Starting phenix.real_space_refine on Tue Feb 13 18:18:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x9b_33070/02_2024/7x9b_33070_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x9b_33070/02_2024/7x9b_33070.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x9b_33070/02_2024/7x9b_33070_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/7x9b_33070/02_2024/7x9b_33070_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x9b_33070/02_2024/7x9b_33070_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x9b_33070/02_2024/7x9b_33070.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x9b_33070/02_2024/7x9b_33070.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x9b_33070/02_2024/7x9b_33070_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x9b_33070/02_2024/7x9b_33070_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 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= 0.003 sd= 0.053 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 45 5.16 5 C 4634 2.51 5 N 1242 2.21 5 O 1321 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 ASP 26": "OD1" <-> "OD2" Residue "A PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 216": "OE1" <-> "OE2" Residue "A ARG 242": "NH1" <-> "NH2" Residue "A ASP 261": "OD1" <-> "OD2" Residue "A TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 308": "OE1" <-> "OE2" Residue "A PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 12": "OE1" <-> "OE2" Residue "B ASP 20": "OD1" <-> "OD2" Residue "B ASP 27": "OD1" <-> "OD2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 68": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B ASP 154": "OD1" <-> "OD2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B ASP 258": "OD1" <-> "OD2" Residue "B ASP 298": "OD1" <-> "OD2" Residue "B ASP 312": "OD1" <-> "OD2" Residue "C ASP 36": "OD1" <-> "OD2" Residue "C TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 96": "OD1" <-> "OD2" Residue "R ARG 163": "NH1" <-> "NH2" Residue "R TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 262": "NH1" <-> "NH2" Residue "R ASP 294": "OD1" <-> "OD2" Residue "R ARG 333": "NH1" <-> "NH2" Residue "R PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 341": "NH1" <-> "NH2" Residue "P TYR 1": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7242 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1684 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 39 Chain: "B" Number of atoms: 2523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2523 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 50 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ARG:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 45 Chain: "C" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 391 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 49} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "R" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2362 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 10, 'TRANS': 291} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 20 Chain: "P" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 282 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 31} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 13 Time building chain proxies: 4.34, per 1000 atoms: 0.60 Number of scatterers: 7242 At special positions: 0 Unit cell: (111.52, 125.46, 84.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 45 16.00 O 1321 8.00 N 1242 7.00 C 4634 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 123 " - pdb=" SG CYS R 203 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.83 Conformation dependent library (CDL) restraints added in 1.4 seconds 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1794 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 8 sheets defined 40.3% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'A' and resid 8 through 32 removed outlier: 3.619A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 49 removed outlier: 4.010A pdb=" N ILE A 49 " --> pdb=" O LYS A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 215 removed outlier: 4.961A pdb=" N HIS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N CYS A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N PHE A 215 " --> pdb=" O TRP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 231 removed outlier: 3.856A pdb=" N TYR A 230 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 227 through 231' Processing helix chain 'A' and resid 243 through 254 removed outlier: 3.623A pdb=" N LEU A 249 " --> pdb=" O ALA A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 279 removed outlier: 3.636A pdb=" N GLU A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 307 removed outlier: 3.740A pdb=" N PHE A 307 " --> pdb=" O ILE A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 348 removed outlier: 3.796A pdb=" N ILE A 344 " --> pdb=" O THR A 340 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS A 345 " --> pdb=" O ASP A 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 24 Processing helix chain 'B' and resid 34 through 36 No H-bonds generated for 'chain 'B' and resid 34 through 36' Processing helix chain 'C' and resid 10 through 23 removed outlier: 4.291A pdb=" N LYS C 14 " --> pdb=" O ALA C 10 