Starting phenix.real_space_refine on Wed Jun 26 00:09:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbe_38215/06_2024/8xbe_38215_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbe_38215/06_2024/8xbe_38215.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbe_38215/06_2024/8xbe_38215_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbe_38215/06_2024/8xbe_38215_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbe_38215/06_2024/8xbe_38215_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbe_38215/06_2024/8xbe_38215.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbe_38215/06_2024/8xbe_38215.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbe_38215/06_2024/8xbe_38215_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbe_38215/06_2024/8xbe_38215_updated.pdb" } resolution = 3.4 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.533 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 67 5.16 5 C 5702 2.51 5 N 1513 2.21 5 O 1654 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "S GLU 46": "OE1" <-> "OE2" Residue "S TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 14": "OE1" <-> "OE2" Residue "B GLU 25": "OE1" <-> "OE2" Residue "B ASP 200": "OD1" <-> "OD2" Residue "B GLU 207": "OE1" <-> "OE2" Residue "B GLU 216": "OE1" <-> "OE2" Residue "C ASP 83": "OD1" <-> "OD2" Residue "C ASP 154": "OD1" <-> "OD2" Residue "C ASP 163": "OD1" <-> "OD2" Residue "C ASP 246": "OD1" <-> "OD2" Residue "C ASP 247": "OD1" <-> "OD2" Residue "C ASP 290": "OD1" <-> "OD2" Residue "C ASP 298": "OD1" <-> "OD2" Residue "D TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 323": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 8937 Number of models: 1 Model: "" Number of chains: 6 Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "B" Number of atoms: 1706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1706 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "D" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 407 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "A" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2420 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 292} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'KW0': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.21, per 1000 atoms: 0.58 Number of scatterers: 8937 At special positions: 0 Unit cell: (128.455, 122.87, 91.594, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 67 16.00 P 1 15.00 O 1654 8.00 N 1513 7.00 C 5702 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.04 Simple disulfide: pdb=" SG CYS C 103 " - pdb=" SG CYS C 114 " distance=2.05 Simple disulfide: pdb=" SG CYS A 46 " - pdb=" SG CYS A 299 " distance=2.03 Simple disulfide: pdb=" SG CYS A 127 " - pdb=" SG CYS A 204 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.53 Conformation dependent library (CDL) restraints added in 1.7 seconds 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2126 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 13 sheets defined 35.6% alpha, 21.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.91 Creating SS restraints... Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 53 through 55 No H-bonds generated for 'chain 'S' and resid 53 through 55' Processing helix chain 'S' and resid 74 through 76 No H-bonds generated for 'chain 'S' and resid 74 through 76' Processing helix chain 'S' and resid 88 through 90 No H-bonds generated for 'chain 'S' and resid 88 through 90' Processing helix chain 'S' and resid 209 through 211 No H-bonds generated for 'chain 'S' and resid 209 through 211' Processing helix chain 'B' and resid 7 through 32 removed outlier: 3.718A pdb=" N ARG B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 53 Processing helix chain 'B' and resid 208 through 210 No H-bonds generated for 'chain 'B' and resid 208 through 210' Processing helix chain 'B' and resid 212 through 215 Processing helix chain 'B' and resid 228 through 230 No H-bonds generated for 'chain 'B' and resid 228 through 230' Processing helix chain 'B' and resid 242 through 254 Processing helix chain 'B' and resid 271 through 279 removed outlier: 4.182A pdb=" N LYS B 279 " --> pdb=" O GLU B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 285 No H-bonds generated for 'chain 'B' and resid 283 through 285' Processing helix chain 'B' and resid 296 through 310 removed outlier: 3.668A pdb=" N LEU B 310 " --> pdb=" O GLN B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 351 Processing helix chain 'C' and resid 7 through 24 Processing helix chain 'C' and resid 30 through 36 removed outlier: 6.004A pdb=" N ASN C 36 " --> pdb=" O GLN C 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 21 Processing helix chain 'D' and resid 30 through 43 removed outlier: 3.824A pdb=" N ALA D 35 " --> pdb=" O SER D 31 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASP D 36 " --> pdb=" O LYS D 32 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU D 37 " --> pdb=" O ALA D 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 80 removed outlier: 3.587A pdb=" N LEU A 80 " --> pdb=" O LEU A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 116 removed outlier: 3.755A pdb=" N LEU A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) Proline residue: A 108 - end of helix removed outlier: 3.928A pdb=" N TYR A 113 " --> pdb=" O PHE A 109 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N HIS A 114 " --> pdb=" O ARG A 110 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN A 116 " --> pdb=" O MET A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 156 removed outlier: 4.341A pdb=" N TYR A 135 " --> pdb=" O GLY A 131 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 194 Processing helix chain 'A' and resid 214 through 251 removed outlier: 3.556A pdb=" N MET A 226 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE A 227 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 294 removed outlier: 3.635A pdb=" N PHE A 269 " --> pdb=" O ALA A 265 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU A 272 " --> pdb=" O SER A 268 " (cutoff:3.500A) Proline residue: A 281 - end of helix removed outlier: 3.542A pdb=" N PHE A 285 " --> pdb=" O PRO A 281 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N PHE A 287 " --> pdb=" O HIS A 283 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ILE A 288 " --> pdb=" O ALA A 284 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 294 " --> pdb=" O ILE A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 330 removed outlier: 3.734A pdb=" N ILE A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN A 319 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N SER A 320 " --> pdb=" O SER A 316 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N CYS A 321 " --> pdb=" O SER A 317 " (cutoff:3.500A) Proline residue: A 324 - end of helix Processing helix chain 'A' and resid 332 through 341 Processing sheet with id= A, first strand: chain 'S' and resid 4 through 7 removed outlier: 3.518A pdb=" N ARG S 18 " --> pdb=" O MET S 83 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.798A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ALA S 40 " --> pdb=" O LEU S 45 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU S 45 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'S' and resid 128 through 130 Processing sheet with id= D, first strand: chain 'S' and resid 134 through 136 removed outlier: 7.206A pdb=" N LYS S 232 " --> pdb=" O VAL S 135 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'S' and resid 214 through 219 removed outlier: 6.168A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 319 through 323 removed outlier: 6.952A pdb=" N ILE B 264 " --> pdb=" O TYR B 320 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N HIS B 322 " --> pdb=" O ILE B 264 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU B 266 " --> pdb=" O HIS B 322 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.910A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 100 through 105 removed outlier: 3.716A pdb=" N MET C 101 " --> pdb=" O GLY C 115 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER C 122 " --> pdb=" O CYS C 114 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG C 137 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 178 through 181 removed outlier: 3.939A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN C 156 " --> pdb=" O ASP C 153 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP C 153 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N VAL C 158 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N PHE C 151 " --> pdb=" O VAL C 158 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.903A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.755A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 294 through 298 Processing sheet with id= M, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.830A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N PHE C 335 " --> pdb=" O SER C 331 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER C 331 " --> pdb=" O PHE C 335 " (cutoff:3.500A) 408 hydrogen bonds defined for protein. 1176 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.44 Time building geometry restraints manager: 3.