb=" O1A G2P B 501 " pdb=" PA G2P B 501 " ideal model delta sigma weight residual 1.507 1.611 -0.104 2.00e-02 2.50e+03 2.68e+01 bond pdb=" O1B G2P B 501 " pdb=" PB G2P B 501 " ideal model delta sigma weight residual 1.510 1.609 -0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" C5 GTP A 501 " pdb=" C6 GTP A 501 " ideal model delta sigma weight residual 1.390 1.481 -0.091 2.00e-02 2.50e+03 2.06e+01 bond pdb=" O3A ANP C1401 " pdb=" PB ANP C1401 " ideal model delta sigma weight residual 1.700 1.610 0.090 2.00e-02 2.50e+03 2.03e+01 ... (remaining 9860 not shown) Histogram of bond angle deviations from ideal: 99.45 - 106.79: 300 106.79 - 114.14: 5755 114.14 - 121.48: 5071 121.48 - 128.82: 2219 128.82 - 136.17: 62 Bond angle restraints: 13407 Sorted by residual: angle pdb=" C THR C 205 " pdb=" CA THR C 205 " pdb=" CB THR C 205 " ideal model delta sigma weight residual 110.42 124.13 -13.71 1.99e+00 2.53e-01 4.75e+01 angle pdb=" C HIS C 204 " pdb=" N THR C 205 " pdb=" CA THR C 205 " ideal model delta sigma weight residual 121.54 111.50 10.04 1.91e+00 2.74e-01 2.76e+01 angle pdb=" N SER C 215 " pdb=" CA SER C 215 " pdb=" C SER C 215 " ideal model delta sigma weight residual 110.91 115.77 -4.86 1.17e+00 7.31e-01 1.73e+01 angle pdb=" PA G2P B 501 " pdb=" C3A G2P B 501 " pdb=" PB G2P B 501 " ideal model delta sigma weight residual 120.83 109.51 11.32 3.00e+00 1.11e-01 1.42e+01 angle pdb=" N THR C 208 " pdb=" CA THR C 208 " pdb=" C THR C 208 " ideal model delta sigma weight residual 108.96 103.00 5.96 1.59e+00 3.96e-01 1.41e+01 ... (remaining 13402 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.70: 5774 33.70 - 67.39: 119 67.39 - 101.08: 13 101.08 - 134.78: 2 134.78 - 168.47: 4 Dihedral angle restraints: 5912 sinusoidal: 2282 harmonic: 3630 Sorted by residual: dihedral pdb=" C THR C 205 " pdb=" N THR C 205 " pdb=" CA THR C 205 " pdb=" CB THR C 205 " ideal model delta harmonic sigma weight residual -122.00 -147.69 25.69 0 2.50e+00 1.60e-01 1.06e+02 dihedral pdb=" N THR C 205 " pdb=" C THR C 205 " pdb=" CA THR C 205 " pdb=" CB THR C 205 " ideal model delta harmonic sigma weight residual 123.40 142.70 -19.30 0 2.50e+00 1.60e-01 5.96e+01 dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -122.26 -168.47 1 2.00e+01 2.50e-03 4.75e+01 ... (remaining 5909 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.199: 1503 0.199 - 0.398: 1 0.398 - 0.597: 0 0.597 - 0.796: 0 0.796 - 0.995: 1 Chirality restraints: 1505 Sorted by residual: chirality pdb=" CA THR C 205 " pdb=" N THR C 205 " pdb=" C THR C 205 " pdb=" CB THR C 205 " both_signs ideal model delta sigma weight residual False 2.53 1.53 0.99 2.00e-01 2.50e+01 2.47e+01 chirality pdb=" CA HIS C 204 " pdb=" N HIS C 204 " pdb=" C HIS C 204 " pdb=" CB HIS C 204 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" C3' ANP C1401 " pdb=" C2' ANP C1401 " pdb=" C4' ANP C1401 " pdb=" O3' ANP C1401 " both_signs ideal model delta sigma weight residual False -2.36 -2.54 0.19 2.00e-01 2.50e+01 8.76e-01 ... (remaining 1502 not shown) Planarity restraints: 1749 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA C 202 " -0.009 2.00e-02 2.50e+03 1.82e-02 3.30e+00 pdb=" C ALA C 202 " 0.031 2.00e-02 2.50e+03 pdb=" O ALA C 202 " -0.012 2.00e-02 2.50e+03 pdb=" N ARG C 203 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET B 269 " 0.030 5.00e-02 4.00e+02 4.53e-02 3.28e+00 pdb=" N PRO B 270 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 270 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 270 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 31 " -0.025 5.00e-02 4.00e+02 3.81e-02 2.32e+00 pdb=" N PRO B 32 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 32 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 32 " -0.021 5.00e-02 4.00e+02 ... (remaining 1746 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.31: 64 2.31 - 2.96: 5398 2.96 - 3.61: 15704 3.61 - 4.25: 22971 4.25 - 4.90: 36351 Nonbonded interactions: 80488 Sorted by model distance: nonbonded pdb=" O ARG C 203 " pdb=" O GLY C 206 " model vdw 1.666 3.040 nonbonded pdb=" O2A G2P B 501 " pdb="MG MG B 502 " model vdw 1.777 2.170 nonbonded pdb=" C GLY C 199 " pdb=" NH1 ARG C 203 " model vdw 1.818 3.350 nonbonded pdb=" O2G G2P B 501 " pdb="MG MG B 502 " model vdw 1.923 2.170 nonbonded pdb=" OH TYR C 145 " pdb=" NH2 ARG C 203 " model vdw 1.968 2.520 ... (remaining 80483 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=0.41 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.050 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: 0.870 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 30.540 Find NCS groups from input model: 0.280 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: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 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 : 0.006 0.105 9865 Z= 0.399 Angle : 0.854 13.713 13407 Z= 0.458 Chirality : 0.051 0.995 1505 Planarity : 0.004 0.045 1749 Dihedral : 15.605 168.471 3576 Min Nonbonded Distance : 1.666 Molprobity Statistics. All-atom Clashscore : 29.