Starting phenix.real_space_refine on Thu Mar 14 15:15:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew3_31346/03_2024/7ew3_31346_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew3_31346/03_2024/7ew3_31346.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew3_31346/03_2024/7ew3_31346_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew3_31346/03_2024/7ew3_31346_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew3_31346/03_2024/7ew3_31346_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew3_31346/03_2024/7ew3_31346.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew3_31346/03_2024/7ew3_31346.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew3_31346/03_2024/7ew3_31346_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew3_31346/03_2024/7ew3_31346_updated.pdb" } resolution = 3.1 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= 0.131 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 48 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 68 5.16 5 C 5794 2.51 5 N 1531 2.21 5 O 1678 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 14": "OE1" <-> "OE2" Residue "A ARG 15": "NH1" <-> "NH2" Residue "A GLU 25": "OE1" <-> "OE2" Residue "A GLU 43": "OE1" <-> "OE2" Residue "A ARG 205": "NH1" <-> "NH2" Residue "A GLU 275": "OE1" <-> "OE2" Residue "A GLU 297": "OE1" <-> "OE2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "C GLU 58": "OE1" <-> "OE2" Residue "C ARG 62": "NH1" <-> "NH2" Residue "R GLU 20": "OE1" <-> "OE2" Residue "R GLU 56": "OE1" <-> "OE2" Residue "R ARG 73": "NH1" <-> "NH2" Residue "R ARG 114": "NH1" <-> "NH2" Residue "R GLU 115": "OE1" <-> "OE2" Residue "R ARG 144": "NH1" <-> "NH2" Residue "R ARG 217": "NH1" <-> "NH2" Residue "R ARG 237": "NH1" <-> "NH2" Residue "R ARG 243": "NH1" <-> "NH2" Residue "R ARG 307": "NH1" <-> "NH2" Residue "S GLU 153": "OE1" <-> "OE2" Residue "S ARG 160": "NH1" <-> "NH2" Residue "S ARG 218": "NH1" <-> "NH2" 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: 9072 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1813 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2611 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "C" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 474 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 4, 'TRANS': 56} Chain: "R" Number of atoms: 2294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2294 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 281} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 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: "R" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 97 Unusual residues: {'PLM': 4, 'S1P': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 4.78, per 1000 atoms: 0.53 Number of scatterers: 9072 At special positions: 0 Unit cell: (94.76, 124.2, 134.32, 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 68 16.00 P 1 15.00 O 1678 8.00 N 1531 7.00 C 5794 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 178 " - pdb=" SG CYS R 185 " distance=2.03 Simple disulfide: pdb=" SG CYS R 269 " - pdb=" SG CYS R 274 " distance=2.03 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " 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: 3.00 Conformation dependent library (CDL) restraints added in 1.6 seconds 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2152 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 13 sheets defined 33.2% alpha, 21.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 7 through 27 removed outlier: 3.983A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 32 No H-bonds generated for 'chain 'A' and resid 30 through 32' Processing helix chain 'A' and resid 48 through 52 Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 272 through 280 removed outlier: 4.321A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 310 removed outlier: 3.778A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 351 Processing helix chain 'B' and resid 2 through 25 removed outlier: 3.857A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 35 Processing helix chain 'C' and resid 8 through 22 removed outlier: 3.608A pdb=" N MET C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 47 removed outlier: 4.918A pdb=" N LYS C 46 " --> pdb=" O GLU C 42 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N GLU C 47 " --> pdb=" O ALA C 43 " (cutoff:3.500A) Processing helix chain 'R' and resid 17 through 25 Processing helix chain 'R' and resid 41 through 66 Processing helix chain 'R' and resid 74 through 98 Processing helix chain 'R' and resid 108 through 141 