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1579 1.33 - 1.45: 2409 1.45 - 1.57: 5027 1.57 - 1.70: 3 1.70 - 1.82: 98 Bond restraints: 9116 Sorted by residual: bond pdb=" C18 KW0 A 401 " pdb=" O2 KW0 A 401 " ideal model delta sigma weight residual 1.409 1.328 0.081 2.00e-02 2.50e+03 1.62e+01 bond pdb=" C22 KW0 A 401 " pdb=" C23 KW0 A 401 " ideal model delta sigma weight residual 1.545 1.469 0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" O4 KW0 A 401 " pdb=" P1 KW0 A 401 " ideal model delta sigma weight residual 1.676 1.606 0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" O7 KW0 A 401 " pdb=" P1 KW0 A 401 " ideal model delta sigma weight residual 1.674 1.605 0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C20 KW0 A 401 " pdb=" O4 KW0 A 401 " ideal model delta sigma weight residual 1.400 1.468 -0.068 2.00e-02 2.50e+03 1.17e+01 ... (remaining 9111 not shown) Histogram of bond angle deviations from ideal: 98.46 - 105.57: 106 105.57 - 112.68: 4822 112.68 - 119.80: 2966 119.80 - 126.91: 4336 126.91 - 134.02: 95 Bond angle restraints: 12325 Sorted by residual: angle pdb=" C10 KW0 A 401 " pdb=" C9 KW0 A 401 " pdb=" C8 KW0 A 401 " ideal model delta sigma weight residual 152.63 126.83 25.80 3.00e+00 1.11e-01 7.40e+01 angle pdb=" C11 KW0 A 401 " pdb=" C10 KW0 A 401 " pdb=" C9 KW0 A 401 " ideal model delta sigma weight residual 112.23 127.88 -15.65 3.00e+00 1.11e-01 2.72e+01 angle pdb=" CA CYS C 103 " pdb=" CB CYS C 103 " pdb=" SG CYS C 103 " ideal model delta sigma weight residual 114.40 125.39 -10.99 2.30e+00 1.89e-01 2.28e+01 angle pdb=" C ALA C 113 " pdb=" N CYS C 114 " pdb=" CA CYS C 114 " ideal model delta sigma weight residual 121.86 114.90 6.96 1.58e+00 4.01e-01 1.94e+01 angle pdb=" N ILE A 166 " pdb=" CA ILE A 166 " pdb=" C ILE A 166 " ideal model delta sigma weight residual 112.83 108.68 4.15 9.90e-01 1.02e+00 1.76e+01 ... (remaining 12320 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.71: 5290 31.71 - 63.42: 117 63.42 - 95.13: 13 95.13 - 126.83: 1 126.83 - 158.54: 1 Dihedral angle restraints: 5422 sinusoidal: 2123 harmonic: 3299 Sorted by residual: dihedral pdb=" CB CYS A 46 " pdb=" SG CYS A 46 " pdb=" SG CYS A 299 " pdb=" CB CYS A 299 " ideal model delta sinusoidal sigma weight residual 93.00 20.15 72.85 1 1.00e+01 1.00e-02 6.77e+01 dihedral pdb=" CB CYS S 147 " pdb=" SG CYS S 147 " pdb=" SG CYS S 217 " pdb=" CB CYS S 217 " ideal model delta sinusoidal sigma weight residual 93.00 132.57 -39.57 1 1.00e+01 1.00e-02 2.20e+01 dihedral pdb=" C15 KW0 A 401 " pdb=" C16 KW0 A 401 " pdb=" C17 KW0 A 401 " pdb=" C18 KW0 A 401 " ideal model delta sinusoidal sigma weight residual 196.90 38.36 158.54 1 3.00e+01 1.11e-03 2.06e+01 ... (remaining 5419 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1020 0.043 - 0.087: 297 0.087 - 0.130: 72 0.130 - 0.174: 12 0.174 - 0.217: 1 Chirality restraints: 1402 Sorted by residual: chirality pdb=" CA TYR S 178 " pdb=" N TYR S 178 " pdb=" C TYR S 178 " pdb=" CB TYR S 178 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA CYS C 103 " pdb=" N CYS C 103 " pdb=" C CYS C 103 " pdb=" CB CYS C 103 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.98e-01 chirality pdb=" CB THR C 47 " pdb=" CA THR C 47 " pdb=" OG1 THR C 47 " pdb=" CG2 THR C 47 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.71e-01 ... (remaining 1399 not shown) Planarity restraints: 1546 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 KW0 A 401 " -0.069 2.00e-02 2.50e+03 5.27e-02 2.78e+01 pdb=" C11 KW0 A 401 " 0.029 2.00e-02 2.50e+03 pdb=" C8 KW0 A 401 " -0.028 2.00e-02 2.50e+03 pdb=" C9 KW0 A 401 " 0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN S 13 " 0.066 5.00e-02 4.00e+02 9.73e-02 1.51e+01 pdb=" N PRO S 14 " -0.168 5.00e-02 4.00e+02 pdb=" CA PRO S 14 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO S 14 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " 0.056 5.00e-02 4.00e+02 8.45e-02 1.14e+01 pdb=" N PRO S 75 " -0.146 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " 0.046 5.00e-02 4.00e+02 ... (remaining 1543 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 156 2.67 - 3.23: 8592 3.23 - 3.79: 13477 3.79 - 4.34: 18978 4.34 - 4.90: 30888 Nonbonded interactions: 72091 Sorted by model distance: nonbonded pdb=" OG SER C 245 " pdb=" OD1 ASP C 247 " model vdw 2.118 2.440 nonbonded pdb=" OE1 GLN C 176 " pdb=" OG1 THR C 179 " model vdw 2.134 2.440 nonbonded pdb=" OG SER C 147 " pdb=" OG SER C 160 " model vdw 2.151 2.440 nonbonded pdb=" O ILE C 58 " pdb=" OG SER C 316 " model vdw 2.233 2.440 nonbonded pdb=" O PHE S 32 " pdb=" NH2 ARG S 72 " model vdw 2.254 2.520 ... (remaining 72086 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.130 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: 0.760 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 27.280 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 9116 Z= 0.264 Angle : 0.724 25.802 12325 Z= 0.376 Chirality : 0.043 0.217 1402 Planarity : 0.005 0.097 1546 Dihedral : 13.784 158.543 3281 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.08 % Favored : 94.83 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.41 (0.25), residues: 1121 helix: 0.66 (0.26), residues: 398 sheet: -0.06 (0.32), residues: 277 loop : -1.20 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 211 HIS 0.003 0.001 HIS S 220 PHE 0.012 0.001 PHE C 234 TYR 0.027 0.001 TYR S 178 ARG 