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU C 15 " --> pdb=" O GLN C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 43 removed outlier: 3.611A pdb=" N ASP C 36 " --> pdb=" O LYS C 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 47 through 77 Processing helix chain 'R' and resid 84 through 103 Processing helix chain 'R' and resid 105 through 111 removed outlier: 3.882A pdb=" N TYR R 110 " --> pdb=" O PHE R 106 " (cutoff:3.500A) Processing helix chain 'R' and resid 122 through 124 No H-bonds generated for 'chain 'R' and resid 122 through 124' Processing helix chain 'R' and resid 126 through 152 Processing helix chain 'R' and resid 162 through 183 removed outlier: 3.969A pdb=" N SER R 181 " --> pdb=" O ALA R 177 " (cutoff:3.500A) Proline residue: R 182 - end of helix Processing helix chain 'R' and resid 214 through 248 Proline residue: R 231 - end of helix Processing helix chain 'R' and resid 258 through 293 removed outlier: 3.672A pdb=" N GLN R 261 " --> pdb=" O HIS R 258 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL R 276 " --> pdb=" O VAL R 273 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N PHE R 277 " --> pdb=" O VAL R 274 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N SER R 280 " --> pdb=" O PHE R 277 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N TRP R 281 " --> pdb=" O ALA R 278 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LEU R 282 " --> pdb=" O VAL R 279 " (cutoff:3.500A) Proline residue: R 283 - end of helix removed outlier: 3.563A pdb=" N ILE R 293 " --> pdb=" O ALA R 290 " (cutoff:3.500A) Processing helix chain 'R' and resid 303 through 327 removed outlier: 4.474A pdb=" N SER R 317 " --> pdb=" O ILE R 313 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N THR R 318 " --> pdb=" O ALA R 314 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE R 319 " --> pdb=" O MET R 315 " (cutoff:3.500A) Proline residue: R 322 - end of helix Processing helix chain 'R' and resid 330 through 339 removed outlier: 3.764A pdb=" N LEU R 337 " --> pdb=" O ARG R 333 " (cutoff:3.500A) Processing helix chain 'P' and resid 14 through 31 Processing sheet with id= A, first strand: chain 'A' and resid 320 through 323 removed outlier: 3.831A pdb=" N HIS A 322 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 9.051A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.374A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER B 72 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 178 through 180 removed outlier: 3.755A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA B 167 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL B 158 " --> pdb=" O ARG B 150 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 207 through 211 removed outlier: 3.850A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER B 201 " --> pdb=" O LYS B 209 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 240 through 242 removed outlier: 4.133A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 294 through 296 removed outlier: 3.580A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 47 through 51 removed outlier: 7.583A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 120 through 125 removed outlier: 3.505A pdb=" N CYS B 121 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) 307 hydrogen bonds defined for protein. 828 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: 1.94 Time building geometry restraints manager: 3.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2338 1.34 - 1.46: 1525 1.46 - 1.58: 3466 1.58 - 1.69: 0 1.69 - 1.81: 62 Bond restraints: 7391 Sorted by residual: bond pdb=" CB TYC P 36 " pdb=" CG TYC P 36 " ideal model delta sigma weight residual 1.528 1.389 0.139 2.00e-02 2.50e+03 4.84e+01 bond pdb=" C TYC P 36 " pdb=" NXT TYC P 36 " ideal model delta sigma weight residual 1.451 1.329 0.122 2.00e-02 2.50e+03 3.72e+01 bond pdb=" C TYC P 36 " pdb=" O TYC P 36 " ideal model delta sigma weight residual 1.185 1.231 -0.046 2.00e-02 2.50e+03 5.20e+00 bond pdb=" CZ TYC P 36 " pdb=" OH TYC P 36 " ideal model delta sigma weight residual 1.401 1.360 0.041 2.00e-02 2.50e+03 4.10e+00 bond pdb=" N TYC P 36 " pdb=" CA TYC P 36 " ideal model delta sigma weight residual 1.452 1.479 -0.027 2.00e-02 2.50e+03 1.76e+00 ... (remaining 7386 not shown) Histogram of bond angle deviations from ideal: 100.47 - 107.17: 174 107.17 - 113.87: 4263 113.87 - 120.57: 2842 120.57 - 127.27: 2693 127.27 - 133.97: 78 Bond angle restraints: 10050 Sorted by residual: angle pdb=" N ILE B 270 " pdb=" CA ILE B 270 " pdb=" C ILE B 270 " ideal model delta sigma weight residual 113.20 109.50 3.70 9.60e-01 1.09e+00 1.48e+01 angle pdb=" CE2 TYC P 36 " pdb=" CZ TYC P 36 " pdb=" OH TYC P 36 " ideal model delta sigma weight residual 129.45 120.01 9.44 3.00e+00 1.11e-01 9.90e+00 angle pdb=" CE1 TYC P 36 " pdb=" CZ TYC P 36 " pdb=" OH TYC P 36 " ideal model delta sigma weight residual 110.51 119.90 -9.39 3.00e+00 1.11e-01 9.80e+00 angle pdb=" N THR B 164 " pdb=" CA THR B 164 " pdb=" CB THR B 164 " ideal model delta sigma weight residual 113.65 109.47 4.18 1.47e+00 4.63e-01 8.07e+00 angle pdb=" C GLU R 210 " pdb=" N GLU R 211 " pdb=" CA GLU R 211 " ideal model delta sigma weight residual 121.54 126.72 -5.18 1.91e+00 2.74e-01 7.37e+00 ... (remaining 