removed outlier: 3.545A pdb=" N MET R 118 " --> pdb=" O ARG R 114 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER R 128 " --> pdb=" O ALA R 124 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N LEU R 129 " --> pdb=" O SER R 125 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU R 130 " --> pdb=" O THR R 126 " (cutoff:3.500A) Processing helix chain 'R' and resid 152 through 174 Proline residue: R 172 - end of helix Processing helix chain 'R' and resid 194 through 228 removed outlier: 4.122A pdb=" N ILE R 218 " --> pdb=" O LEU R 214 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N TYR R 219 " --> pdb=" O TYR R 215 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N PHE R 220 " --> pdb=" O ALA R 216 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N LEU R 221 " --> pdb=" O ARG R 217 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LYS R 228 " --> pdb=" O SER R 224 " (cutoff:3.500A) Processing helix chain 'R' and resid 232 through 268 removed outlier: 3.763A pdb=" N CYS R 255 " --> pdb=" O VAL R 251 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TRP R 256 " --> pdb=" O PHE R 252 " (cutoff:3.500A) Proline residue: R 258 - end of helix Processing helix chain 'R' and resid 276 through 278 No H-bonds generated for 'chain 'R' and resid 276 through 278' Processing helix chain 'R' and resid 280 through 297 removed outlier: 4.299A pdb=" N VAL R 285 " --> pdb=" O TRP R 282 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN R 294 " --> pdb=" O SER R 291 " (cutoff:3.500A) Proline residue: R 295 - end of helix Processing helix chain 'R' and resid 303 through 311 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 88 through 90 No H-bonds generated for 'chain 'S' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.834A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N HIS A 195 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N LEU A 36 " --> pdb=" O HIS A 195 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LYS A 197 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N LEU A 38 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N PHE A 199 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N GLY A 40 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.032A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.722A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.903A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.056A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 262 through 264 removed outlier: 3.814A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.406A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 46 through 52 removed outlier: 6.951A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'S' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'S' and resid 115 through 117 removed outlier: 3.741A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 146 through 148 removed outlier: 7.242A pdb=" N LYS S 244 " --> pdb=" O VAL S 147 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'S' and resid 155 through 160 Processing sheet with id= M, first strand: chain 'S' and resid 226 through 231 removed outlier: 3.502A pdb=" N PHE S 177 " --> pdb=" O TYR S 228 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) 395 hydrogen bonds defined for protein. 1104 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: 2.48 Time building geometry restraints manager: 3.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2904 1.35 - 1.46: 2234 1.46 - 1.58: 4010 1.58 - 1.70: 1 1.70 - 1.82: 99 Bond restraints: 9248 Sorted by residual: bond pdb=" C13 S1P R 401 " pdb=" C14 S1P R 401 " ideal model delta sigma weight residual 1.569 1.451 0.118 2.00e-02 2.50e+03 3.48e+01 bond pdb=" C14 S1P R 401 " pdb=" C15 S1P R 401 " ideal model delta sigma weight residual 1.557 1.443 0.114 2.00e-02 2.50e+03 3.24e+01 bond pdb=" C12 S1P R 401 " pdb=" C13 S1P R 401 " ideal model delta sigma weight residual 1.569 1.458 0.111 2.00e-02 2.50e+03 3.07e+01 bond pdb=" C15 S1P R 401 " pdb=" C16 S1P R 401 " ideal model delta sigma weight residual 1.561 1.455 0.106 2.00e-02 2.50e+03 2.82e+01 bond pdb=" C8 S1P R 401 " pdb=" C9 S1P R 401 " ideal model delta sigma weight residual 1.554 1.452 0.102 2.00e-02 2.50e+03 2.61e+01 ... (remaining 9243 not shown) Histogram of bond angle deviations from ideal: 99.05 - 106.05: 147 106.05 - 113.04: 4998 113.04 - 120.03: 3107 120.03 - 127.02: 4134 127.02 - 134.01: 98 Bond angle restraints: 12484 Sorted by residual: angle pdb=" O1 S1P R 401 " pdb=" P22 S1P R 401 " pdb=" O24 S1P R 401 " ideal model delta sigma