0.003 0.000 ARG S 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 0.990 Fit side-chains revert: symmetry clash REVERT: S 6 GLU cc_start: 0.7282 (mp0) cc_final: 0.6869 (mp0) REVERT: S 67 ARG cc_start: 0.8563 (mtm110) cc_final: 0.8273 (ttm110) REVERT: S 73 ASP cc_start: 0.7178 (t0) cc_final: 0.6750 (t0) REVERT: S 160 THR cc_start: 0.7972 (t) cc_final: 0.7745 (t) REVERT: S 218 MET cc_start: 0.8441 (ttp) cc_final: 0.8074 (ttt) REVERT: B 269 ASN cc_start: 0.7616 (m-40) cc_final: 0.7327 (m-40) REVERT: C 280 LYS cc_start: 0.8643 (tttp) cc_final: 0.8427 (ttmm) REVERT: C 303 ASP cc_start: 0.6849 (m-30) cc_final: 0.6628 (m-30) REVERT: A 72 ASN cc_start: 0.7622 (m110) cc_final: 0.6967 (m110) REVERT: A 240 LYS cc_start: 0.7583 (mtpt) cc_final: 0.7356 (mtpp) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.2173 time to fit residues: 65.7071 Evaluate side-chains 195 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 3.9990 chunk 84 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 44 optimal weight: 20.0000 chunk 87 optimal weight: 0.9980 chunk 33 optimal weight: 30.0000 chunk 52 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 chunk 100 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 241 ASN B 255 ASN C 176 GLN C 239 ASN C 340 ASN A 72 ASN A 114 HIS A 306 HIS A 319 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 9116 Z= 0.288 Angle : 0.619 9.977 12325 Z= 0.328 Chirality : 0.045 0.233 1402 Planarity : 0.005 0.064 1546 Dihedral : 8.359 176.986 1252 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.64 % Favored : 95.27 % Rotamer: Outliers : 2.26 % Allowed : 9.47 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.23 (0.25), residues: 1121 helix: 1.26 (0.25), residues: 406 sheet: -0.31 (0.31), residues: 284 loop : -1.37 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 99 HIS 0.004 0.001 HIS A 83 PHE 0.021 0.002 PHE A 318 TYR 0.027 0.002 TYR S 178 ARG 0.004 0.000 ARG C 52 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 198 time to evaluate : 0.963 Fit side-chains revert: symmetry clash REVERT: S 6 GLU cc_start: 0.7077 (mp0) cc_final: 0.6708 (mp0) REVERT: S 67 ARG cc_start: 0.8561 (mtm110) cc_final: 0.8305 (ttm110) REVERT: S 218 MET cc_start: 0.8797 (ttp) cc_final: 0.8507 (ttt) REVERT: B 14 GLU cc_start: 0.7380 (tt0) cc_final: 0.7177 (tt0) REVERT: B 269 ASN cc_start: 0.7800 (m-40) cc_final: 0.7434 (m-40) REVERT: B 320 TYR cc_start: 0.6839 (m-10) cc_final: 0.6162 (m-10) REVERT: C 215 GLU cc_start: 0.7144 (mp0) cc_final: 0.6891 (mp0) REVERT: C 280 LYS cc_start: 0.8655 (tttp) cc_final: 0.8432 (ttmm) REVERT: D 42 GLU cc_start: 0.7906 (tp30) cc_final: 0.7426 (tp30) REVERT: A 104 ILE cc_start: 0.7099 (OUTLIER) cc_final: 0.6814 (mp) REVERT: A 240 LYS cc_start: 0.7561 (mtpt) cc_final: 0.7211 (mtpt) REVERT: A 330 MET cc_start: 0.6303 (mmp) cc_final: 0.5695 (mmt) outliers start: 22 outliers final: 18 residues processed: 209 average time/residue: 0.2138 time to fit residues: 60.7246 Evaluate side-chains 202 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 183 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 157 ASN Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 346 ASN Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 249 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 83 optimal weight: 20.0000 chunk 68 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 89 optimal weight: 20.0000 chunk 34 optimal weight: 7.9990 chunk 81 optimal weight: 0.9980 chunk 99 optimal weight: 6.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 176 GLN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9116 Z= 0.263 Angle : 0.594 10.873 12325 Z= 0.313 Chirality : 0.044 0.225 1402 Planarity : 0.004 0.044 1546 Dihedral : 7.560 137.134 1252 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.37 % Favored : 95.54 % Rotamer: Outliers : 2.88 % Allowed : 12.96 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.14 (0.25), residues: 1121 helix: 1.46 (0.26), residues: 406 sheet: -0.43 (0.31), residues: 290 loop : -1.33 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 99 HIS 0.004 0.001 HIS S 220 PHE 0.020 0.002 PHE A 79 TYR 0.027 0.002 TYR S 178 ARG 0.002 0.000 ARG C 52 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 192 time to evaluate : 1.048 Fit side-chains revert: symmetry clash REVERT: S 6 GLU cc_start: 0.7220 (mp0) cc_final: 0.6574 (mp0) REVERT: S 18 ARG cc_start: 0.8350 (tpp-160) cc_final: 0.7832 (tpp-160) REVERT: S 160 THR cc_start: 0.8241 (OUTLIER) cc_final: 0.7971 (t) REVERT: S 218 MET cc_start: 0.8852 (ttp) cc_final: 0.8577 (ttt) REVERT: B 14 GLU cc_start: 0.7331 (tt0) cc_final: 0.7120 (tt0) REVERT: B 269 ASN cc_start: 0.7770 (m-40) cc_final: 0.7451 (m-40) REVERT: B 320 TYR cc_start: 0.6866 (m-10) cc_final: 0.6147 (m-10) REVERT: C 280 LYS cc_start: 0.8628 (tttp) cc_final: 0.8413 (ttmm) REVERT: A 104 ILE cc_start: 0.6946 (OUTLIER) cc_final: 0.6674 (mp) REVERT: A 157 ASN cc_start: 0.7487 (t0) cc_final: 0.7254 (t0) REVERT: A 312 MET cc_start: 0.7180 (mmt) cc_final: 0.6689 (mmt) outliers start: 28 outliers final: 23 residues processed: 203 average time/residue: 0.2086 time to fit residues: 58.1586 Evaluate side-chains 213 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 188 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 157 ASN Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 346 ASN Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 212 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 48 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 107 optimal weight: 8.9990 chunk 96 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 89 optimal weight: 30.0000 chunk 60 optimal weight: 6.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 95 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9116 Z= 0.244 Angle : 0.582 11.411 12325 Z= 0.306 Chirality : 0.044 0.232 1402 Planarity : 0.004 0.042 1546 Dihedral : 6.953 95.811 1252 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.64 % Favored : 95.27 % Rotamer: Outliers : 4.22 % Allowed : 14.92 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.04 (0.26), residues: 1121 helix: 1.62 (0.26), residues: 406 sheet: -0.41 (0.30), residues: 292 loop : -1.35 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 99 HIS 0.004 0.001 HIS S 220 PHE 0.017 0.002 PHE A 318 TYR 0.026 0.002 TYR S 178 ARG 0.002 0.000 ARG C 52 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 187 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 6 GLU cc_start: 0.7262 (mp0) cc_final: 0.6549 (mp0) REVERT: S 18 ARG cc_start: 0.8317 (tpp-160) cc_final: 0.7815 (tpp-160) REVERT: S 19 LYS cc_start: 0.8079 (ttpt) cc_final: 0.7472 (mtmm) REVERT: S 67 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.8315 (ttp80) REVERT: S 160 THR cc_start: 0.8134 (OUTLIER) cc_final: 0.7914 (t) REVERT: S 179 ARG cc_start: 0.7477 (OUTLIER) cc_final: 0.6399 (mpt180) REVERT: S 218 MET cc_start: 0.8879 (ttp) cc_final: 0.8607 (ttt) REVERT: B 14 GLU cc_start: 0.7290 (tt0) cc_final: 0.7079 (tt0) REVERT: B 23 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7928 (mp) REVERT: B 269 ASN cc_start: 0.7749 (m-40) cc_final: 0.7333 (m-40) REVERT: B 320 TYR cc_start: 0.6855 (m-10) cc_final: 0.6159 (m-10) REVERT: C 188 MET cc_start: 0.8574 (mmm) cc_final: 0.8351 (mmm) REVERT: C 280 LYS cc_start: 0.8627 (tttp) cc_final: 0.8400 (ttmm) REVERT: A 104 ILE cc_start: 0.6998 (OUTLIER) cc_final: 0.6732 (mp) REVERT: A 148 ILE cc_start: 0.7811 (mt) cc_final: 0.7538 (mt) REVERT: A 312 MET cc_start: 0.7158 (mmt) cc_final: 0.6742 (mmt) REVERT: A 330 MET cc_start: 0.6233 (mmp) cc_final: 0.5513 (mmt) outliers start: 41 outliers final: 28 residues processed: 210 average time/residue: 0.2014 time to fit residues: 58.0839 Evaluate side-chains 212 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 179 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 149 SER Chi-restraints excluded: chain S residue 157 ASN Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 179 ARG Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 346 ASN Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 212 ASN Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 317 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 20.0000 chunk 79 optimal weight: 9.9990 chunk 44 optimal weight: 20.0000 chunk 91 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 54 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 36 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 130 GLN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 72 ASN ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 9116 Z= 0.346 Angle : 0.659 12.638 12325 Z= 0.345 Chirality : 0.046 0.252 1402 Planarity : 0.004 0.044 1546 Dihedral : 7.204 89.962 1252 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.44 % Favored : 94.47 % Rotamer: Outliers : 4.42 % Allowed : 16.77 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.32 (0.25), residues: 1121 helix: 1.43 (0.26), residues: 407 sheet: -0.70 (0.30), residues: 291 loop : -1.43 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 211 HIS 0.005 0.001 HIS A 83 PHE 0.020 0.002 PHE A 79 TYR 0.028 0.002 TYR S 178 ARG 0.003 0.000 ARG S 67 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 183 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 6 GLU cc_start: 0.7339 (mp0) cc_final: 0.6623 (mp0) REVERT: S 160 THR cc_start: 0.8231 (OUTLIER) cc_final: 0.8030 (t) REVERT: S 179 ARG cc_start: 0.7521 (OUTLIER) cc_final: 0.6531 (mpt180) REVERT: S 182 ASN cc_start: 0.6729 (p0) cc_final: 0.6498 (p0) REVERT: B 14 GLU cc_start: 0.7320 (tt0) cc_final: 0.7102 (tt0) REVERT: B 23 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7843 (mp) REVERT: B 269 ASN cc_start: 0.7944 (m-40) cc_final: 0.7498 (m-40) REVERT: B 