10045 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 4053 17.96 - 35.92: 262 35.92 - 53.88: 48 53.88 - 71.84: 5 71.84 - 89.80: 2 Dihedral angle restraints: 4370 sinusoidal: 1605 harmonic: 2765 Sorted by residual: dihedral pdb=" CB CYS R 123 " pdb=" SG CYS R 123 " pdb=" SG CYS R 203 " pdb=" CB CYS R 203 " ideal model delta sinusoidal sigma weight residual -86.00 -153.21 67.21 1 1.00e+01 1.00e-02 5.88e+01 dihedral pdb=" CA ASP B 298 " pdb=" CB ASP B 298 " pdb=" CG ASP B 298 " pdb=" OD1 ASP B 298 " ideal model delta sinusoidal sigma weight residual -30.00 -88.31 58.31 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CA SER A 326 " pdb=" C SER A 326 " pdb=" N THR A 327 " pdb=" CA THR A 327 " ideal model delta harmonic sigma weight residual 180.00 -164.58 -15.42 0 5.00e+00 4.00e-02 9.51e+00 ... (remaining 4367 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 691 0.027 - 0.054: 311 0.054 - 0.081: 107 0.081 - 0.109: 54 0.109 - 0.136: 20 Chirality restraints: 1183 Sorted by residual: chirality pdb=" CB ILE R 66 " pdb=" CA ILE R 66 " pdb=" CG1 ILE R 66 " pdb=" CG2 ILE R 66 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.60e-01 chirality pdb=" CA ILE R 194 " pdb=" N ILE R 194 " pdb=" C ILE R 194 " pdb=" CB ILE R 194 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.14e-01 chirality pdb=" CA ILE B 81 " pdb=" N ILE B 81 " pdb=" C ILE B 81 " pdb=" CB ILE B 81 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.05e-01 ... (remaining 1180 not shown) Planarity restraints: 1262 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS P 4 " 0.042 5.00e-02 4.00e+02 6.41e-02 6.57e+00 pdb=" N PRO P 5 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO P 5 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO P 5 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 226 " 0.008 2.00e-02 2.50e+03 1.53e-02 2.34e+00 pdb=" C ILE R 226 " -0.026 2.00e-02 2.50e+03 pdb=" O ILE R 226 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU R 227 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER R 238 " 0.006 2.00e-02 2.50e+03 1.28e-02 1.63e+00 pdb=" C SER R 238 " -0.022 2.00e-02 2.50e+03 pdb=" O SER R 238 " 0.008 2.00e-02 2.50e+03 pdb=" N TYR R 239 " 0.008 2.00e-02 2.50e+03 ... (remaining 1259 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 2114 2.81 - 3.33: 6994 3.33 - 3.85: 12060 3.85 - 4.38: 13545 4.38 - 4.90: 23546 Nonbonded interactions: 58259 Sorted by model distance: nonbonded pdb=" OH TYR A 290 " pdb=" OE2 GLU A 298 " model vdw 2.284 2.440 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.289 2.440 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.306 2.440 nonbonded pdb=" OD1 ASP A 341 " pdb=" NE2 HIS R 249 " model vdw 2.323 2.520 nonbonded pdb=" O ARG P 25 " pdb=" ND2 ASN P 29 " model vdw 2.324 2.520 ... (remaining 58254 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: 1.370 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: 4.720 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 24.010 Find NCS groups from input model: 0.270 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 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 : 0.003 0.139 7391 Z= 0.139 Angle : 0.529 9.438 10050 Z= 0.278 Chirality : 0.039 0.136 1183 Planarity : 0.003 0.064 1262 Dihedral : 12.106 89.805 2573 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.13 % Allowed : 3.17 % Favored : 96.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.52 (0.23), residues: 931 helix: -0.99 (0.23), residues: 398 sheet: -3.11 (0.39), residues: 137 loop : -3.48 (0.23), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 82 HIS 0.002 0.000 HIS B 142 PHE 0.010 0.001 PHE R 340 TYR 0.005 0.001 TYR R 228 ARG 0.001 0.000 ARG C 27 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 248 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.9007 (tm-30) cc_final: 0.8761 (tm-30) REVERT: A 25 GLU cc_start: 0.8852 (tm-30) cc_final: 0.8419 (tm-30) REVERT: A 33 GLU cc_start: 0.9020 (pp20) cc_final: 0.8485 (pp20) REVERT: A 191 PHE cc_start: 0.8324 (t80) cc_final: 0.8011 (t80) REVERT: A 195 HIS cc_start: 0.8167 (m-70) cc_final: 0.7646 (m-70) REVERT: A 224 CYS cc_start: 0.7098 (t) cc_final: 0.6577 (t) REVERT: A 261 ASP cc_start: 0.7874 (t0) cc_final: 0.7586 (t0) REVERT: A 276 GLU cc_start: 0.9229 (mp0) cc_final: 0.8954 (mp0) REVERT: A 337 ASP cc_start: 0.8219 (m-30) cc_final: 0.7875 (m-30) REVERT: B 266 HIS cc_start: 0.7811 (t-170) cc_final: 0.7355 (t-170) REVERT: B 339 TRP cc_start: 0.8625 (m100) cc_final: 0.7954 (m-10) REVERT: B 340 ASN cc_start: 0.7249 (t0) cc_final: 0.6573 (t0) REVERT: C 40 TYR cc_start: 0.8674 (t80) cc_final: 0.8463 (t80) REVERT: R 86 ASN cc_start: 0.8522 (m-40) cc_final: 0.8255 (m-40) REVERT: R 262 ARG cc_start: 0.7373 (mtp85) cc_final: 0.7040 (mtm180) REVERT: R 301 LYS cc_start: 0.8392 (tttt) cc_final: 0.8121 (ttmm) REVERT: P 34 GLN cc_start: 0.7893 (tm-30) cc_final: 0.7421 (tm-30) outliers start: 1 outliers final: 0 residues processed: 248 average time/residue: 0.2219 time to fit residues: 70.2340 Evaluate side-chains 166 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 38 optimal weight: 9.9990 chunk 23 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 27 optimal weight: 9.9990 chunk 43 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS B 176 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN R 100 ASN R 155 HIS ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 260 HIS R 261 GLN R 288 GLN R 311 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7391 Z= 0.190 Angle : 0.611 9.159 10050 Z= 0.306 Chirality : 0.043 0.260 1183 Planarity : 0.005 0.050 1262 Dihedral : 3.534 17.566 1018 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.30 % Allowed : 15.06 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.26), residues: 931 helix: 0.07 (0.26), residues: 398 sheet: -2.94 (0.35), residues: 169 loop : -2.94 (0.27), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 116 HIS 0.009 0.001 HIS R 73 PHE 0.016 0.001 PHE R 340 TYR 0.030 0.001 TYR P 21 ARG 0.007 0.001 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 190 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ARG cc_start: 0.8275 (ttt90) cc_final: 0.8015 (ttt90) REVERT: A 18 MET cc_start: 0.8237 (tpp) cc_final: 0.6780 (tpp) REVERT: A 21 ARG cc_start: 0.8751 (ttp80) cc_final: 0.7819 (ttp80) REVERT: A 33 GLU cc_start: 0.9039 (pp20) cc_final: 0.8562 (pp20) REVERT: A 191 PHE cc_start: 0.8284 (t80) cc_final: 0.8013 (t80) REVERT: A 205 ARG cc_start: 0.7726 (mtm-85) cc_final: 0.7506 (mtm-85) REVERT: A 261 ASP cc_start: 0.7895 (t0) cc_final: 0.7506 (t0) REVERT: A 276 GLU cc_start: 0.9295 (mp0) cc_final: 0.9015 (mp0) REVERT: A 337 ASP cc_start: 0.8377 (m-30) cc_final: 0.7820 (m-30) REVERT: B 17 GLN cc_start: 0.8138 (tm-30) cc_final: 0.7892 (tm-30) REVERT: B 72 SER cc_start: 0.8129 (m) cc_final: 0.7762 (p) REVERT: B 266 HIS cc_start: 0.7814 (t-170) cc_final: 0.7355 (t-170) REVERT: B 339 TRP cc_start: 0.8570 (m100) cc_final: 0.8278 (m100) REVERT: C 40 TYR cc_start: 0.8732 (t80) cc_final: 0.8499 (t80) REVERT: R 262 ARG cc_start: 0.7457 (mtp85) cc_final: 0.7132 (mtm-85) REVERT: R 301 LYS cc_start: 0.8436 (tttt) cc_final: 0.8198 (ttmm) REVERT: P 15 GLU cc_start: 0.8327 (pm20) cc_final: 0.7996 (pm20) outliers start: 25 outliers final: 14 residues processed: 204 average time/residue: 0.2171 time to fit residues: 57.7503 Evaluate side-chains 176 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 162 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 263 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 8.9990 chunk 25 optimal weight: 0.0010 chunk 69 optimal weight: 4.9990 chunk 56 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 67 optimal weight: 0.5980 overall best weight: 0.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS B 62 HIS B 88 ASN B 259 GLN R 135 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7391 Z= 0.164 Angle : 0.583 7.899 10050 Z= 0.289 Chirality : 0.043 0.200 1183 Planarity : 0.004 0.049 1262 Dihedral : 3.619 17.066 1018 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.96 % Allowed : 17.70 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.27), residues: 931 helix: 0.36 (0.26), residues: 394 sheet: -2.58 (0.39), residues: 161 loop : -2.54 (0.28), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 297 HIS 0.004 0.001 HIS B 91 PHE 0.017 0.001 PHE B 292 TYR 0.016 0.001 TYR P 20 ARG 0.006 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 180 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8874 (tm-30) cc_final: 0.8197 (pp20) REVERT: A 33 GLU cc_start: 0.8977 (pp20) cc_final: 0.8606 (pp20) REVERT: A 191 PHE cc_start: 0.8277 (t80) cc_final: 0.8026 (t80) REVERT: A 261 ASP cc_start: 0.7902 (t0) cc_final: 0.7480 (t0) REVERT: A 276 GLU cc_start: 0.9300 (mp0) cc_final: 0.8992 (mp0) REVERT: A 315 ASP cc_start: 0.7523 (p0) cc_final: 0.7224 (p0) REVERT: A 337 ASP cc_start: 0.8359 (m-30) cc_final: 0.7720 (m-30) REVERT: B 59 TYR cc_start: 0.8158 (m-80) cc_final: 0.7782 (m-80) REVERT: B 339 TRP cc_start: 0.8565 (m100) cc_final: 0.8309 (m100) REVERT: C 40 TYR cc_start: 0.8714 (t80) cc_final: 0.8468 (t80) REVERT: R 146 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8320 (mm) REVERT: R 262 ARG cc_start: 0.7458 (mtp85) cc_final: 0.7119 (mtm-85) REVERT: R 301 LYS cc_start: 0.8491 (tttt) cc_final: 0.8219 (ttmm) REVERT: R 302 GLU cc_start: 0.8357 (mm-30) cc_final: 0.8131 (mm-30) REVERT: P 21 TYR cc_start: 0.7624 (m-80) cc_final: 0.7374 (m-80) outliers start: 30 outliers final: 13 residues processed: 195 average time/residue: 0.1980 time to fit residues: 50.5787 Evaluate side-chains 179 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 165 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 146 LEU Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 204 THR Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 259 TYR Chi-restraints excluded: chain R residue 263 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 23 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 296 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7391 Z= 0.203 Angle : 0.592 7.689 10050 Z= 0.296 Chirality : 0.043 0.169 1183 Planarity : 0.004 0.049 1262 Dihedral : 3.777 19.120 1018 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 4.62 % Allowed : 18.63 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.27), residues: 931 helix: 0.43 (0.26), residues: 393 sheet: -2.39 (0.40), residues: 159 loop : -2.34 (0.29), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 297 HIS 