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.22), residues: 1172 helix: -1.24 (0.20), residues: 491 sheet: -1.23 (0.31), residues: 198 loop : -2.37 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 346 HIS 0.008 0.002 HIS C 298 PHE 0.016 0.002 PHE C 248 TYR 0.013 0.002 TYR B 432 ARG 0.006 0.000 ARG C 258 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 299 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 119 ILE cc_start: 0.8786 (mt) cc_final: 0.8345 (mm) REVERT: C 149 TYR cc_start: 0.8704 (t80) cc_final: 0.8442 (t80) REVERT: C 151 GLU cc_start: 0.9099 (mp0) cc_final: 0.8634 (mp0) REVERT: C 182 LYS cc_start: 0.8830 (tttp) cc_final: 0.8427 (ttmt) REVERT: C 218 HIS cc_start: 0.8399 (m-70) cc_final: 0.7744 (m-70) REVERT: C 225 LEU cc_start: 0.8888 (tp) cc_final: 0.8623 (tp) REVERT: C 274 GLN cc_start: 0.9144 (mt0) cc_final: 0.8111 (pt0) REVERT: C 301 TYR cc_start: 0.9198 (m-80) cc_final: 0.8717 (m-80) REVERT: A 18 ASN cc_start: 0.8886 (m-40) cc_final: 0.8559 (t0) REVERT: A 116 ASP cc_start: 0.9437 (m-30) cc_final: 0.8869 (p0) REVERT: A 118 VAL cc_start: 0.9722 (m) cc_final: 0.9413 (p) REVERT: A 127 ASP cc_start: 0.8830 (m-30) cc_final: 0.8551 (m-30) REVERT: A 155 GLU cc_start: 0.9357 (tp30) cc_final: 0.8858 (tp30) REVERT: A 196 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8413 (mm-30) REVERT: A 216 ASN cc_start: 0.9193 (m-40) cc_final: 0.8719 (m110) REVERT: A 363 VAL cc_start: 0.9237 (t) cc_final: 0.8895 (p) REVERT: A 401 LYS cc_start: 0.9489 (tppt) cc_final: 0.9274 (tppt) REVERT: A 430 LYS cc_start: 0.9453 (tptt) cc_final: 0.8912 (tppt) REVERT: A 433 GLU cc_start: 0.9157 (tm-30) cc_final: 0.8424 (tm-30) REVERT: B 26 ASP cc_start: 0.9318 (t0) cc_final: 0.9078 (t70) REVERT: B 37 HIS cc_start: 0.8802 (m-70) cc_final: 0.8292 (m90) REVERT: B 108 TYR cc_start: 0.8550 (t80) cc_final: 0.8322 (t80) REVERT: B 156 LYS cc_start: 0.9458 (mttt) cc_final: 0.9101 (mmpt) REVERT: B 166 MET cc_start: 0.7478 (mmm) cc_final: 0.7047 (mtm) REVERT: B 199 ASP cc_start: 0.8421 (m-30) cc_final: 0.7889 (m-30) REVERT: B 214 PHE cc_start: 0.8809 (t80) cc_final: 0.8581 (t80) REVERT: B 219 LEU cc_start: 0.8663 (mt) cc_final: 0.8311 (mt) REVERT: B 306 ASP cc_start: 0.9007 (m-30) cc_final: 0.8696 (t70) REVERT: B 309 HIS cc_start: 0.9000 (m170) cc_final: 0.8352 (m-70) REVERT: B 332 MET cc_start: 0.9291 (mmt) cc_final: 0.8944 (mmm) REVERT: B 373 MET cc_start: 0.8297 (ptp) cc_final: 0.7957 (mtp) REVERT: B 394 GLN cc_start: 0.8879 (mm-40) cc_final: 0.8677 (tp40) REVERT: B 413 MET cc_start: 0.9131 (mmm) cc_final: 0.8697 (mmm) REVERT: B 416 MET cc_start: 0.9093 (mmm) cc_final: 0.8126 (tpt) outliers start: 0 outliers final: 0 residues processed: 299 average time/residue: 0.2504 time to fit residues: 99.3495 Evaluate side-chains 212 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 5.9990 chunk 93 optimal weight: 10.0000 chunk 51 optimal weight: 30.0000 chunk 31 optimal weight: 40.0000 chunk 62 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 96 optimal weight: 0.9990 chunk 37 optimal weight: 50.0000 chunk 58 optimal weight: 9.9990 chunk 71 optimal weight: 7.9990 chunk 111 optimal weight: 0.5980 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 18 ASN A 28 HIS A 31 GLN A 101 ASN A 380 ASN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN B 14 ASN B 337 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9865 Z= 0.204 Angle : 0.683 9.717 13407 Z= 0.338 Chirality : 0.044 0.188 1505 Planarity : 0.005 0.059 1749 Dihedral : 10.971 151.582 1435 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 21.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.73 % Allowed : 17.88 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.23), residues: 1172 helix: -0.11 (0.23), residues: 483 sheet: -0.94 (0.32), residues: 211 loop : -1.55 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 21 HIS 0.005 0.001 HIS C 298 PHE 0.021 0.002 PHE B 262 TYR 0.041 0.002 TYR C 71 ARG 0.011 0.001 ARG C 154 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 254 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 149 TYR cc_start: 0.8687 (t80) cc_final: 0.8438 (t80) REVERT: C 151 GLU cc_start: 0.9031 (mp0) cc_final: 0.8429 (mp0) REVERT: C 167 GLN cc_start: 0.8710 (mt0) cc_final: 0.8473 (mt0) REVERT: C 182 LYS cc_start: 0.8727 (tttp) cc_final: 0.8300 (ttmt) REVERT: C 218 HIS cc_start: 0.8346 (m-70) cc_final: 0.7856 (m-70) REVERT: C 274 GLN cc_start: 0.9157 (mt0) cc_final: 0.8470 (pp30) REVERT: C 280 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9118 (mm) REVERT: C 301 TYR cc_start: 0.9221 (m-80) cc_final: 0.8784 (m-80) REVERT: C 305 LYS cc_start: 0.8714 (mttp) cc_final: 0.8507 (mtmt) REVERT: A 86 LEU cc_start: 0.9311 (mt) cc_final: 0.8896 (mt) REVERT: A 116 ASP cc_start: 0.9273 (m-30) cc_final: 0.9023 (p0) REVERT: A 196 GLU cc_start: 0.8584 (mm-30) cc_final: 0.8289 (mm-30) REVERT: A 272 TYR cc_start: 0.8415 (t80) cc_final: 0.7988 (t80) REVERT: A 363 VAL cc_start: 0.9243 (t) cc_final: 0.8863 (p) REVERT: A 372 GLN cc_start: 0.8927 (mp10) cc_final: 0.8697 (mm-40) REVERT: A 413 MET cc_start: 0.9156 (mmm) cc_final: 0.8865 (mmm) REVERT: A 430 LYS cc_start: 0.9499 (tptt) cc_final: 0.9239 (tppt) REVERT: A 433 GLU cc_start: 0.9166 (tm-30) cc_final: 0.8935 (tm-30) REVERT: A 434 GLU cc_start: 0.8961 (mt-10) cc_final: 0.8666 (mt-10) REVERT: B 26 ASP cc_start: 0.9263 (t0) cc_final: 0.9012 (t70) REVERT: B 37 HIS cc_start: 0.8788 (m-70) cc_final: 0.8267 (m90) REVERT: B 68 VAL cc_start: 0.9317 (p) cc_final: 0.9077 (m) REVERT: B 69 ASP cc_start: 0.7555 (t70) cc_final: 0.7316 (t70) REVERT: B 108 TYR cc_start: 0.8526 (t80) cc_final: 0.8319 (t80) REVERT: B 156 LYS cc_start: 0.9443 (mttt) cc_final: 0.9038 (mmtm) REVERT: B 159 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7885 (mt-10) REVERT: B 219 LEU cc_start: 0.8509 (mt) cc_final: 0.8155 (mt) REVERT: B 267 PHE cc_start: 0.8919 (m-10) cc_final: 0.8374 (m-10) REVERT: B 302 MET cc_start: 0.9129 (OUTLIER) cc_final: 0.8474 (mmm) REVERT: B 306 ASP cc_start: 0.8967 (m-30) cc_final: 0.8747 (t0) REVERT: B 309 HIS cc_start: 0.8880 (m170) cc_final: 0.8204 (m-70) REVERT: B 332 MET cc_start: 0.9342 (mmt) cc_final: 0.8971 (mmm) REVERT: B 373 MET cc_start: 0.8425 (ptp) cc_final: 0.7986 (mtm) REVERT: B 413 MET cc_start: 0.9106 (mmm) cc_final: 0.8675 (mmm) REVERT: B 416 MET cc_start: 0.8923 (mmm) cc_final: 0.7817 (tpt) REVERT: B 419 THR cc_start: 0.9586 (OUTLIER) cc_final: 0.9386 (p) outliers start: 27 outliers final: 14 residues processed: 264 average time/residue: 0.2167 time to fit residues: 78.3745 Evaluate side-chains 232 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 215 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 309 HIS Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 59 ASN Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 419 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 40.0000 chunk 34 optimal weight: 70.0000 chunk 92 optimal weight: 20.0000 chunk 76 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 chunk 111 optimal weight: 40.0000 chunk 120 optimal weight: 10.0000 chunk 99 optimal weight: 6.9990 chunk 110 optimal weight: 50.0000 chunk 38 optimal weight: 60.0000 chunk 89 optimal weight: 20.0000 overall best weight: 10.