weight residual 109.47 99.05 10.42 3.00e+00 1.11e-01 1.21e+01 angle pdb=" C3 S1P R 401 " pdb=" C2 S1P R 401 " pdb=" N2 S1P R 401 " ideal model delta sigma weight residual 109.50 99.16 10.34 3.00e+00 1.11e-01 1.19e+01 angle pdb=" C1 S1P R 401 " pdb=" O1 S1P R 401 " pdb=" P22 S1P R 401 " ideal model delta sigma weight residual 118.48 127.34 -8.86 3.00e+00 1.11e-01 8.73e+00 angle pdb=" N THR R 103 " pdb=" CA THR R 103 " pdb=" C THR R 103 " ideal model delta sigma weight residual 111.28 114.12 -2.84 1.09e+00 8.42e-01 6.77e+00 angle pdb=" O1 S1P R 401 " pdb=" P22 S1P R 401 " pdb=" O23 S1P R 401 " ideal model delta sigma weight residual 109.50 116.69 -7.19 3.00e+00 1.11e-01 5.75e+00 ... (remaining 12479 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.59: 5140 22.59 - 45.17: 342 45.17 - 67.76: 28 67.76 - 90.35: 13 90.35 - 112.93: 2 Dihedral angle restraints: 5525 sinusoidal: 2193 harmonic: 3332 Sorted by residual: dihedral pdb=" CB CYS R 178 " pdb=" SG CYS R 178 " pdb=" SG CYS R 185 " pdb=" CB CYS R 185 " ideal model delta sinusoidal sigma weight residual 93.00 50.01 42.99 1 1.00e+01 1.00e-02 2.58e+01 dihedral pdb=" C11 S1P R 401 " pdb=" C10 S1P R 401 " pdb=" C9 S1P R 401 " pdb=" C8 S1P R 401 " ideal model delta sinusoidal sigma weight residual 241.31 128.38 112.93 1 3.00e+01 1.11e-03 1.48e+01 dihedral pdb=" C12 S1P R 401 " pdb=" C10 S1P R 401 " pdb=" C11 S1P R 401 " pdb=" C9 S1P R 401 " ideal model delta sinusoidal sigma weight residual 141.65 -122.25 -96.10 1 3.00e+01 1.11e-03 1.18e+01 ... (remaining 5522 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 879 0.027 - 0.054: 313 0.054 - 0.081: 136 0.081 - 0.108: 52 0.108 - 0.134: 33 Chirality restraints: 1413 Sorted by residual: chirality pdb=" CB VAL A 201 " pdb=" CA VAL A 201 " pdb=" CG1 VAL A 201 " pdb=" CG2 VAL A 201 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.13 2.00e-01 2.50e+01 4.51e-01 chirality pdb=" CA PRO R 172 " pdb=" N PRO R 172 " pdb=" C PRO R 172 " pdb=" CB PRO R 172 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.80e-01 chirality pdb=" CA ILE S 216 " pdb=" N ILE S 216 " pdb=" C ILE S 216 " pdb=" CB ILE S 216 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.79e-01 ... (remaining 1410 not shown) Planarity restraints: 1566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG S 180 " -0.025 5.00e-02 4.00e+02 3.78e-02 2.28e+00 pdb=" N PRO S 181 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO S 181 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO S 181 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.023 5.00e-02 4.00e+02 3.48e-02 1.94e+00 pdb=" N PRO B 236 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 246 " -0.007 2.00e-02 2.50e+03 1.31e-02 1.71e+00 pdb=" C ASP B 246 " 0.023 2.00e-02 2.50e+03 pdb=" O ASP B 246 " -0.008 2.00e-02 2.50e+03 pdb=" N ASP B 247 " -0.008 2.00e-02 2.50e+03 ... (remaining 1563 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2174 2.80 - 3.32: 7900 3.32 - 3.85: 13947 3.85 - 4.37: 15856 4.37 - 4.90: 29216 Nonbonded interactions: 69093 Sorted by model distance: nonbonded pdb=" O LEU R 168 " pdb=" OH TYR R 196 " model vdw 2.274 2.440 nonbonded pdb=" NH1 ARG S 67 " pdb=" O SER S 85 " model vdw 2.309 2.520 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.320 2.440 nonbonded pdb=" O PHE S 32 " pdb=" NH2 ARG S 72 " model vdw 2.330 2.520 nonbonded pdb=" NH1 ARG S 87 " pdb=" OE2 GLU S 89 " model vdw 2.340 2.520 ... (remaining 69088 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 3.990 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 25.220 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 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 0.118 9248 Z= 0.285 Angle : 0.500 10.415 12484 Z= 0.262 Chirality : 0.039 0.134 1413 Planarity : 0.003 0.038 1566 Dihedral : 14.443 112.934 3364 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.36 (0.25), residues: 1133 helix: 2.58 (0.26), residues: 385 sheet: 1.16 (0.32), residues: 270 loop : -0.70 (0.26), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 111 HIS 0.001 0.000 HIS S 35 PHE 0.010 0.001 PHE R 260 TYR 0.005 0.001 TYR S 190 ARG 0.009 0.000 ARG S 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 1.002 Fit side-chains REVERT: A 229 ASP cc_start: 0.7905 (m-30) cc_final: 0.7553 (m-30) REVERT: C 21 MET cc_start: 0.7835 (mmm) cc_final: 0.6929 (ptm) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.2233 time to fit residues: 40.2980 Evaluate side-chains 109 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 89 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 103 optimal weight: 7.