0.003 0.001 HIS B 91 PHE 0.011 0.001 PHE A 250 TYR 0.018 0.001 TYR R 110 ARG 0.007 0.001 ARG P 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 167 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8901 (tm-30) cc_final: 0.8606 (pp20) REVERT: A 33 GLU cc_start: 0.9051 (pp20) cc_final: 0.8617 (pp20) REVERT: A 191 PHE cc_start: 0.8272 (t80) cc_final: 0.7991 (t80) REVERT: A 195 HIS cc_start: 0.8044 (m-70) cc_final: 0.7039 (m-70) REVERT: A 261 ASP cc_start: 0.7940 (t0) cc_final: 0.7509 (t0) REVERT: A 276 GLU cc_start: 0.9323 (mp0) cc_final: 0.8983 (mp0) REVERT: A 315 ASP cc_start: 0.7539 (p0) cc_final: 0.7215 (p0) REVERT: A 337 ASP cc_start: 0.8390 (m-30) cc_final: 0.7681 (m-30) REVERT: B 59 TYR cc_start: 0.8310 (m-80) cc_final: 0.7956 (m-80) REVERT: B 215 GLU cc_start: 0.8608 (mm-30) cc_final: 0.7907 (tm-30) REVERT: B 266 HIS cc_start: 0.7707 (t-170) cc_final: 0.7267 (t-170) REVERT: B 292 PHE cc_start: 0.7609 (m-10) cc_final: 0.7245 (m-80) REVERT: B 339 TRP cc_start: 0.8652 (m100) cc_final: 0.8349 (m100) REVERT: C 40 TYR cc_start: 0.8733 (t80) cc_final: 0.8475 (t80) REVERT: R 110 TYR cc_start: 0.8084 (t80) cc_final: 0.7861 (t80) REVERT: R 135 GLN cc_start: 0.8725 (mm-40) cc_final: 0.8263 (mm-40) REVERT: R 146 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8447 (mm) REVERT: R 262 ARG cc_start: 0.7532 (mtp85) cc_final: 0.7169 (mtm180) REVERT: R 301 LYS cc_start: 0.8485 (tttt) cc_final: 0.8184 (ttmm) outliers start: 35 outliers final: 23 residues processed: 190 average time/residue: 0.2016 time to fit residues: 51.2489 Evaluate side-chains 181 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 157 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 146 LEU Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 188 GLU Chi-restraints excluded: chain R residue 194 ILE Chi-restraints excluded: chain R residue 197 ASP Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 258 HIS Chi-restraints excluded: chain R residue 259 TYR Chi-restraints excluded: chain R residue 263 ARG Chi-restraints excluded: chain R residue 274 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 66 optimal weight: 8.9990 chunk 36 optimal weight: 10.0000 chunk 75 optimal weight: 0.0270 chunk 61 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 45 optimal weight: 8.9990 chunk 79 optimal weight: 0.8980 chunk 22 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 overall best weight: 1.7844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 100 ASN R 288 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7391 Z= 0.229 Angle : 0.594 8.102 10050 Z= 0.297 Chirality : 0.043 0.264 1183 Planarity : 0.004 0.047 1262 Dihedral : 3.915 18.866 1018 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 4.62 % Allowed : 20.74 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.27), residues: 931 helix: 0.46 (0.26), residues: 392 sheet: -2.18 (0.42), residues: 153 loop : -2.24 (0.29), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP R 116 HIS 0.005 0.001 HIS R 124 PHE 0.011 0.001 PHE A 250 TYR 0.013 0.001 TYR R 110 ARG 0.005 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 164 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.9041 (pp20) cc_final: 0.8628 (pp20) REVERT: A 35 LYS cc_start: 0.9006 (mppt) cc_final: 0.8568 (mptt) REVERT: A 191 PHE cc_start: 0.8266 (t80) cc_final: 0.7981 (t80) REVERT: A 195 HIS cc_start: 0.8060 (m-70) cc_final: 0.7068 (m-70) REVERT: A 261 ASP cc_start: 0.7949 (t0) cc_final: 0.7508 (t0) REVERT: A 276 GLU cc_start: 0.9323 (mp0) cc_final: 0.8956 (mp0) REVERT: A 315 ASP cc_start: 0.7557 (p0) cc_final: 0.7205 (p0) REVERT: A 337 ASP cc_start: 0.8490 (m-30) cc_final: 0.7740 (m-30) REVERT: B 59 TYR cc_start: 0.8381 (m-80) cc_final: 0.8105 (m-80) REVERT: B 215 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8011 (tm-30) REVERT: B 266 HIS cc_start: 0.7774 (t-170) cc_final: 0.7321 (t-170) REVERT: B 292 PHE cc_start: 0.7738 (m-10) cc_final: 0.7515 (m-80) REVERT: B 339 TRP cc_start: 0.8706 (m100) cc_final: 0.8392 (m100) REVERT: C 36 ASP cc_start: 0.8746 (m-30) cc_final: 0.8061 (t0) REVERT: C 40 TYR cc_start: 0.8755 (t80) cc_final: 0.8499 (t80) REVERT: R 146 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8513 (mm) REVERT: R 215 TYR cc_start: 0.7265 (m-80) cc_final: 0.6712 (t80) REVERT: R 256 ASN cc_start: 0.8219 (t0) cc_final: 0.7992 (t0) REVERT: R 262 ARG cc_start: 0.7608 (mtp85) cc_final: 0.7174 (mtm-85) REVERT: R 301 LYS cc_start: 0.8461 (tttt) cc_final: 0.8081 (ttmm) REVERT: R 302 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7900 (mp0) REVERT: P 21 TYR cc_start: 0.7992 (m-80) cc_final: 0.7550 (m-80) outliers start: 35 outliers final: 27 residues processed: 184 average time/residue: 0.1954 time to fit residues: 47.5532 Evaluate side-chains 182 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 154 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 146 LEU Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 194 ILE Chi-restraints excluded: chain R residue 197 ASP Chi-restraints excluded: chain R residue 204 THR Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 258 HIS Chi-restraints excluded: chain R residue 259 TYR Chi-restraints excluded: chain R residue 263 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 