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 76 GLN ** C 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 ASN B 406 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9865 Z= 0.283 Angle : 0.698 10.460 13407 Z= 0.347 Chirality : 0.042 0.151 1505 Planarity : 0.004 0.048 1749 Dihedral : 10.681 160.762 1435 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 24.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 4.14 % Allowed : 20.20 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -1.06 (0.24), residues: 1172 helix: 0.12 (0.23), residues: 484 sheet: -0.83 (0.32), residues: 207 loop : -1.41 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 346 HIS 0.006 0.002 HIS C 298 PHE 0.016 0.002 PHE A 49 TYR 0.021 0.002 TYR C 71 ARG 0.007 0.001 ARG C 154 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 219 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 71 TYR cc_start: 0.8598 (t80) cc_final: 0.8049 (t80) REVERT: C 119 ILE cc_start: 0.8319 (OUTLIER) cc_final: 0.8090 (tp) REVERT: C 151 GLU cc_start: 0.9041 (mp0) cc_final: 0.8451 (mp0) REVERT: C 167 GLN cc_start: 0.8613 (mt0) cc_final: 0.8399 (mt0) REVERT: C 182 LYS cc_start: 0.8702 (tttp) cc_final: 0.8333 (ttmt) REVERT: C 218 HIS cc_start: 0.8408 (m-70) cc_final: 0.7812 (m-70) REVERT: C 274 GLN cc_start: 0.9165 (mt0) cc_final: 0.8665 (mt0) REVERT: C 301 TYR cc_start: 0.9242 (m-80) cc_final: 0.8807 (m-80) REVERT: C 305 LYS cc_start: 0.8689 (mttp) cc_final: 0.8432 (mtmt) REVERT: A 22 GLU cc_start: 0.8991 (pt0) cc_final: 0.8703 (pt0) REVERT: A 86 LEU cc_start: 0.9352 (mt) cc_final: 0.9042 (mt) REVERT: A 116 ASP cc_start: 0.9357 (m-30) cc_final: 0.8912 (p0) REVERT: A 127 ASP cc_start: 0.8857 (m-30) cc_final: 0.8628 (m-30) REVERT: A 196 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8238 (mm-30) REVERT: A 272 TYR cc_start: 0.8535 (t80) cc_final: 0.8228 (t80) REVERT: A 297 GLU cc_start: 0.9006 (tm-30) cc_final: 0.8792 (tm-30) REVERT: A 363 VAL cc_start: 0.9210 (t) cc_final: 0.8890 (p) REVERT: A 372 GLN cc_start: 0.9064 (mp10) cc_final: 0.8738 (mm-40) REVERT: A 375 VAL cc_start: 0.9476 (t) cc_final: 0.9206 (p) REVERT: A 413 MET cc_start: 0.9311 (mmm) cc_final: 0.9059 (mmm) REVERT: A 430 LYS cc_start: 0.9540 (tptt) cc_final: 0.9192 (tppt) REVERT: A 433 GLU cc_start: 0.9151 (tm-30) cc_final: 0.8898 (tm-30) REVERT: A 434 GLU cc_start: 0.8983 (mt-10) cc_final: 0.8552 (mt-10) REVERT: B 26 ASP cc_start: 0.9315 (t0) cc_final: 0.9072 (t70) REVERT: B 156 LYS cc_start: 0.9496 (mttt) cc_final: 0.9005 (mmpt) REVERT: B 159 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7922 (mt-10) REVERT: B 306 ASP cc_start: 0.8918 (m-30) cc_final: 0.8711 (t0) REVERT: B 309 HIS cc_start: 0.8913 (m170) cc_final: 0.8172 (m-70) REVERT: B 332 MET cc_start: 0.9380 (mmt) cc_final: 0.8987 (mmm) REVERT: B 373 MET cc_start: 0.8497 (ptp) cc_final: 0.8072 (mtp) REVERT: B 395 PHE cc_start: 0.9131 (t80) cc_final: 0.8761 (t80) REVERT: B 398 MET cc_start: 0.9339 (mtp) cc_final: 0.9044 (mmt) REVERT: B 413 MET cc_start: 0.9152 (mmm) cc_final: 0.8859 (mmm) REVERT: B 416 MET cc_start: 0.9034 (mmm) cc_final: 0.8006 (tpt) REVERT: B 419 THR cc_start: 0.9626 (OUTLIER) cc_final: 0.9367 (p) outliers start: 41 outliers final: 27 residues processed: 238 average time/residue: 0.2212 time to fit residues: 72.6052 Evaluate side-chains 227 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 198 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 309 HIS Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 59 ASN Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 419 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 20.0000 chunk 84 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 12 optimal weight: 40.0000 chunk 53 optimal weight: 30.0000 chunk 75 optimal weight: 40.0000 chunk 112 optimal weight: 20.0000 chunk 118 optimal weight: 7.9990 chunk 106 optimal weight: 6.9990 chunk 32 optimal weight: 50.0000 chunk 99 optimal weight: 30.0000 overall best weight: 9.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 342 GLN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9865 Z= 0.260 Angle : 0.683 12.077 13407 Z= 0.336 Chirality : 0.043 0.377 1505 Planarity : 0.004 0.045 1749 Dihedral : 10.620 166.251 1435 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 23.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 4.34 % Allowed : 22.73 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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 (0.24), residues: 1172 helix: 0.27 (0.23), residues: 484 sheet: -0.67 (0.33), residues: 203 loop : -1.34 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 346 HIS 0.005 0.001 HIS A 28 PHE 0.012 0.001 PHE C 248 TYR 0.022 0.002 TYR A 224 ARG 0.005 0.000 ARG C 154 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 221 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 71 TYR cc_start: 0.8840 (t80) cc_final: 0.8380 (t80) REVERT: C 119 ILE cc_start: 0.8383 (OUTLIER) cc_final: 0.8181 (tp) REVERT: C 151 GLU cc_start: 0.8971 (mp0) cc_final: 0.8500 (mp0) REVERT: C 182 LYS cc_start: 0.8709 (tttp) cc_final: 0.8328 (ttmm) REVERT: C 210 LEU cc_start: 0.5283 (OUTLIER) cc_final: 0.4499 (tt) REVERT: C 218 HIS cc_start: 0.8530 (m-70) cc_final: 0.7941 (m-70) REVERT: C 268 ARG cc_start: 0.8968 (mtm110) cc_final: 0.8487 (ptt90) REVERT: C 274 GLN cc_start: 0.9134 (mt0) cc_final: 0.8500 (pp30) REVERT: C 301 TYR cc_start: 