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN ** R 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9248 Z= 0.155 Angle : 0.462 5.740 12484 Z= 0.241 Chirality : 0.040 0.157 1413 Planarity : 0.003 0.038 1566 Dihedral : 7.412 115.516 1313 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.72 % Allowed : 6.96 % Favored : 92.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.46 (0.25), residues: 1133 helix: 3.00 (0.27), residues: 376 sheet: 1.01 (0.32), residues: 270 loop : -0.75 (0.26), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 111 HIS 0.004 0.001 HIS S 35 PHE 0.010 0.001 PHE B 199 TYR 0.008 0.001 TYR S 190 ARG 0.001 0.000 ARG S 202 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 104 time to evaluate : 0.985 Fit side-chains REVERT: C 21 MET cc_start: 0.7868 (mmm) cc_final: 0.7135 (ptm) outliers start: 7 outliers final: 5 residues processed: 108 average time/residue: 0.2419 time to fit residues: 35.5118 Evaluate side-chains 105 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 100 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain S residue 217 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 86 optimal weight: 0.4980 chunk 70 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 112 optimal weight: 3.9990 chunk 92 optimal weight: 8.9990 chunk 102 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9248 Z= 0.324 Angle : 0.583 10.665 12484 Z= 0.305 Chirality : 0.044 0.152 1413 Planarity : 0.004 0.038 1566 Dihedral : 7.513 90.071 1313 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.33 % Allowed : 9.93 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.25), residues: 1133 helix: 2.83 (0.27), residues: 375 sheet: 0.79 (0.31), residues: 282 loop : -0.98 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 256 HIS 0.007 0.001 HIS S 35 PHE 0.019 0.002 PHE B 199 TYR 0.012 0.001 TYR S 59 ARG 0.007 0.000 ARG S 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 93 time to evaluate : 0.914 Fit side-chains REVERT: C 21 MET cc_start: 0.7936 (mmm) cc_final: 0.7049 (ptm) REVERT: R 140 MET cc_start: 0.8375 (mmm) cc_final: 0.7956 (mmm) REVERT: R 150 LYS cc_start: 0.6213 (ptmt) cc_final: 0.5872 (ttpt) REVERT: S 46 GLU cc_start: 0.7521 (pt0) cc_final: 0.7288 (pt0) outliers start: 13 outliers final: 8 residues processed: 102 average time/residue: 0.2648 time to fit residues: 35.7445 Evaluate side-chains 95 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 87 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 296 VAL Chi-restraints excluded: chain S residue 177 PHE Chi-restraints excluded: chain S residue 217 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 104 optimal weight: 40.0000 chunk 110 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 chunk 98 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 9248 Z= 0.360 Angle : 0.600 10.544 12484 Z= 0.313 Chirality : 0.045 0.150 1413 Planarity : 0.004 0.039 1566 Dihedral : 7.472 83.237 1313 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.05 % Allowed : 12.38 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1133 helix: 2.64 (0.26), residues: 376 sheet: 0.54 (0.31), residues: 277 loop : -1.13 (0.25), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 82 HIS 0.006 0.001 HIS S 35 PHE 0.020 0.002 PHE B 199 TYR 0.011 0.002 TYR S 102 ARG 0.003 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 92 time to evaluate : 1.076 Fit side-chains REVERT: B 338 ILE cc_start: 0.8470 (OUTLIER) cc_final: 0.8231 (mp) REVERT: C 21 MET cc_start: 0.7928 (mmm) cc_final: 0.7165 (ptm) REVERT: R 140 MET cc_start: 0.8347 (mmm) cc_final: 0.8025 (mmm) outliers start: 20 outliers final: 14 residues processed: 106 average time/residue: 0.2691 time to fit residues: 37.9180 Evaluate side-chains 101 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 86 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 296 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 177 PHE Chi-restraints excluded: chain S residue 217 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 56 optimal weight: 8.9990 chunk 98 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9248 Z= 0.203 Angle : 0.492 7.007 12484 Z= 0.260 Chirality : 0.041 0.149 1413 Planarity : 0.003 0.039 1566 Dihedral : 6.828 84.090 1313 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.94 % Allowed : 13.61 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.00 (0.25), residues: 1133 helix: 2.96 (0.27), residues: 374 sheet: 0.51 (0.31), residues: 271 loop : -1.15 (0.25), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.004 