320 TYR cc_start: 0.7134 (m-10) cc_final: 0.6193 (m-10) REVERT: C 145 TYR cc_start: 0.8483 (p90) cc_final: 0.8137 (p90) REVERT: C 186 ASP cc_start: 0.8506 (OUTLIER) cc_final: 0.8159 (m-30) REVERT: C 280 LYS cc_start: 0.8675 (tttp) cc_final: 0.8443 (ttmm) REVERT: A 104 ILE cc_start: 0.7013 (OUTLIER) cc_final: 0.6728 (mp) REVERT: A 148 ILE cc_start: 0.8049 (mt) cc_final: 0.7808 (mt) REVERT: A 312 MET cc_start: 0.7289 (mmt) cc_final: 0.6825 (mmt) REVERT: A 330 MET cc_start: 0.6257 (mmp) cc_final: 0.5719 (mmt) outliers start: 43 outliers final: 35 residues processed: 209 average time/residue: 0.2079 time to fit residues: 59.7216 Evaluate side-chains 216 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 176 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 149 SER Chi-restraints excluded: chain S residue 157 ASN Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 179 ARG Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 220 HIS Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 212 ASN Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 326 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 89 optimal weight: 20.0000 chunk 49 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 chunk 56 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 130 GLN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 9116 Z= 0.448 Angle : 0.735 15.162 12325 Z= 0.384 Chirality : 0.049 0.279 1402 Planarity : 0.005 0.048 1546 Dihedral : 7.468 83.686 1252 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.33 % Favored : 93.58 % Rotamer: Outliers : 5.45 % Allowed : 16.98 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.68 (0.25), residues: 1121 helix: 1.07 (0.25), residues: 405 sheet: -0.87 (0.30), residues: 290 loop : -1.57 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 99 HIS 0.006 0.001 HIS A 83 PHE 0.017 0.003 PHE A 318 TYR 0.030 0.003 TYR S 178 ARG 0.003 0.001 ARG S 190 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 183 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 179 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.6791 (mpt180) REVERT: B 14 GLU cc_start: 0.7317 (tt0) cc_final: 0.7111 (tt0) REVERT: B 23 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7747 (mp) REVERT: B 269 ASN cc_start: 0.7920 (m-40) cc_final: 0.7426 (m-40) REVERT: C 38 ASP cc_start: 0.7855 (OUTLIER) cc_final: 0.7602 (p0) REVERT: C 130 GLU cc_start: 0.7348 (mm-30) cc_final: 0.7043 (mm-30) REVERT: C 186 ASP cc_start: 0.8533 (OUTLIER) cc_final: 0.8102 (m-30) REVERT: A 104 ILE cc_start: 0.6883 (OUTLIER) cc_final: 0.6629 (mp) REVERT: A 148 ILE cc_start: 0.8226 (mt) cc_final: 0.8015 (mt) REVERT: A 312 MET cc_start: 0.7391 (mmt) cc_final: 0.6890 (mmt) outliers start: 53 outliers final: 36 residues processed: 218 average time/residue: 0.2043 time to fit residues: 61.2288 Evaluate side-chains 220 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 179 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 157 ASN Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 179 ARG Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 220 HIS Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 212 ASN Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 326 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 30.0000 chunk 60 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 106 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 130 GLN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9116 Z= 0.190 Angle : 0.604 14.147 12325 Z= 0.309 Chirality : 0.043 0.264 1402 Planarity : 0.004 0.039 1546 Dihedral : 7.190 89.515 1252 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.10 % Favored : 95.81 % Rotamer: Outliers : 4.22 % Allowed : 19.44 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.23 (0.25), residues: 1121 helix: 1.54 (0.26), residues: 404 sheet: -0.54 (0.31), residues: 265 loop : -1.46 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 99 HIS 0.003 0.001 HIS S 220 PHE 0.016 0.002 PHE A 79 TYR 0.028 0.002 TYR S 178 ARG 0.004 0.000 ARG S 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 182 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 18 ARG cc_start: 0.8381 (tpp-160) cc_final: 0.7959 (tpp80) REVERT: S 46 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.7040 (mt-10) REVERT: S 65 LYS cc_start: 0.8492 (tptp) cc_final: 0.7807 (tppt) REVERT: S 67 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.8274 (ttp80) REVERT: S 179 ARG cc_start: 0.7543 (OUTLIER) cc_final: 0.6267 (mpt180) REVERT: B 14 GLU cc_start: 0.7228 (tt0) cc_final: 0.7017 (tt0) REVERT: B 269 ASN cc_start: 0.7950 (m-40) cc_final: 0.7392 (m110) REVERT: C 215 GLU cc_start: 0.7400 (mp0) cc_final: 0.6899 (mp0) REVERT: D 42 GLU cc_start: 0.7855 (tp30) cc_final: 0.7564 (tp30) REVERT: A 85 LYS cc_start: 0.8365 (tppt) cc_final: 0.7965 (tppt) REVERT: A 104 ILE cc_start: 0.6953 (OUTLIER) cc_final: 