89 optimal weight: 30.0000 chunk 73 optimal weight: 0.2980 chunk 41 optimal weight: 6.9990 chunk 7 optimal weight: 0.7980 chunk 29 optimal weight: 9.9990 chunk 46 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 155 HIS R 288 GLN ** P 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7391 Z= 0.249 Angle : 0.613 11.916 10050 Z= 0.308 Chirality : 0.045 0.396 1183 Planarity : 0.004 0.046 1262 Dihedral : 4.078 22.491 1018 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 5.02 % Allowed : 21.66 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.27), residues: 931 helix: 0.55 (0.27), residues: 386 sheet: -2.05 (0.42), residues: 155 loop : -2.14 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP R 116 HIS 0.004 0.001 HIS B 142 PHE 0.010 0.001 PHE A 250 TYR 0.007 0.001 TYR B 105 ARG 0.006 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 160 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.8380 (pp20) REVERT: A 33 GLU cc_start: 0.9044 (pp20) cc_final: 0.8626 (pp20) REVERT: A 35 LYS cc_start: 0.9015 (mppt) cc_final: 0.8560 (mptt) REVERT: A 191 PHE cc_start: 0.8261 (t80) cc_final: 0.8012 (t80) REVERT: A 195 HIS cc_start: 0.8100 (m-70) cc_final: 0.7129 (m-70) REVERT: A 261 ASP cc_start: 0.8015 (t0) cc_final: 0.7589 (t0) REVERT: A 276 GLU cc_start: 0.9327 (mp0) cc_final: 0.8940 (mp0) REVERT: A 315 ASP cc_start: 0.7640 (p0) cc_final: 0.7256 (p0) REVERT: A 337 ASP cc_start: 0.8482 (m-30) cc_final: 0.7737 (m-30) REVERT: B 215 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8010 (tm-30) REVERT: B 266 HIS cc_start: 0.7825 (t-170) cc_final: 0.7352 (t-170) REVERT: B 284 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8369 (pp) REVERT: B 339 TRP cc_start: 0.8729 (m100) cc_final: 0.8378 (m100) REVERT: C 36 ASP cc_start: 0.8775 (m-30) cc_final: 0.8103 (t0) REVERT: C 40 TYR cc_start: 0.8751 (t80) cc_final: 0.8478 (t80) REVERT: R 116 TRP cc_start: 0.7817 (t60) cc_final: 0.7526 (t60) REVERT: R 146 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8564 (mm) REVERT: R 262 ARG cc_start: 0.7624 (mtp85) cc_final: 0.7221 (mtm-85) REVERT: R 301 LYS cc_start: 0.8445 (tttt) cc_final: 0.8115 (ttmm) outliers start: 38 outliers final: 27 residues processed: 183 average time/residue: 0.2047 time to fit residues: 49.2793 Evaluate side-chains 186 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 156 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 146 LEU Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 194 ILE Chi-restraints excluded: chain R residue 197 ASP Chi-restraints excluded: chain R residue 204 THR Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 258 HIS Chi-restraints excluded: chain R residue 259 TYR Chi-restraints excluded: chain R residue 263 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 65 optimal weight: 0.8980 chunk 74 optimal weight: 9.9990 chunk 49 optimal weight: 0.8980 chunk 88 optimal weight: 8.9990 chunk 55 optimal weight: 20.0000 chunk 54 optimal weight: 0.7980 chunk 40 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 52 optimal weight: 0.0970 overall best weight: 1.1380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 155 HIS ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 288 GLN P 26 HIS ** P 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7391 Z= 0.192 Angle : 0.623 13.716 10050 Z= 0.311 Chirality : 0.044 0.396 1183 Planarity : 0.004 0.043 1262 Dihedral : 4.052 22.545 1018 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 4.10 % Allowed : 23.12 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.28), residues: 931 helix: 0.63 (0.27), residues: 384 sheet: -1.98 (0.43), residues: 153 loop : -1.96 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 297 HIS 0.003 0.001 HIS B 183 PHE 0.009 0.001 PHE B 292 TYR 0.031 0.001 TYR P 21 ARG 0.011 0.001 ARG P 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 160 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8423 (pp20) REVERT: A 33 GLU cc_start: 0.9031 (pp20) cc_final: 0.8625 (pp20) REVERT: A 35 LYS cc_start: 0.8999 (mppt) cc_final: 0.8549 (mptt) REVERT: A 195 HIS cc_start: 0.8060 (m-70) cc_final: 0.7749 (m-70) REVERT: A 261 ASP cc_start: 0.8004 (t0) cc_final: 0.7626 (t0) REVERT: A 276 GLU cc_start: 0.9304 (mp0) cc_final: 0.8925 (mp0) REVERT: A 315 ASP cc_start: 0.7648 (p0) cc_final: 0.7262 (p0) REVERT: A 337 ASP cc_start: 0.8499 (m-30) cc_final: 0.7750 (m-30) REVERT: B 78 LYS cc_start: 0.8175 (mmmt) cc_final: 0.7456 (mmmt) REVERT: B 215 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8023 (tm-30) REVERT: B 266 HIS cc_start: 0.7786 (t-170) cc_final: 0.7319 (t-170) REVERT: B 292 PHE cc_start: 0.7866 (m-80) cc_final: 0.7505 (m-80) REVERT: B 339 TRP cc_start: 0.8679 (m100) cc_final: 0.8350 (m100) REVERT: C 36 ASP cc_start: 0.8756 (m-30) cc_final: 0.8106 (t0) REVERT: C 40 TYR cc_start: 0.8735 (t80) cc_final: 0.8453 (t80) REVERT: R 116 TRP cc_start: 0.7728 (t-100) cc_final: 0.7508 (t60) REVERT: R 146 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8557 (mm) REVERT: R 262 ARG cc_start: 0.7592 (mtp85) cc_final: 0.7176 (mtm-85) REVERT: R 301 LYS cc_start: 0.8407 (tttt) cc_final: 0.8031 (ttmm) REVERT: P 20 TYR cc_start: 0.8067 (t80) cc_final: 0.7846 (t80) outliers start: 31 outliers final: 25 residues processed: 179 