0.9256 (m-80) cc_final: 0.8822 (m-80) REVERT: C 305 LYS cc_start: 0.8706 (mttp) cc_final: 0.8437 (mtmt) REVERT: A 22 GLU cc_start: 0.9034 (pt0) cc_final: 0.8718 (pt0) REVERT: A 86 LEU cc_start: 0.9358 (mt) cc_final: 0.9038 (mt) REVERT: A 116 ASP cc_start: 0.9358 (m-30) cc_final: 0.8891 (p0) REVERT: A 127 ASP cc_start: 0.8916 (m-30) cc_final: 0.8691 (m-30) REVERT: A 196 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8306 (mm-30) REVERT: A 203 MET cc_start: 0.7846 (ttt) cc_final: 0.7476 (tpt) REVERT: A 272 TYR cc_start: 0.8471 (t80) cc_final: 0.8189 (t80) REVERT: A 285 GLN cc_start: 0.2827 (OUTLIER) cc_final: 0.1854 (mt0) REVERT: A 363 VAL cc_start: 0.9214 (t) cc_final: 0.8905 (p) REVERT: A 372 GLN cc_start: 0.8956 (mp10) cc_final: 0.8705 (mm-40) REVERT: A 375 VAL cc_start: 0.9463 (t) cc_final: 0.9179 (p) REVERT: A 413 MET cc_start: 0.9331 (mmm) cc_final: 0.9087 (mmm) REVERT: A 430 LYS cc_start: 0.9550 (tptt) cc_final: 0.9190 (tppt) REVERT: A 433 GLU cc_start: 0.9164 (tm-30) cc_final: 0.8906 (tm-30) REVERT: A 434 GLU cc_start: 0.8957 (mt-10) cc_final: 0.8520 (mt-10) REVERT: B 26 ASP cc_start: 0.9308 (t0) cc_final: 0.9050 (t70) REVERT: B 107 HIS cc_start: 0.8516 (t70) cc_final: 0.7790 (t70) REVERT: B 302 MET cc_start: 0.9097 (mmm) cc_final: 0.8657 (mtt) REVERT: B 306 ASP cc_start: 0.8910 (m-30) cc_final: 0.8639 (t0) REVERT: B 309 HIS cc_start: 0.8889 (m170) cc_final: 0.8078 (m-70) REVERT: B 332 MET cc_start: 0.9359 (mmt) cc_final: 0.8990 (mmm) REVERT: B 373 MET cc_start: 0.8510 (ptp) cc_final: 0.8024 (mtp) REVERT: B 398 MET cc_start: 0.9305 (mtp) cc_final: 0.9011 (mmt) REVERT: B 413 MET cc_start: 0.9166 (mmm) cc_final: 0.8770 (mmm) REVERT: B 416 MET cc_start: 0.9004 (mmm) cc_final: 0.7990 (tpt) REVERT: B 419 THR cc_start: 0.9544 (OUTLIER) cc_final: 0.9134 (p) outliers start: 43 outliers final: 29 residues processed: 239 average time/residue: 0.2184 time to fit residues: 72.1264 Evaluate side-chains 230 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 197 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 285 GLN Chi-restraints excluded: chain A residue 309 HIS Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 59 ASN Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 419 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 5.9990 chunk 1 optimal weight: 50.0000 chunk 88 optimal weight: 9.9990 chunk 49 optimal weight: 20.0000 chunk 101 optimal weight: 40.0000 chunk 82 optimal weight: 9.9990 chunk 0 optimal weight: 50.0000 chunk 60 optimal weight: 6.9990 chunk 106 optimal weight: 8.9990 chunk 30 optimal weight: 50.0000 chunk 40 optimal weight: 9.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 167 GLN ** C 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 GLN ** C 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9865 Z= 0.244 Angle : 0.690 13.409 13407 Z= 0.337 Chirality : 0.042 0.163 1505 Planarity : 0.004 0.038 1749 Dihedral : 10.633 169.926 1435 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 22.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 4.85 % Allowed : 23.94 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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 (0.24), residues: 1172 helix: 0.42 (0.24), residues: 483 sheet: -0.52 (0.34), residues: 201 loop : -1.27 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP B 346 HIS 0.005 0.001 HIS C 298 PHE 0.022 0.001 PHE B 262 TYR 0.018 0.001 TYR A 224 ARG 0.006 0.000 ARG C 154 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 217 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 71 TYR cc_start: 0.8987 (t80) cc_final: 0.8492 (t80) REVERT: C 119 ILE cc_start: 0.8365 (OUTLIER) cc_final: 0.8133 (tp) REVERT: C 151 GLU cc_start: 0.9038 (mp0) cc_final: 0.8378 (mp0) REVERT: C 210 LEU cc_start: 0.5257 (OUTLIER) cc_final: 0.4499 (tt) REVERT: C 268 ARG cc_start: 0.8968 (mtm110) cc_final: 0.8568 (ptt90) REVERT: C 274 GLN cc_start: 0.9016 (mt0) cc_final: 0.8467 (pp30) REVERT: C 301 TYR cc_start: 0.9230 (m-80) cc_final: 0.8780 (m-80) REVERT: C 305 LYS cc_start: 0.8672 (mttp) cc_final: 0.8409 (mtmt) REVERT: A 22 GLU cc_start: 0.8989 (pt0) cc_final: 0.8640 (pt0) REVERT: A 86 LEU cc_start: 0.9314 (mt) cc_final: 0.8973 (mt) REVERT: A 116 ASP cc_start: 0.9357 (m-30) cc_final: 0.8886 (p0) REVERT: A 127 ASP cc_start: 0.8927 (m-30) cc_final: 0.8674 (m-30) REVERT: A 196 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8311 (mm-30) REVERT: A 272 TYR cc_start: 0.8494 (t80) cc_final: 0.8218 (t80) REVERT: A 276 ILE cc_start: 0.9465 (tp) cc_final: 0.9246 (tp) REVERT: A 302 MET cc_start: 0.8241 (mpp) cc_final: 0.7994 (mpp) REVERT: A 363 VAL cc_start: 0.9218 (t) cc_final: 0.8918 (p) REVERT: A 372 GLN cc_start: 0.8944 (mp10) cc_final: 0.8716 (mm-40) REVERT: A 375 VAL cc_start: 0.9457 (t) cc_final: 0.9171 (p) REVERT: A 380 ASN cc_start: 0.7793 (m-40) cc_final: 0.7501 (m-40) REVERT: A 413 MET cc_start: 0.9313 (mmm) cc_final: 0.9070 (mmm) REVERT: A 430 LYS cc_start: 0.9563 (tptt) cc_final: 0.9191 (tppt) REVERT: A 433 GLU cc_start: 0.9173 (tm-30) cc_final: 0.8899 (tm-30) REVERT: A 434 GLU cc_start: 0.8963 (mt-10) cc_final: 0.8525 (mt-10) REVERT: B 26 ASP cc_start: 0.9269 (t0) cc_final: 0.8982 (t70) REVERT: B 107 HIS cc_start: 0.8558 (t70) cc_final: 0.7838 (t70) REVERT: B 156 LYS cc_start: 0.9546 (mttt) cc_final: 0.9300 (tppt) REVERT: B 267 PHE cc_start: 0.8963 (m-10) cc_final: 0.8553 (m-10) REVERT: B 302 MET cc_start: 0.8972 (mmm) cc_final: 0.8601 (mtt) REVERT: B 309 HIS cc_start: 0.8875 (m170) cc_final: 0.8188 (m-70) REVERT: B 332 MET cc_start: 0.9385 (mmt) cc_final: 0.9001 (mmm) REVERT: B 373 MET cc_start: 0.8497 (ptp) cc_final: 0.7962 (mtp) REVERT: B 398 MET cc_start: 0.9297 (mtp) cc_final: 0.8980 (mmt) REVERT: B 413 MET cc_start: 0.9136 (mmm) cc_final: 0.8743 (mmm) REVERT: B 416 MET cc_start: 0.9010 (mmm) cc_final: 0.7818 (tpp) REVERT: B 419 THR cc_start: 0.9350 (OUTLIER) cc_final: 0.9136 (p) outliers start: 48 outliers final: 34 residues processed: 238 average time/residue: 0.2145 time to fit residues: 71.0089 Evaluate side-chains 246 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 209 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 309 HIS Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 59 ASN Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 419 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 9.9990 chunk 23 optimal weight: 40.0000 chunk 69 optimal weight: 5.9990 chunk 29 optimal weight: 50.0000 chunk 119 optimal weight: 0.0570 chunk 98 optimal weight: 20.0000 chunk 55 optimal weight: 30.0000 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 chunk 62 optimal weight: 30.0000 chunk 114 optimal weight: 7.9990 overall best weight: 5.