Starting phenix.real_space_refine on Sat Apr 6 18:15:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6b_25712/04_2024/7t6b_25712_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6b_25712/04_2024/7t6b_25712.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6b_25712/04_2024/7t6b_25712_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6b_25712/04_2024/7t6b_25712_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6b_25712/04_2024/7t6b_25712_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6b_25712/04_2024/7t6b_25712.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6b_25712/04_2024/7t6b_25712.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6b_25712/04_2024/7t6b_25712_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6b_25712/04_2024/7t6b_25712_updated.pdb" } resolution = 3.19 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= 0.109 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 55 5.16 5 C 5571 2.51 5 N 1497 2.21 5 O 1631 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 69": "NH1" <-> "NH2" Residue "A GLU 212": "OE1" <-> "OE2" Residue "A ARG 230": "NH1" <-> "NH2" Residue "A ARG 232": "NH1" <-> "NH2" Residue "A ASP 315": "OD1" <-> "OD2" Residue "A ASP 336": "OD1" <-> "OD2" Residue "A PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 356": "NH1" <-> "NH2" Residue "A ASP 369": "OD1" <-> "OD2" Residue "C TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 195": "OD1" <-> "OD2" Residue "C GLU 226": "OE1" <-> "OE2" Residue "C ASP 254": "OD1" <-> "OD2" Residue "C ASP 312": "OD1" <-> "OD2" Residue "D GLU 22": "OE1" <-> "OE2" Residue "D ASP 26": "OD1" <-> "OD2" Residue "E PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 42": "OE1" <-> "OE2" Residue "E ASP 73": "OD1" <-> "OD2" Residue "E GLU 89": "OE1" <-> "OE2" Residue "E GLU 220": "OE1" <-> "OE2" Residue "E GLU 222": "OE1" <-> "OE2" Residue "E ASP 223": "OD1" <-> "OD2" Residue "R GLU 16": "OE1" <-> "OE2" Residue "R ARG 33": "NH1" <-> "NH2" Residue "R PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 50": "OE1" <-> "OE2" Residue "R ARG 60": "NH1" <-> "NH2" Residue "R PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 79": "OD1" <-> "OD2" Residue "R ARG 147": "NH1" <-> "NH2" Residue "R GLU 177": "OE1" <-> "OE2" Residue "R TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 256": "OD1" <-> "OD2" Residue "R PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 8755 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1849 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 225, 1848 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 3, 'TRANS': 221} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 225, 1848 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 3, 'TRANS': 221} Chain breaks: 2 bond proxies already assigned to first conformer: 1874 Chain: "C" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "D" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 454 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 4, 'TRANS': 54} Chain: "E" Number of atoms: 1782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1782 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "R" Number of atoms: 2063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2063 Unusual residues: {'S1P': 1} Classifications: {'peptide': 264, 'undetermined': 1} Link IDs: {'PTRANS': 7, 'TRANS': 256, None: 1} Not linked: pdbres="TRP R 290 " pdbres="S1P R 401 " Chain breaks: 2 Time building chain proxies: 5.70, per 1000 atoms: 0.65 Number of scatterers: 8755 At special positions: 0 Unit cell: (99.356, 121.248, 114.512, 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 55 16.00 P 1 15.00 O 1631 8.00 N 1497 7.00 C 5571 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.04 Simple disulfide: pdb=" SG CYS R 172 " - pdb=" SG CYS R 179 " distance=2.03 Simple disulfide: pdb=" SG CYS R 259 " - pdb=" SG CYS R 264 " 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: 3.18 Conformation dependent library (CDL) restraints added in 1.7 seconds 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2096 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 19 helices and 16 sheets defined 30.4% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 7 through 28 