average time/residue: 0.2195 time to fit residues: 51.8895 Evaluate side-chains 180 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 153 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 146 LEU Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 194 ILE Chi-restraints excluded: chain R residue 197 ASP Chi-restraints excluded: chain R residue 204 THR Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 259 TYR Chi-restraints excluded: chain R residue 263 ARG Chi-restraints excluded: chain R residue 298 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 4.9990 chunk 17 optimal weight: 0.3980 chunk 56 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 80 optimal weight: 0.1980 chunk 84 optimal weight: 0.0770 chunk 77 optimal weight: 0.9990 chunk 82 optimal weight: 0.3980 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 155 HIS ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 288 GLN ** P 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7391 Z= 0.160 Angle : 0.635 15.208 10050 Z= 0.309 Chirality : 0.044 0.455 1183 Planarity : 0.004 0.045 1262 Dihedral : 4.003 24.253 1018 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 3.04 % Allowed : 25.36 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.28), residues: 931 helix: 0.63 (0.27), residues: 392 sheet: -1.77 (0.43), residues: 153 loop : -1.89 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 297 HIS 0.004 0.001 HIS P 26 PHE 0.010 0.001 PHE A 191 TYR 0.017 0.001 TYR R 110 ARG 0.009 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 167 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8490 (pp20) REVERT: A 33 GLU cc_start: 0.9020 (pp20) cc_final: 0.8272 (pp20) REVERT: A 35 LYS cc_start: 0.8974 (mppt) cc_final: 0.8596 (mptt) REVERT: A 195 HIS cc_start: 0.8062 (m-70) cc_final: 0.6906 (m-70) REVERT: A 208 ARG cc_start: 0.8399 (mtm110) cc_final: 0.8020 (ttp80) REVERT: A 261 ASP cc_start: 0.7968 (t0) cc_final: 0.7608 (t0) REVERT: A 276 GLU cc_start: 0.9285 (mp0) cc_final: 0.8920 (mp0) REVERT: A 315 ASP cc_start: 0.7680 (p0) cc_final: 0.7302 (p0) REVERT: A 337 ASP cc_start: 0.8463 (m-30) cc_final: 0.7749 (m-30) REVERT: B 78 LYS cc_start: 0.8043 (mmmt) cc_final: 0.7402 (mmmt) REVERT: B 215 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8036 (tm-30) REVERT: B 266 HIS cc_start: 0.7644 (t-170) cc_final: 0.7216 (t-170) REVERT: B 292 PHE cc_start: 0.7772 (m-80) cc_final: 0.7445 (m-80) REVERT: B 339 TRP cc_start: 0.8603 (m100) cc_final: 0.8344 (m100) REVERT: C 36 ASP cc_start: 0.8685 (m-30) cc_final: 0.8046 (t0) REVERT: C 40 TYR cc_start: 0.8727 (t80) cc_final: 0.8428 (t80) REVERT: R 146 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8518 (mm) REVERT: R 215 TYR cc_start: 0.7286 (m-80) cc_final: 0.6729 (t80) REVERT: R 262 ARG cc_start: 0.7477 (mtp85) cc_final: 0.7068 (mtm-85) REVERT: R 301 LYS cc_start: 0.8363 (tttt) cc_final: 0.8049 (ttmm) REVERT: P 19 ARG cc_start: 0.8286 (ttm110) cc_final: 0.7628 (mtm-85) REVERT: P 21 TYR cc_start: 0.7912 (m-80) cc_final: 0.7499 (m-80) outliers start: 23 outliers final: 16 residues processed: 181 average time/residue: 0.1983 time to fit residues: 47.4553 Evaluate side-chains 174 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 156 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 146 LEU Chi-restraints excluded: chain R residue 194 ILE Chi-restraints excluded: chain R residue 204 THR Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 263 ARG Chi-restraints excluded: chain R residue 298 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 6.9990 chunk 49 optimal weight: 0.3980 chunk 35 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 25 optimal weight: 6.9990 chunk 74 optimal weight: 7.9990 chunk 78 optimal weight: 0.0570 chunk 82 optimal weight: 0.0030 chunk 54 optimal weight: 6.9990 chunk 87 optimal weight: 0.1980 chunk 53 optimal weight: 3.9990 overall best weight: 0.3108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7391 Z= 0.161 Angle : 0.650 15.410 10050 Z= 0.317 Chirality : 0.045 0.436 1183 Planarity : 0.004 0.045 1262 Dihedral : 3.976 25.330 1018 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 2.77 % Allowed : 26.68 % Favored : 70.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.28), residues: 931 helix: 0.64 (0.27), residues: 397 sheet: -1.78 (0.42), residues: 161 loop : -1.86 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 82 HIS 0.005 0.001 HIS P 26 PHE 0.009 0.001 PHE A 191 TYR 0.015 0.001 TYR A 230 ARG 0.009 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 162 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8879 (OUTLIER) cc_final: 0.8495 (pp20) REVERT: A 33 GLU cc_start: 0.9019 (pp20) cc_final: 0.8256 (pp20) REVERT: A 35 LYS cc_start: 0.8973 (mppt) cc_final: 0.8589 (mptt) REVERT: A 208 ARG cc_start: 0.8327 (mtm110) cc_final: 0.7983 (ttp80) REVERT: A 261 ASP cc_start: 0.7953 (t0) cc_final: 0.7636 (t0) REVERT: A 276 GLU cc_start: 0.9277 (mp0) cc_final: 0.8965 (mp0) REVERT: A 315 ASP cc_start: 0.7684 (p0) cc_final: 0.7298 (p0) REVERT: A 337 ASP cc_start: 0.8455 (m-30) cc_final: 0.7744 (m-30) REVERT: B 59 TYR cc_start: 0.7908 (m-80) cc_final: 0.7595 (m-80) REVERT: B 215 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8040 (tm-30) REVERT: B 266 HIS cc_start: 