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 11 GLN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9865 Z= 0.204 Angle : 0.680 12.543 13407 Z= 0.331 Chirality : 0.042 0.175 1505 Planarity : 0.004 0.044 1749 Dihedral : 10.497 167.980 1435 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 21.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 4.75 % Allowed : 24.55 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -0.58 (0.24), residues: 1172 helix: 0.50 (0.24), residues: 473 sheet: -0.33 (0.34), residues: 202 loop : -1.20 (0.29), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 346 HIS 0.004 0.001 HIS C 298 PHE 0.027 0.001 PHE B 262 TYR 0.016 0.001 TYR A 224 ARG 0.008 0.000 ARG A 121 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 232 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 71 TYR cc_start: 0.9041 (t80) cc_final: 0.8556 (t80) REVERT: C 102 TYR cc_start: 0.7477 (t80) cc_final: 0.7254 (t80) REVERT: C 119 ILE cc_start: 0.8477 (OUTLIER) cc_final: 0.8121 (tp) REVERT: C 151 GLU cc_start: 0.8986 (mp0) cc_final: 0.7990 (mp0) REVERT: C 182 LYS cc_start: 0.8763 (tttp) cc_final: 0.8386 (tttp) REVERT: C 192 VAL cc_start: 0.9057 (t) cc_final: 0.8853 (p) REVERT: C 210 LEU cc_start: 0.5259 (OUTLIER) cc_final: 0.4498 (tt) REVERT: C 250 PHE cc_start: 0.8644 (m-10) cc_final: 0.8299 (m-10) REVERT: C 268 ARG cc_start: 0.9005 (mtm110) cc_final: 0.8586 (ptt90) REVERT: C 274 GLN cc_start: 0.9008 (mt0) cc_final: 0.8496 (pp30) REVERT: C 301 TYR cc_start: 0.9266 (m-80) cc_final: 0.8862 (m-80) REVERT: C 305 LYS cc_start: 0.8777 (mttp) cc_final: 0.8568 (mtpt) REVERT: A 22 GLU cc_start: 0.9015 (pt0) cc_final: 0.8649 (pt0) REVERT: A 86 LEU cc_start: 0.9310 (mt) cc_final: 0.8963 (mt) REVERT: A 116 ASP cc_start: 0.9359 (m-30) cc_final: 0.8894 (p0) REVERT: A 127 ASP cc_start: 0.8956 (m-30) cc_final: 0.8702 (m-30) REVERT: A 196 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8368 (mm-30) REVERT: A 203 MET cc_start: 0.7856 (ttt) cc_final: 0.7098 (tpt) REVERT: A 267 PHE cc_start: 0.9374 (m-80) cc_final: 0.9148 (m-80) REVERT: A 272 TYR cc_start: 0.8461 (t80) cc_final: 0.8181 (t80) REVERT: A 276 ILE cc_start: 0.9447 (tp) cc_final: 0.9222 (tp) REVERT: A 302 MET cc_start: 0.8276 (mpp) cc_final: 0.8060 (ptp) REVERT: A 304 LYS cc_start: 0.9070 (tttm) cc_final: 0.8854 (tttt) REVERT: A 363 VAL cc_start: 0.9223 (t) cc_final: 0.8929 (p) REVERT: A 372 GLN cc_start: 0.8970 (mp10) cc_final: 0.8707 (mm-40) REVERT: A 375 VAL cc_start: 0.9431 (t) cc_final: 0.9123 (p) REVERT: A 380 ASN cc_start: 0.7763 (m-40) cc_final: 0.7393 (m-40) REVERT: A 413 MET cc_start: 0.9246 (mmm) cc_final: 0.9045 (mmm) REVERT: A 430 LYS cc_start: 0.9591 (tptt) cc_final: 0.9282 (tppt) REVERT: A 433 GLU cc_start: 0.9168 (tm-30) cc_final: 0.8895 (tm-30) REVERT: A 434 GLU cc_start: 0.9037 (mt-10) cc_final: 0.8512 (mt-10) REVERT: B 26 ASP cc_start: 0.9241 (t0) cc_final: 0.8943 (t70) REVERT: B 107 HIS cc_start: 0.8599 (t70) cc_final: 0.7836 (t70) REVERT: B 156 LYS cc_start: 0.9537 (mttt) cc_final: 0.9242 (mmtt) REVERT: B 159 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8194 (mt-10) REVERT: B 267 PHE cc_start: 0.8839 (m-10) cc_final: 0.8599 (m-10) REVERT: B 302 MET cc_start: 0.8865 (mmm) cc_final: 0.8487 (mtt) REVERT: B 306 ASP cc_start: 0.8128 (t0) cc_final: 0.7617 (t0) REVERT: B 309 HIS cc_start: 0.8479 (m170) cc_final: 0.8084 (m-70) REVERT: B 373 MET cc_start: 0.8468 (ptp) cc_final: 0.7962 (mtp) REVERT: B 398 MET cc_start: 0.9248 (mtp) cc_final: 0.8928 (mmt) REVERT: B 413 MET cc_start: 0.9186 (mmm) cc_final: 0.8767 (mmm) REVERT: B 416 MET cc_start: 0.8973 (mmm) cc_final: 0.7797 (tpp) outliers start: 47 outliers final: 39 residues processed: 251 average time/residue: 0.2058 time to fit residues: 71.8868 Evaluate side-chains 258 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 217 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 342 TYR Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 309 HIS Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 59 ASN Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 357 ASP Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 387 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 9.9990 chunk 67 optimal weight: 7.9990 chunk 86 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 chunk 118 optimal weight: 6.9990 chunk 74 optimal weight: 0.5980 chunk 72 optimal weight: 3.9990 chunk 54 optimal weight: 30.0000 chunk 73 optimal weight: 7.9990 chunk 47 optimal weight: 20.0000 overall best weight: 5.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9865 Z= 0.206 Angle : 0.703 13.243 13407 Z= 0.337 Chirality : 0.043 0.174 1505 Planarity : 0.004 0.039 1749 Dihedral : 10.437 166.705 1435 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 21.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 5.15 % Allowed : 25.25 % Favored : 69.