0.001 HIS B 91 PHE 0.015 0.001 PHE B 241 TYR 0.011 0.001 TYR S 190 ARG 0.003 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 90 time to evaluate : 0.947 Fit side-chains REVERT: C 21 MET cc_start: 0.7947 (mmm) cc_final: 0.7118 (ptm) REVERT: R 140 MET cc_start: 0.8295 (mmm) cc_final: 0.8058 (mmm) outliers start: 19 outliers final: 9 residues processed: 105 average time/residue: 0.2522 time to fit residues: 35.3603 Evaluate side-chains 97 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 88 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 257 SER Chi-restraints excluded: chain R residue 296 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 177 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 2.9990 chunk 99 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 110 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9248 Z= 0.287 Angle : 0.552 9.087 12484 Z= 0.288 Chirality : 0.043 0.158 1413 Planarity : 0.004 0.040 1566 Dihedral : 7.020 85.289 1313 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.46 % Allowed : 13.72 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 (0.25), residues: 1133 helix: 2.78 (0.27), residues: 377 sheet: 0.40 (0.31), residues: 276 loop : -1.16 (0.25), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.005 0.001 HIS B 91 PHE 0.017 0.002 PHE B 199 TYR 0.010 0.001 TYR S 190 ARG 0.003 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 93 time to evaluate : 0.932 Fit side-chains REVERT: C 21 MET cc_start: 0.7930 (mmm) cc_final: 0.7098 (ptm) REVERT: R 140 MET cc_start: 0.8348 (mmm) cc_final: 0.8066 (mmm) outliers start: 24 outliers final: 16 residues processed: 110 average time/residue: 0.2536 time to fit residues: 37.0907 Evaluate side-chains 106 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 90 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 59 MET Chi-restraints excluded: chain R residue 257 SER Chi-restraints excluded: chain R residue 296 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 177 PHE Chi-restraints excluded: chain S residue 217 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 109 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9248 Z= 0.200 Angle : 0.503 10.313 12484 Z= 0.263 Chirality : 0.042 0.146 1413 Planarity : 0.003 0.039 1566 Dihedral : 6.795 82.453 1313 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.25 % Allowed : 13.82 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.99 (0.25), residues: 1133 helix: 2.94 (0.27), residues: 375 sheet: 0.41 (0.31), residues: 277 loop : -1.11 (0.25), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.004 0.001 HIS B 91 PHE 0.015 0.001 PHE B 241 TYR 0.010 0.001 TYR S 190 ARG 0.003 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 94 time to evaluate : 1.050 Fit side-chains REVERT: B 234 PHE cc_start: 0.8910 (OUTLIER) cc_final: 0.7849 (t80) REVERT: C 21 MET cc_start: 0.7942 (mmm) cc_final: 0.7122 (ptm) REVERT: R 140 MET cc_start: 0.8315 (mmm) cc_final: 0.8094 (mmm) outliers start: 22 outliers final: 16 residues processed: 110 average time/residue: 0.2621 time to fit residues: 38.3655 Evaluate side-chains 108 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 91 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 59 MET Chi-restraints excluded: chain R residue 257 SER Chi-restraints excluded: chain R residue 296 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 177 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 86 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 105 optimal weight: 20.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9248 Z= 0.279 Angle : 0.553 11.309 12484 Z= 0.286 Chirality : 0.043 0.165 1413 Planarity : 0.004 0.039 1566 Dihedral : 6.894 84.345 1313 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.66 % Allowed : 13.61 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.89 (0.25), residues: 1133 helix: 2.80 (0.27), residues: 377 sheet: 0.42 (0.31), residues: 273 loop : -1.17 (0.25), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.006 0.001 HIS B 91 PHE 0.016 0.002 PHE B 199 TYR 0.010 0.001 TYR S 190 ARG 0.002 0.000 ARG S 202 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 91 time to evaluate : 1.056 Fit side-chains REVERT: C 21 MET cc_start: 0.7933 (mmm) cc_final: 0.7096 (ptm) REVERT: R 140 MET cc_start: 0.8342 (mmm) cc_final: 0.8079 (mmm) REVERT: R 143 MET cc_start: 0.8760 (mmt) cc_final: 0.8355 (mmp) REVERT: S 140 MET cc_start: 0.7148 (mmt) cc_final: 0.6304 (mmt) outliers start: 26 outliers final: 20 residues processed: 109 average time/residue: 0.2588 time to fit residues: 37.6303 Evaluate side-chains 111 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 91 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 59 MET Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 257 SER Chi-restraints excluded: chain R residue 296 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 177 PHE Chi-restraints excluded: chain S residue 217 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 105 optimal weight: 20.0000 chunk 61 optimal weight: 0.9990 chunk 44 optimal weight: 0.4980 chunk 80 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 66 optimal weight: 9.