0.6638 (mp) REVERT: A 312 MET cc_start: 0.7215 (mmt) cc_final: 0.6681 (mmt) REVERT: A 326 MET cc_start: 0.6304 (OUTLIER) cc_final: 0.6041 (mtp) REVERT: A 330 MET cc_start: 0.5894 (mmp) cc_final: 0.5495 (mmt) outliers start: 41 outliers final: 30 residues processed: 206 average time/residue: 0.2112 time to fit residues: 59.2660 Evaluate side-chains 214 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 179 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 157 ASN Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 179 ARG Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 220 HIS Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 212 ASN Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 326 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 68 optimal weight: 9.9990 chunk 72 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 0.0020 chunk 84 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 102 optimal weight: 9.9990 chunk 93 optimal weight: 5.9990 chunk 99 optimal weight: 7.9990 overall best weight: 2.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 17 GLN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9116 Z= 0.282 Angle : 0.636 13.934 12325 Z= 0.327 Chirality : 0.045 0.294 1402 Planarity : 0.004 0.041 1546 Dihedral : 7.198 82.183 1252 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.53 % Favored : 94.38 % Rotamer: Outliers : 4.42 % Allowed : 19.65 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.33 (0.25), residues: 1121 helix: 1.47 (0.26), residues: 404 sheet: -0.82 (0.30), residues: 284 loop : -1.37 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 82 HIS 0.003 0.001 HIS S 35 PHE 0.015 0.002 PHE A 318 TYR 0.027 0.002 TYR S 178 ARG 0.005 0.000 ARG C 52 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 181 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 46 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.7049 (mt-10) REVERT: S 65 LYS cc_start: 0.8458 (tptp) cc_final: 0.7790 (tppt) REVERT: S 179 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.6394 (mpt180) REVERT: B 269 ASN cc_start: 0.7967 (m-40) cc_final: 0.7406 (m110) REVERT: C 130 GLU cc_start: 0.7412 (mm-30) cc_final: 0.7077 (mm-30) REVERT: C 215 GLU cc_start: 0.7349 (mp0) cc_final: 0.6859 (mp0) REVERT: D 42 GLU cc_start: 0.7848 (tp30) cc_final: 0.7545 (tp30) REVERT: A 85 LYS cc_start: 0.8345 (tppt) cc_final: 0.7957 (tppt) REVERT: A 104 ILE cc_start: 0.6994 (OUTLIER) cc_final: 0.6673 (mp) REVERT: A 312 MET cc_start: 0.7259 (mmt) cc_final: 0.6770 (mmt) REVERT: A 326 MET cc_start: 0.6296 (OUTLIER) cc_final: 0.5884 (mtp) REVERT: A 330 MET cc_start: 0.5896 (mmp) cc_final: 0.5602 (mmt) outliers start: 43 outliers final: 36 residues processed: 207 average time/residue: 0.2035 time to fit residues: 57.9285 Evaluate side-chains 220 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 180 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 133 SER Chi-restraints excluded: chain S residue 157 ASN Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 179 ARG Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 220 HIS Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 212 ASN Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 326 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 20.0000 chunk 60 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 78 optimal weight: 30.0000 chunk 30 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 94 optimal weight: 0.3980 chunk 99 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 105 optimal weight: 0.3980 chunk 64 optimal weight: 0.9980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 130 GLN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9116 Z= 0.150 Angle : 0.560 13.470 12325 Z= 0.286 Chirality : 0.042 0.278 1402 Planarity : 0.003 0.038 1546 Dihedral : 6.859 89.391 1252 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.48 % Favored : 96.43 % Rotamer: Outliers : 3.29 % Allowed : 20.68 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.26), residues: 1121 helix: 1.92 (0.26), residues: 399 sheet: -0.42 (0.31), residues: 269 loop : -1.40 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 82 HIS 0.003 0.001 HIS S 220 PHE 0.012 0.001 PHE C 151 TYR 0.025 0.001 TYR S 178 ARG 0.004 0.000 ARG C 52 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 188 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 6 GLU cc_start: 0.7115 (mp0) cc_final: 0.6691 (mp0) REVERT: S 18 ARG cc_start: 0.8499 (tpp-160) cc_final: 0.7754 (tpp-160) REVERT: S 46 GLU cc_start: 0.7205 (tm-30) cc_final: 0.7000 (mt-10) REVERT: S 65 LYS cc_start: 0.8436 (tptp) cc_final: 0.7709 (tppt) REVERT: S 67 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.8183 (ttp80) REVERT: S 80 PHE cc_start: 0.6466 (m-10) cc_final: 0.6248 (m-10) REVERT: S 179 ARG cc_start: 0.7436 (OUTLIER) cc_final: 0.5394 (mpt180) REVERT: S 