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -0.54 (0.25), residues: 1172 helix: 0.44 (0.24), residues: 475 sheet: -0.31 (0.34), residues: 201 loop : -1.09 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 346 HIS 0.006 0.001 HIS C 142 PHE 0.016 0.001 PHE B 262 TYR 0.015 0.001 TYR C 93 ARG 0.006 0.000 ARG B 278 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 226 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 71 TYR cc_start: 0.9049 (t80) cc_final: 0.8596 (t80) REVERT: C 102 TYR cc_start: 0.7247 (t80) cc_final: 0.6984 (t80) REVERT: C 119 ILE cc_start: 0.8442 (OUTLIER) cc_final: 0.8073 (tp) REVERT: C 151 GLU cc_start: 0.9121 (mp0) cc_final: 0.8594 (mp0) REVERT: C 210 LEU cc_start: 0.5248 (OUTLIER) cc_final: 0.4539 (tt) REVERT: C 268 ARG cc_start: 0.9002 (mtm110) cc_final: 0.8538 (ptt90) REVERT: C 274 GLN cc_start: 0.9066 (mt0) cc_final: 0.8463 (pp30) REVERT: C 301 TYR cc_start: 0.9228 (m-80) cc_final: 0.8784 (m-80) REVERT: C 305 LYS cc_start: 0.8743 (mttp) cc_final: 0.8501 (mtmt) REVERT: A 22 GLU cc_start: 0.9043 (pt0) cc_final: 0.8706 (pt0) REVERT: A 86 LEU cc_start: 0.9284 (mt) cc_final: 0.8917 (mt) REVERT: A 116 ASP cc_start: 0.9376 (m-30) cc_final: 0.8931 (p0) REVERT: A 127 ASP cc_start: 0.8963 (m-30) cc_final: 0.8696 (m-30) REVERT: A 154 MET cc_start: 0.9264 (ttt) cc_final: 0.8869 (ttt) REVERT: A 196 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8465 (mm-30) REVERT: A 203 MET cc_start: 0.7826 (ttt) cc_final: 0.7291 (tpt) REVERT: A 224 TYR cc_start: 0.9123 (OUTLIER) cc_final: 0.8746 (m-80) REVERT: A 267 PHE cc_start: 0.9356 (m-80) cc_final: 0.9145 (m-80) REVERT: A 272 TYR cc_start: 0.8396 (t80) cc_final: 0.8058 (t80) REVERT: A 276 ILE cc_start: 0.9433 (tp) cc_final: 0.9209 (tp) REVERT: A 363 VAL cc_start: 0.9236 (t) cc_final: 0.8939 (p) REVERT: A 372 GLN cc_start: 0.8962 (mp10) cc_final: 0.8697 (mm-40) REVERT: A 375 VAL cc_start: 0.9430 (t) cc_final: 0.9124 (p) REVERT: A 380 ASN cc_start: 0.7754 (m-40) cc_final: 0.7386 (m-40) REVERT: A 430 LYS cc_start: 0.9610 (tptt) cc_final: 0.9175 (tppt) REVERT: A 433 GLU cc_start: 0.9158 (tm-30) cc_final: 0.8859 (tm-30) REVERT: A 434 GLU cc_start: 0.9064 (mt-10) cc_final: 0.8562 (mt-10) REVERT: B 26 ASP cc_start: 0.9247 (t0) cc_final: 0.8956 (t70) REVERT: B 107 HIS cc_start: 0.8699 (t70) cc_final: 0.7994 (t70) REVERT: B 156 LYS cc_start: 0.9529 (mttt) cc_final: 0.9183 (tppt) REVERT: B 159 GLU cc_start: 0.8347 (mt-10) cc_final: 0.8006 (mt-10) REVERT: B 267 PHE cc_start: 0.8712 (m-10) cc_final: 0.8499 (m-10) REVERT: B 302 MET cc_start: 0.8759 (mmm) cc_final: 0.8470 (mtt) REVERT: B 306 ASP cc_start: 0.8160 (t0) cc_final: 0.7665 (t0) REVERT: B 309 HIS cc_start: 0.8549 (m170) cc_final: 0.8175 (m-70) REVERT: B 373 MET cc_start: 0.8414 (ptp) cc_final: 0.8143 (mtp) REVERT: B 398 MET cc_start: 0.9218 (mtp) cc_final: 0.8894 (mmt) REVERT: B 413 MET cc_start: 0.9148 (mmm) cc_final: 0.8678 (mmm) outliers start: 51 outliers final: 40 residues processed: 245 average time/residue: 0.2080 time to fit residues: 70.7737 Evaluate side-chains 253 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 210 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 167 GLN Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 342 TYR Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 309 HIS Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 59 ASN Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 357 ASP Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 387 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 0.9990 chunk 35 optimal weight: 50.0000 chunk 23 optimal weight: 8.9990 chunk 22 optimal weight: 6.9990 chunk 75 optimal weight: 20.0000 chunk 80 optimal weight: 40.0000 chunk 58 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 107 optimal weight: 30.0000 chunk 113 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 101 ASN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9865 Z= 0.193 Angle : 0.715 14.095 13407 Z= 0.343 Chirality : 0.042 0.186 1505 Planarity : 0.004 0.039 1749 Dihedral : 10.262 162.479 1435 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 20.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 4.55 % Allowed : 26.87 % Favored : 68.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -0.47 (0.25), residues: 1172 helix: 0.51 (0.24), residues: 476 sheet: -0.26 (0.35), residues: 198 loop : -1.06 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 346 HIS 0.005 0.001 HIS C 142 PHE 0.019 0.001 PHE B 272 TYR 0.016 0.001 TYR C 93 ARG 0.007 0.000 ARG B 278 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 227 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 71 TYR cc_start: 0.9047 (t80) cc_final: 0.8582 (t80) REVERT: C 102 TYR cc_start: 0.7440 (t80) cc_final: 0.7219 (t80) REVERT: C 119 ILE cc_start: 0.8347 (OUTLIER) cc_final: 0.7896 (tp) REVERT: C 151 GLU cc_start: 0.9054 (mp0) cc_final: 0.7930 (mp0) REVERT: C 152 GLU cc_start: 0.9292 (mm-30) cc_final: 0.8891 (mp0) REVERT: C 182 LYS cc_start: 0.8796 (tttp) cc_final: 0.8422 (tttp) REVERT: C 210 LEU cc_start: 0.4912 (OUTLIER) cc_final: 0.4236 (tt) REVERT: C 268 ARG cc_start: 0.9024 (mtm110) cc_final: 0.8723 (ptt90) REVERT: C 301 TYR cc_start: 0.9250 (m-80) cc_final: 0.8806 (m-80) REVERT: C 305 LYS cc_start: 0.8799 (mttp) cc_final: 0.8534 (mtmt) REVERT: A 18 ASN cc_start: 0.8704 (m110) cc_final: 0.8407 (t0) REVERT: A 22 GLU cc_start: 0.9040 (pt0) cc_final: 0.8653 (pt0) REVERT: A 86 LEU cc_start: 0.9266 (mt) cc_final: 0.8894 (mt) REVERT: A 116 ASP cc_start: 0.9375 (m-30) cc_final: 0.8936 (p0) REVERT: A 124 LYS cc_start: 0.9534 (ttpt) cc_final: 0.9232 (ttpp) REVERT: A 127 ASP cc_start: 0.8965 (m-30) cc_final: 0.8679 (m-30) REVERT: A 154 MET cc_start: 0.9217 (ttt) cc_final: 0.8805 (ttt) REVERT: A 203 MET cc_start: 0.7793 (ttt) cc_final: 0.7305 (tpt) REVERT: A 224 TYR cc_start: 0.9180 (OUTLIER) cc_final: 0.8813 (m-80) REVERT: A 272 TYR cc_start: 0.8361 (t80) cc_final: 0.8044 (t80) REVERT: A 363 VAL cc_start: 0.9251 (t) cc_final: 0.8947 (p) REVERT: A 372 GLN cc_start: 0.8933 (mp10) cc_final: 0.8672 (mm-40) REVERT: A 380 ASN cc_start: 0.7740 (m-40) cc_final: 