Processing helix chain 'A' and resid 61 through 71 Processing helix chain 'A' and resid 264 through 276 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 320 through 333 removed outlier: 4.742A pdb=" N LYS A 333 " --> pdb=" O CYS A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 373 removed outlier: 4.239A pdb=" N LYS A 372 " --> pdb=" O HIS A 368 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN A 373 " --> pdb=" O ASP A 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 25 removed outlier: 3.824A pdb=" N CYS C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 23 Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'R' and resid 14 through 21 removed outlier: 3.917A pdb=" N THR R 21 " --> pdb=" O HIS R 17 " (cutoff:3.500A) Processing helix chain 'R' and resid 34 through 60 removed outlier: 4.124A pdb=" N ALA R 38 " --> pdb=" O GLN R 34 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N PHE R 39 " --> pdb=" O VAL R 35 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE R 40 " --> pdb=" O ALA R 36 " (cutoff:3.500A) Processing helix chain 'R' and resid 68 through 93 removed outlier: 3.705A pdb=" N ASN R 74 " --> pdb=" O LEU R 70 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU R 75 " --> pdb=" O PHE R 71 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N PHE R 86 " --> pdb=" O ALA R 82 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU R 91 " --> pdb=" O VAL R 87 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N LEU R 92 " --> pdb=" O ALA R 88 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER R 93 " --> pdb=" O ASN R 89 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 135 removed outlier: 3.826A pdb=" N THR R 115 " --> pdb=" O SER R 111 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU R 116 " --> pdb=" O ALA R 112 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER R 119 " --> pdb=" O THR R 115 " (cutoff:3.500A) Processing helix chain 'R' and resid 147 through 164 Processing helix chain 'R' and resid 190 through 218 Processing helix chain 'R' and resid 229 through 258 removed outlier: 3.709A pdb=" N LYS R 233 " --> pdb=" O LEU R 229 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N THR R 234 " --> pdb=" O ALA R 230 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N VAL R 238 " --> pdb=" O THR R 234 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N LEU R 239 " --> pdb=" O VAL R 235 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N GLY R 240 " --> pdb=" O THR R 236 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N VAL R 241 " --> pdb=" O ILE R 237 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N PHE R 242 " --> pdb=" O VAL R 238 " (cutoff:3.500A) Proline residue: R 248 - end of helix Processing helix chain 'R' and resid 267 through 287 removed outlier: 4.986A pdb=" N HIS R 271 " --> pdb=" O TYR R 268 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ASN R 280 " --> pdb=" O SER R 277 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ASN R 284 " --> pdb=" O SER R 281 " (cutoff:3.500A) Proline residue: R 285 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 48 through 53 removed outlier: 7.613A pdb=" N ILE A 51 " --> pdb=" O PRO A 217 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LYS A 219 " --> pdb=" O ILE A 51 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N LEU A 53 " --> pdb=" O LYS A 219 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL A 221 " --> pdb=" O LEU A 53 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 244 through 248 removed outlier: 6.302A pdb=" N ILE A 287 " --> pdb=" O PHE A 245 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N VAL A 247 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N PHE A 289 " --> pdb=" O VAL A 247 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'C' and resid 100 through 103 removed outlier: 7.011A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.942A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 190 through 192 removed outlier: 4.469A pdb=" N SER C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 294 through 298 removed outlier: 3.546A pdb=" N ALA C 287 " --> pdb=" O ASN C 295 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 327 through 330 removed