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 21 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9248 Z= 0.152 Angle : 0.477 12.316 12484 Z= 0.247 Chirality : 0.041 0.221 1413 Planarity : 0.003 0.039 1566 Dihedral : 6.425 78.831 1313 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.84 % Allowed : 14.84 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.10 (0.25), residues: 1133 helix: 3.03 (0.27), residues: 376 sheet: 0.45 (0.30), residues: 285 loop : -1.05 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.004 0.001 HIS A 188 PHE 0.014 0.001 PHE B 241 TYR 0.010 0.001 TYR S 190 ARG 0.001 0.000 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 93 time to evaluate : 0.974 Fit side-chains REVERT: B 234 PHE cc_start: 0.8899 (OUTLIER) cc_final: 0.7895 (t80) REVERT: C 21 MET cc_start: 0.7931 (mmm) cc_final: 0.7115 (ptm) REVERT: S 140 MET cc_start: 0.7024 (mmt) cc_final: 0.6205 (mmt) outliers start: 18 outliers final: 14 residues processed: 107 average time/residue: 0.2792 time to fit residues: 39.9085 Evaluate side-chains 105 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 90 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 257 SER Chi-restraints excluded: chain R residue 296 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 177 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 104 optimal weight: 30.0000 chunk 90 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 96 optimal weight: 0.3980 chunk 27 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9248 Z= 0.202 Angle : 0.517 12.651 12484 Z= 0.263 Chirality : 0.042 0.212 1413 Planarity : 0.003 0.040 1566 Dihedral : 6.438 78.813 1313 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.54 % Allowed : 15.46 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.25), residues: 1133 helix: 3.01 (0.27), residues: 376 sheet: 0.45 (0.31), residues: 276 loop : -1.06 (0.25), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.005 0.001 HIS A 188 PHE 0.017 0.001 PHE B 241 TYR 0.010 0.001 TYR S 190 ARG 0.001 0.000 ARG S 202 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 94 time to evaluate : 1.032 Fit side-chains REVERT: B 234 PHE cc_start: 0.8908 (OUTLIER) cc_final: 0.7871 (t80) REVERT: C 21 MET cc_start: 0.7930 (mmm) cc_final: 0.7114 (ptm) REVERT: R 140 MET cc_start: 0.8280 (mmm) cc_final: 0.8043 (mmm) REVERT: S 140 MET cc_start: 0.7024 (mmt) cc_final: 0.6191 (mmt) outliers start: 15 outliers final: 14 residues processed: 106 average time/residue: 0.2652 time to fit residues: 37.1370 Evaluate side-chains 109 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 94 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 257 SER Chi-restraints excluded: chain R residue 296 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 177 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 90 optimal weight: 10.0000 chunk 37 optimal weight: 0.4980 chunk 93 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 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 = 0.3972 r_free = 0.3972 target = 0.169597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.126342 restraints weight = 10518.235| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.71 r_work: 0.3124 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9248 Z= 0.167 Angle : 0.492 12.582 12484 Z= 0.251 Chirality : 0.041 0.202 1413 Planarity : 0.003 0.040 1566 Dihedral : 6.262 77.529 1313 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.84 % Allowed : 15.15 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.14 (0.25), residues: 1133 helix: 3.07 (0.27), residues: 376 sheet: 0.43 (0.31), residues: 279 loop : -1.00 (0.26), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.004 0.001 HIS A 188 PHE 0.016 0.001 PHE B 241 TYR 0.010 0.001 TYR S 190 ARG 0.001 0.000 ARG S 202 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2112.27 seconds wall clock time: 38 minutes 35.25 seconds (2315.25 seconds total)