0.7331 (m-40) REVERT: A 433 GLU cc_start: 0.9153 (tm-30) cc_final: 0.8906 (tm-30) REVERT: B 26 ASP cc_start: 0.9239 (t0) cc_final: 0.8944 (t70) REVERT: B 47 GLU cc_start: 0.9050 (tp30) cc_final: 0.8749 (tp30) REVERT: B 107 HIS cc_start: 0.8712 (t70) cc_final: 0.8007 (t70) REVERT: B 156 LYS cc_start: 0.9510 (mttt) cc_final: 0.9190 (tppt) REVERT: B 159 GLU cc_start: 0.8361 (mt-10) cc_final: 0.7999 (mt-10) REVERT: B 302 MET cc_start: 0.8789 (mmm) cc_final: 0.8315 (mtt) REVERT: B 306 ASP cc_start: 0.8128 (t0) cc_final: 0.7678 (t0) REVERT: B 309 HIS cc_start: 0.8518 (m170) cc_final: 0.8115 (m-70) REVERT: B 398 MET cc_start: 0.9179 (mtp) cc_final: 0.8870 (mmt) REVERT: B 413 MET cc_start: 0.9205 (mmm) cc_final: 0.8676 (mmm) REVERT: B 416 MET cc_start: 0.8728 (ptp) cc_final: 0.8242 (tpt) outliers start: 45 outliers final: 38 residues processed: 246 average time/residue: 0.2243 time to fit residues: 78.1589 Evaluate side-chains 255 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 214 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 167 GLN Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 342 TYR Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 309 HIS Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 59 ASN Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 387 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 8.9990 chunk 110 optimal weight: 20.0000 chunk 113 optimal weight: 8.9990 chunk 66 optimal weight: 20.0000 chunk 48 optimal weight: 30.0000 chunk 86 optimal weight: 8.9990 chunk 33 optimal weight: 60.0000 chunk 99 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 chunk 72 optimal weight: 0.0370 chunk 116 optimal weight: 9.9990 overall best weight: 6.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9865 Z= 0.229 Angle : 0.739 14.203 13407 Z= 0.355 Chirality : 0.043 0.205 1505 Planarity : 0.004 0.048 1749 Dihedral : 10.247 161.041 1435 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 22.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.95 % Allowed : 27.47 % Favored : 67.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -0.45 (0.25), residues: 1172 helix: 0.53 (0.24), residues: 473 sheet: -0.17 (0.35), residues: 202 loop : -1.10 (0.29), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 21 HIS 0.011 0.001 HIS A 192 PHE 0.026 0.002 PHE B 267 TYR 0.016 0.001 TYR B 432 ARG 0.007 0.000 ARG B 278 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 217 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 71 TYR cc_start: 0.9027 (t80) cc_final: 0.8614 (t80) REVERT: C 102 TYR cc_start: 0.7482 (t80) cc_final: 0.7245 (t80) REVERT: C 119 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.7979 (tp) REVERT: C 151 GLU cc_start: 0.9141 (mp0) cc_final: 0.7890 (mp0) REVERT: C 152 GLU cc_start: 0.9258 (mm-30) cc_final: 0.8760 (mp0) REVERT: C 182 LYS cc_start: 0.8803 (tttp) cc_final: 0.8520 (tttp) REVERT: C 210 LEU cc_start: 0.4855 (OUTLIER) cc_final: 0.4241 (tt) REVERT: C 218 HIS cc_start: 0.8283 (m-70) cc_final: 0.8002 (m-70) REVERT: C 268 ARG cc_start: 0.9034 (mtm110) cc_final: 0.8658 (ptt90) REVERT: C 274 GLN cc_start: 0.9065 (mt0) cc_final: 0.8470 (mt0) REVERT: C 301 TYR cc_start: 0.9250 (m-80) cc_final: 0.8837 (m-80) REVERT: C 305 LYS cc_start: 0.8803 (mttp) cc_final: 0.8518 (mtmt) REVERT: A 22 GLU cc_start: 0.9057 (pt0) cc_final: 0.8745 (pt0) REVERT: A 86 LEU cc_start: 0.9310 (mt) cc_final: 0.8933 (mt) REVERT: A 116 ASP cc_start: 0.9361 (m-30) cc_final: 0.8911 (p0) REVERT: A 118 VAL cc_start: 0.9621 (m) cc_final: 0.9394 (p) REVERT: A 154 MET cc_start: 0.9318 (ttt) cc_final: 0.8877 (ttt) REVERT: A 203 MET cc_start: 0.7802 (ttt) cc_final: 0.7334 (tpt) REVERT: A 224 TYR cc_start: 0.9141 (OUTLIER) cc_final: 0.8734 (m-80) REVERT: A 272 TYR cc_start: 0.8359 (t80) cc_final: 0.8071 (t80) REVERT: A 297 GLU cc_start: 0.8571 (tm-30) cc_final: 0.8099 (tm-30) REVERT: A 363 VAL cc_start: 0.9243 (t) cc_final: 0.8938 (p) REVERT: A 372 GLN cc_start: 0.8961 (mp10) cc_final: 0.8697 (mm-40) REVERT: A 380 ASN cc_start: 0.7758 (m-40) cc_final: 0.7373 (m-40) REVERT: A 433 GLU cc_start: 0.9218 (tm-30) cc_final: 0.8746 (tm-30) REVERT: A 434 GLU cc_start: 0.9247 (tm-30) cc_final: 0.8950 (pt0) REVERT: B 26 ASP cc_start: 0.9261 (t0) cc_final: 0.8963 (t70) REVERT: B 107 HIS cc_start: 0.8706 (t70) cc_final: 0.8114 (t70) REVERT: B 156 LYS cc_start: 0.9516 (mttt) cc_final: 0.9203 (mmtm) REVERT: B 159 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8186 (mt-10) REVERT: B 169 PHE cc_start: 0.7502 (m-80) cc_final: 0.6936 (m-80) REVERT: B 202 TYR cc_start: 0.8960 (m-80) cc_final: 0.8679 (m-80) REVERT: B 302 MET cc_start: 0.8772 (mmm) cc_final: 0.8319 (mtt) REVERT: B 306 ASP cc_start: 0.8151 (t0) cc_final: 0.7696 (t0) REVERT: B 309 HIS cc_start: 0.8547 (m170) cc_final: 0.8131 (m-70) REVERT: B 323 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.8116 (mpp) REVERT: B 332 MET cc_start: 0.9379 (mmt) cc_final: 0.9051 (mmm) REVERT: B 398 MET cc_start: 0.9147 (mtp) cc_final: 0.8815 (mmt) REVERT: B 413 MET cc_start: 0.9158 (mmm) cc_final: 0.8714 (mmm) REVERT: B 416 MET cc_start: 0.8833 (ptp) cc_final: 0.8244 (tpt) outliers start: 49 outliers final: 36 residues processed: 241 average time/residue: 0.2007 time to fit residues: 68.1834 Evaluate side-chains 249 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 209 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 167 GLN Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 342 TYR Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 309 HIS Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 59 ASN Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 357 ASP Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 377 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 chunk 81 optimal weight: 30.0000 chunk 122 optimal weight: 7.9990 chunk 112 optimal weight: 30.0000 chunk 97 optimal weight: 7.9990 chunk 10 optimal weight: 40.0000 chunk 75 optimal weight: 7.9990 chunk 59 optimal weight: 0.4980 chunk 77 optimal weight: 8.9990 chunk 103 optimal weight: 0.0170 overall best weight: 4.9024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 192 HIS ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9865 Z= 0.209 Angle : 0.764 14.281 13407 Z= 0.361 Chirality : 0.044 0.196 1505 Planarity : 0.004 0.038 1749 Dihedral : 10.084 155.941 1435 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 22.