208 GLU cc_start: 0.7398 (mp0) cc_final: 0.7158 (mp0) REVERT: B 269 ASN cc_start: 0.7808 (m-40) cc_final: 0.7401 (m-40) REVERT: C 188 MET cc_start: 0.8462 (mmm) cc_final: 0.8256 (mmm) REVERT: C 215 GLU cc_start: 0.7377 (mp0) cc_final: 0.6309 (mp0) REVERT: A 85 LYS cc_start: 0.8407 (tppt) cc_final: 0.8028 (tppt) REVERT: A 104 ILE cc_start: 0.6867 (OUTLIER) cc_final: 0.6525 (mp) REVERT: A 201 SER cc_start: 0.7397 (m) cc_final: 0.7075 (t) REVERT: A 312 MET cc_start: 0.7087 (mmt) cc_final: 0.6535 (mmt) REVERT: A 330 MET cc_start: 0.5743 (mmp) cc_final: 0.5417 (mmt) outliers start: 32 outliers final: 24 residues processed: 209 average time/residue: 0.2064 time to fit residues: 59.4006 Evaluate side-chains 202 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 175 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 133 SER Chi-restraints excluded: chain S residue 157 ASN Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 179 ARG Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 212 ASN Chi-restraints excluded: chain A residue 296 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 chunk 110 optimal weight: 0.9990 chunk 101 optimal weight: 8.9990 chunk 88 optimal weight: 0.6980 chunk 9 optimal weight: 9.9990 chunk 68 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 93 optimal weight: 0.3980 chunk 26 optimal weight: 9.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 188 HIS C 125 ASN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9116 Z= 0.203 Angle : 0.587 12.885 12325 Z= 0.300 Chirality : 0.043 0.295 1402 Planarity : 0.004 0.039 1546 Dihedral : 6.748 79.043 1252 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.64 % Favored : 95.27 % Rotamer: Outliers : 2.98 % Allowed : 20.58 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.04 (0.25), residues: 1121 helix: 1.87 (0.26), residues: 399 sheet: -0.45 (0.31), residues: 274 loop : -1.36 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 82 HIS 0.003 0.001 HIS S 220 PHE 0.028 0.002 PHE A 285 TYR 0.023 0.002 TYR S 178 ARG 0.005 0.000 ARG C 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 179 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 6 GLU cc_start: 0.7222 (mp0) cc_final: 0.6686 (mp0) REVERT: S 18 ARG cc_start: 0.8460 (tpp-160) cc_final: 0.7854 (tpp80) REVERT: S 46 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.7014 (mt-10) REVERT: S 65 LYS cc_start: 0.8390 (tptp) cc_final: 0.7676 (tppt) REVERT: S 67 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8127 (ttp80) REVERT: S 80 PHE cc_start: 0.6617 (m-10) cc_final: 0.6352 (m-10) REVERT: S 179 ARG cc_start: 0.7430 (OUTLIER) cc_final: 0.6056 (mpt-90) REVERT: S 208 GLU cc_start: 0.7461 (mp0) cc_final: 0.7187 (mp0) REVERT: B 269 ASN cc_start: 0.7813 (m-40) cc_final: 0.7390 (m-40) REVERT: B 276 GLU cc_start: 0.8039 (tm-30) cc_final: 0.7558 (tm-30) REVERT: C 188 MET cc_start: 0.8597 (mmm) cc_final: 0.8302 (mmm) REVERT: C 215 GLU cc_start: 0.6873 (mp0) cc_final: 0.6370 (mp0) REVERT: C 280 LYS cc_start: 0.8329 (tttm) cc_final: 0.7601 (ttmt) REVERT: A 85 LYS cc_start: 0.8415 (tppt) cc_final: 0.7993 (tppt) REVERT: A 104 ILE cc_start: 0.6889 (OUTLIER) cc_final: 0.6524 (mp) REVERT: A 312 MET cc_start: 0.7195 (mmt) cc_final: 0.6752 (mmt) outliers start: 29 outliers final: 24 residues processed: 196 average time/residue: 0.2193 time to fit residues: 58.2726 Evaluate side-chains 205 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 177 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 133 SER Chi-restraints excluded: chain S residue 157 ASN Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 179 ARG Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 212 ASN Chi-restraints excluded: chain A residue 296 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 6.9990 chunk 13 optimal weight: 20.0000 chunk 24 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.190069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.148991 restraints weight = 10607.850| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.23 r_work: 0.3344 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9116 Z= 0.178 Angle : 0.579 13.024 12325 Z= 0.295 Chirality : 0.043 0.292 1402 Planarity : 0.003 0.039 1546 Dihedral : 6.699 78.342 1252 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.84 % Favored : 96.07 % Rotamer: Outliers : 3.70 % Allowed : 20.16 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.07 (0.25), residues: 1121 helix: 1.88 (0.26), residues: 399 sheet: -0.43 (0.31), residues: 274 loop : -1.33 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 82 HIS 0.003 0.001 HIS S 220 PHE 0.023 0.001 PHE A 285 TYR 0.024 0.001 TYR S 178 ARG 0.005 0.000 ARG C 52 =============================================================================== Job complete usr+sys time: 1995.73 seconds wall clock time: 36 minutes 32.86 seconds (2192.86 seconds total)