0.7577 (t-170) cc_final: 0.7178 (t-170) REVERT: B 292 PHE cc_start: 0.7697 (m-80) cc_final: 0.7364 (m-80) REVERT: B 339 TRP cc_start: 0.8619 (m100) cc_final: 0.8418 (m100) REVERT: C 36 ASP cc_start: 0.8706 (m-30) cc_final: 0.8066 (t0) REVERT: C 40 TYR cc_start: 0.8737 (t80) cc_final: 0.8438 (t80) REVERT: R 146 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8478 (mm) REVERT: R 215 TYR cc_start: 0.7272 (m-80) cc_final: 0.6724 (t80) REVERT: R 262 ARG cc_start: 0.7441 (mtp85) cc_final: 0.7021 (mtm180) REVERT: R 301 LYS cc_start: 0.8298 (tttt) cc_final: 0.7938 (ttmm) REVERT: P 21 TYR cc_start: 0.7932 (m-80) cc_final: 0.7504 (m-80) outliers start: 21 outliers final: 18 residues processed: 173 average time/residue: 0.2000 time to fit residues: 45.6662 Evaluate side-chains 170 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 150 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 146 LEU Chi-restraints excluded: chain R residue 188 GLU Chi-restraints excluded: chain R residue 194 ILE Chi-restraints excluded: chain R residue 204 THR Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 291 VAL Chi-restraints excluded: chain R residue 298 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 9.9990 chunk 60 optimal weight: 0.5980 chunk 91 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 57 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN B 119 ASN ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7391 Z= 0.193 Angle : 0.654 15.426 10050 Z= 0.320 Chirality : 0.045 0.442 1183 Planarity : 0.004 0.044 1262 Dihedral : 4.089 26.534 1018 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 2.91 % Allowed : 26.82 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.28), residues: 931 helix: 0.72 (0.27), residues: 390 sheet: -1.71 (0.42), residues: 160 loop : -1.72 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 82 HIS 0.006 0.001 HIS B 91 PHE 0.019 0.001 PHE R 307 TYR 0.014 0.001 TYR R 228 ARG 0.009 0.001 ARG A 21 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 158 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8558 (pp20) REVERT: A 33 GLU cc_start: 0.9029 (pp20) cc_final: 0.8260 (pp20) REVERT: A 35 LYS cc_start: 0.9011 (mppt) cc_final: 0.8624 (mptt) REVERT: A 208 ARG cc_start: 0.8342 (mtm110) cc_final: 0.7970 (ttp80) REVERT: A 261 ASP cc_start: 0.8016 (t0) cc_final: 0.7667 (t0) REVERT: A 276 GLU cc_start: 0.9279 (mp0) cc_final: 0.8972 (mp0) REVERT: A 315 ASP cc_start: 0.7722 (p0) cc_final: 0.7340 (p0) REVERT: A 337 ASP cc_start: 0.8505 (m-30) cc_final: 0.7789 (m-30) REVERT: B 59 TYR cc_start: 0.8140 (m-80) cc_final: 0.7789 (m-80) REVERT: B 78 LYS cc_start: 0.8076 (mmmt) cc_final: 0.7508 (mmmt) REVERT: B 215 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8046 (tm-30) REVERT: B 266 HIS cc_start: 0.7608 (t-170) cc_final: 0.7193 (t-170) REVERT: B 292 PHE cc_start: 0.7848 (m-80) cc_final: 0.7519 (m-80) REVERT: B 339 TRP cc_start: 0.8626 (m100) cc_final: 0.8391 (m100) REVERT: C 36 ASP cc_start: 0.8701 (m-30) cc_final: 0.8052 (t0) REVERT: C 40 TYR cc_start: 0.8743 (t80) cc_final: 0.8445 (t80) REVERT: R 116 TRP cc_start: 0.7491 (t-100) cc_final: 0.7252 (t-100) REVERT: R 146 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8556 (mm) REVERT: R 215 TYR cc_start: 0.7298 (m-80) cc_final: 0.6748 (t80) REVERT: R 262 ARG cc_start: 0.7460 (mtp85) cc_final: 0.7032 (mtm180) REVERT: R 301 LYS cc_start: 0.8319 (tttt) cc_final: 0.8019 (ttmm) REVERT: P 19 ARG cc_start: 0.8224 (ttm110) cc_final: 0.7705 (mtm-85) REVERT: P 21 TYR cc_start: 0.7983 (m-80) cc_final: 0.7541 (m-80) outliers start: 22 outliers final: 17 residues processed: 170 average time/residue: 0.2029 time to fit residues: 45.5249 Evaluate side-chains 170 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 151 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 146 LEU Chi-restraints excluded: chain R residue 194 ILE Chi-restraints excluded: chain R residue 204 THR Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 232 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 0.0030 chunk 10 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 73 optimal weight: 8.9990 chunk 30 optimal weight: 0.2980 chunk 75 optimal weight: 8.9990 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 34 GLN ** 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 = 0.3910 r_free = 0.3910 target = 0.122688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.097424 restraints weight = 16211.398| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 3.93 r_work: 0.3412 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7391 Z= 0.172 Angle : 0.658 15.606 10050 Z= 0.319 Chirality : 0.044 0.437 1183 Planarity : 0.004 0.041 1262 Dihedral : 4.045 25.194 1018 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 2.77 % Allowed : 27.48 % Favored : 69.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.28), residues: 931 helix: 0.62 (0.27), residues: 395 sheet: -1.62 (0.43), residues: 155 loop : -1.72 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 82 HIS 0.008 0.001 HIS B 91 PHE 0.009 0.001 PHE R 319 TYR 0.018 0.001 TYR R 110 ARG 0.011 0.001 ARG A 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2121.60 seconds wall clock time: 39 minutes 22.34 seconds (2362.34 seconds total)