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 4.14 % Allowed : 27.88 % Favored : 67.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -0.44 (0.25), residues: 1172 helix: 0.50 (0.24), residues: 471 sheet: -0.14 (0.36), residues: 192 loop : -1.05 (0.29), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 21 HIS 0.007 0.001 HIS A 8 PHE 0.020 0.001 PHE B 267 TYR 0.013 0.001 TYR A 224 ARG 0.009 0.000 ARG B 322 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 216 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 71 TYR cc_start: 0.8915 (t80) cc_final: 0.8660 (t80) REVERT: C 102 TYR cc_start: 0.7329 (t80) cc_final: 0.7082 (t80) REVERT: C 119 ILE cc_start: 0.8356 (OUTLIER) cc_final: 0.7996 (tp) REVERT: C 151 GLU cc_start: 0.9111 (mp0) cc_final: 0.8027 (mp0) REVERT: C 182 LYS cc_start: 0.8863 (tttp) cc_final: 0.8404 (tttp) REVERT: C 210 LEU cc_start: 0.4640 (OUTLIER) cc_final: 0.4208 (tt) REVERT: C 218 HIS cc_start: 0.8249 (m-70) cc_final: 0.7912 (m-70) REVERT: C 268 ARG cc_start: 0.9034 (mtm110) cc_final: 0.8626 (ptt90) REVERT: C 274 GLN cc_start: 0.9068 (mt0) cc_final: 0.8464 (pp30) REVERT: C 301 TYR cc_start: 0.9231 (m-80) cc_final: 0.8792 (m-80) REVERT: A 86 LEU cc_start: 0.9263 (mt) cc_final: 0.8802 (mt) REVERT: A 113 GLU cc_start: 0.9280 (mm-30) cc_final: 0.9010 (mp0) REVERT: A 116 ASP cc_start: 0.9348 (m-30) cc_final: 0.9046 (p0) REVERT: A 118 VAL cc_start: 0.9623 (m) cc_final: 0.9376 (p) REVERT: A 127 ASP cc_start: 0.8907 (m-30) cc_final: 0.8621 (m-30) REVERT: A 154 MET cc_start: 0.9263 (ttt) cc_final: 0.8825 (ttt) REVERT: A 203 MET cc_start: 0.7785 (ttt) cc_final: 0.7307 (tpt) REVERT: A 224 TYR cc_start: 0.9138 (OUTLIER) cc_final: 0.8713 (m-80) REVERT: A 272 TYR cc_start: 0.8395 (t80) cc_final: 0.8092 (t80) REVERT: A 297 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8153 (tm-30) REVERT: A 363 VAL cc_start: 0.9235 (t) cc_final: 0.8717 (p) REVERT: A 372 GLN cc_start: 0.8973 (mp10) cc_final: 0.8704 (mm-40) REVERT: A 380 ASN cc_start: 0.7760 (m-40) cc_final: 0.7374 (m-40) REVERT: A 433 GLU cc_start: 0.9228 (tm-30) cc_final: 0.8835 (tm-30) REVERT: A 434 GLU cc_start: 0.9212 (tm-30) cc_final: 0.8944 (pt0) REVERT: B 26 ASP cc_start: 0.9253 (t0) cc_final: 0.8950 (t70) REVERT: B 107 HIS cc_start: 0.8736 (t70) cc_final: 0.8192 (t70) REVERT: B 156 LYS cc_start: 0.9503 (mttt) cc_final: 0.9141 (mmtm) REVERT: B 159 GLU cc_start: 0.8351 (mt-10) cc_final: 0.8139 (mt-10) REVERT: B 169 PHE cc_start: 0.7736 (m-80) cc_final: 0.7354 (m-80) REVERT: B 302 MET cc_start: 0.8794 (mmm) cc_final: 0.8369 (mtt) REVERT: B 309 HIS cc_start: 0.8542 (m170) cc_final: 0.8162 (m-70) REVERT: B 332 MET cc_start: 0.9357 (mmt) cc_final: 0.9023 (mmm) REVERT: B 398 MET cc_start: 0.9153 (mtp) cc_final: 0.8793 (mmt) REVERT: B 413 MET cc_start: 0.9146 (mmm) cc_final: 0.8709 (mmm) outliers start: 41 outliers final: 35 residues processed: 234 average time/residue: 0.2003 time to fit residues: 66.1905 Evaluate side-chains 245 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 207 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 167 GLN Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 338 ASN Chi-restraints excluded: chain C residue 342 TYR Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 309 HIS Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 59 ASN Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 357 ASP Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 377 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 10.0000 chunk 89 optimal weight: 0.9990 chunk 14 optimal weight: 40.0000 chunk 27 optimal weight: 0.0170 chunk 97 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 100 optimal weight: 4.9990 chunk 12 optimal weight: 0.0870 chunk 18 optimal weight: 10.0000 chunk 85 optimal weight: 0.1980 chunk 5 optimal weight: 5.9990 overall best weight: 1.2600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 HIS ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 ASN ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.088686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.070235 restraints weight = 33834.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.072563 restraints weight = 17744.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.074125 restraints weight = 11114.331| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3523 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3523 r_free = 0.3523 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3506 r_free = 0.3506 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3506 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.4528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9865 Z= 0.196 Angle : 0.769 14.430 13407 Z= 0.363 Chirality : 0.043 0.178 1505 Planarity : 0.004 0.046 1749 Dihedral : 9.798 147.169 1435 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 19.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.13 % Allowed : 29.19 % Favored : 67.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.43 (0.25), residues: 1172 helix: 0.49 (0.24), residues: 461 sheet: -0.06 (0.34), residues: 207 loop : -1.04 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 21 HIS 0.006 0.001 HIS C 142 PHE 0.039 0.002 PHE C 153 TYR 0.013 0.001 TYR C 93 ARG 0.009 0.001 ARG B 322 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1990.34 seconds wall clock time: 37 minutes 6.06 seconds (2226.06 seconds total)