outlier: 3.645A pdb=" N ARG C 49 " --> pdb=" O ILE C 338 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 58 through 63 removed outlier: 7.005A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 78 through 82 removed outlier: 3.526A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.568A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 250 through 254 removed outlier: 3.828A pdb=" N LEU C 252 " --> pdb=" O MET C 262 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= M, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.578A pdb=" N THR E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 95 through 99 removed outlier: 3.564A pdb=" N ALA E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.597A pdb=" N LYS E 244 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 155 through 159 removed outlier: 3.559A pdb=" N THR E 213 " --> pdb=" O SER E 206 " (cutoff:3.500A) 344 hydrogen bonds defined for protein. 945 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: 2.32 Time building geometry restraints manager: 3.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2834 1.35 - 1.48: 2215 1.48 - 1.60: 3795 1.60 - 1.73: 1 1.73 - 1.86: 78 Bond restraints: 8923 Sorted by residual: bond pdb=" O1 S1P R 401 " pdb=" P22 S1P R 401 " ideal model delta sigma weight residual 1.661 1.858 -0.197 2.00e-02 2.50e+03 9.72e+01 bond pdb=" C1 S1P R 401 " pdb=" C2 S1P R 401 " ideal model delta sigma weight residual 1.535 1.609 -0.074 2.00e-02 2.50e+03 1.35e+01 bond pdb=" C1 S1P R 401 " pdb=" O1 S1P R 401 " ideal model delta sigma weight residual 1.405 1.355 0.050 2.00e-02 2.50e+03 6.35e+00 bond pdb=" C5 S1P R 401 " pdb=" C6 S1P R 401 " ideal model delta sigma weight residual 1.550 1.509 0.041 2.00e-02 2.50e+03 4.24e+00 bond pdb=" C2 S1P R 401 " pdb=" C3 S1P R 401 " ideal model delta sigma weight residual 1.527 1.568 -0.041 2.00e-02 2.50e+03 4.21e+00 ... (remaining 8918 not shown) Histogram of bond angle deviations from ideal: 98.75 - 105.81: 129 105.81 - 112.87: 4799 112.87 - 119.93: 3034 119.93 - 126.99: 4025 126.99 - 134.06: 96 Bond angle restraints: 12083 Sorted by residual: angle pdb=" N VAL A 302 " pdb=" CA VAL A 302 " pdb=" C VAL A 302 " ideal model delta sigma weight residual 113.53 110.61 2.92 9.80e-01 1.04e+00 8.87e+00 angle pdb=" O1 S1P R 401 " pdb=" P22 S1P R 401 " pdb=" O23 S1P R 401 " ideal model delta sigma weight residual 109.50 100.64 8.86 3.00e+00 1.11e-01 8.73e+00 angle pdb=" CA GLY C 115 " pdb=" C GLY C 115 " pdb=" N GLY C 116 " ideal model delta sigma weight residual 114.58 117.09 -2.51 8.60e-01 1.35e+00 8.55e+00 angle pdb=" CA LEU A 54 " pdb=" CB LEU A 54 " pdb=" CG LEU A 54 " ideal model delta sigma weight residual 116.30 126.52 -10.22 3.50e+00 8.16e-02 8.52e+00 angle pdb=" N SER C 275 " pdb=" CA SER C 275 " pdb=" C SER C 275 " ideal model delta sigma weight residual 108.32 112.94 -4.62 1.64e+00 3.72e-01 7.93e+00 ... (remaining 12078 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 4751 18.01 - 36.01: 466 36.01 - 54.02: 81 54.02 - 72.03: 14 72.03 - 90.03: 5 Dihedral angle restraints: 5317 sinusoidal: 2074 harmonic: 3243 Sorted by residual: dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 96 " pdb=" CB CYS E 96 " ideal model delta sinusoidal sigma weight residual 93.00 156.86 -63.86 1 1.00e+01 1.00e-02 5.37e+01 dihedral pdb=" CA VAL R 238 " pdb=" C VAL R 238 " pdb=" N LEU R 239 " pdb=" CA LEU R 239 " ideal model delta harmonic sigma weight residual 180.00 150.01 29.99 0 5.00e+00 4.00e-02 3.60e+01 dihedral pdb=" CA ALA A 349 " pdb=" C ALA A 349 " pdb=" N ILE A 350 " pdb=" CA ILE A 350 " ideal model delta harmonic sigma weight residual -180.00 -152.44 -27.56 0 5.00e+00 4.00e-02 3.04e+01 ... (remaining 5314 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 841 0.036 - 0.072: 393 0.072 - 0.108: 120 0.108 - 0.144: 35 0.144 - 0.181: 8 Chirality restraints: 1397 Sorted by residual: chirality pdb=" CA VAL C 327 " pdb=" N VAL C 327 " pdb=" C VAL C 327 " pdb=" CB VAL C 327 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.15e-01 chirality pdb=" CA PRO E 41 " pdb=" N PRO E 41 " pdb=" C PRO E 41 " pdb=" CB PRO E 41 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.32e-01 chirality pdb=" CB THR D 52 " pdb=" CA THR D 52 " pdb=" OG1 THR D 52 " pdb=" CG2 THR D 52 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.95e-01 ... (remaining 1394 not shown) Planarity restraints: 1519 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 48 " 0.036 5.00e-02 4.00e+02 5.42e-02 4.70e+00 pdb=" N PRO D 49 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO D 49 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 49 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 235 " 0.035 5.00e-02 4.00e+02 5.23e-02 4.37e+00 pdb=" N PRO C 236 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO C 236 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 236 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 165 " 0.034 5.00e-02 4.00e+02 5.08e-02 4.13e+00 pdb=" N PRO R 166 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO R 166 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO R 166 " 0.029 5.00e-02 4.00e+02 ... (remaining 1516 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 658 2.74 - 3.28: 8459 3.28 - 3.82: 13692 3.82 - 4.36: 16731 4.36 - 4.90: 29407 Nonbonded interactions: 68947 Sorted by model distance: nonbonded pdb=" O THR R 278 " pdb=" OG SER R 281 " model vdw 2.195 2.440 nonbonded pdb=" OG SER C 161 " pdb=" OD1 ASP C 163 " model vdw 2.245 2.440 nonbonded pdb=" O LEU R 162 " pdb=" OH TYR R 190 " model vdw 2.254 2.440 nonbonded pdb=" OG SER C 331 " pdb=" OD1 ASP C 333 " model vdw 2.258 2.440 nonbonded pdb=" OG SER C 281 " pdb=" OD2 ASP D 48 " model vdw 2.296 2.440 ... (remaining 68942 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 1.030 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: 5.460 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 26.930 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 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 : 0.005 0.197 8923 Z= 0.312 Angle : 0.802 10.217 12083 Z= 0.422 Chirality : 0.047 0.181 1397 Planarity : 0.005 0.054 1519 Dihedral : 14.475 90.032 3209 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.21 % Allowed : 4.47 % Favored : 95.32 % 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: -3.82 (0.21), residues: 1099 helix: -1.34 (0.24), residues: 362 sheet: -2.95 (0.27), residues: 277 loop : -3.16 (0.23), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 211 HIS 0.007 0.001 HIS C 91 PHE 0.018 0.002 PHE A 234 TYR 0.016 0.002 TYR C 59 ARG 0.005 0.000 ARG A 47 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 127 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 334 ARG cc_start: 0.5998 (pmt-80) cc_final: 0.5368 (pmt-80) REVERT: A 340 LYS cc_start: 0.7121 (ptmt) cc_final: 0.6253 (mmmt) REVERT: A 369 ASP cc_start: 0.8047 (t0) cc_final: 0.7473 (t0) REVERT: C 42 ARG cc_start: 0.7710 (tpt-90) cc_final: 0.7499 (tpt170) REVERT: C 46 ARG cc_start: 0.7479 (ttt-90) cc_final: 0.6891 (mtp85) REVERT: C 204 CYS cc_start: 0.7246 (t) cc_final: 0.6588 (t) REVERT: D 62 ARG cc_start: 0.6013 (tpm170) cc_final: 0.5685 (ttp-170) outliers start: 2 outliers final: 0 residues processed: 129 average time/residue: 0.2312 time to fit residues: 40.2690 Evaluate side-chains 100 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 55 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 98 optimal weight: 20.0000 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 GLN C 6 GLN C 91 HIS ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 GLN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 GLN E 232 HIS ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 175 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.0943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8923 Z= 0.250 Angle : 0.575 7.445 12083 Z= 0.300 Chirality : 0.042 0.150 1397 Planarity : 0.004 0.045 1519 Dihedral : 6.108 84.985 1224 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 1.14 % Allowed : 11.45 % Favored : 87.41 % 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: -2.68 (0.23), residues: 1099 helix: 0.09 (0.27), residues: 363 sheet: -2.57 (0.28), residues: 277 loop : -2.76 (0.24), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 211 HIS 0.006 0.001 HIS C 91 PHE 0.013 0.002 PHE A 234 TYR 0.016 0.002 TYR C 105 ARG 0.002 0.000 ARG D 13 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 105 time to evaluate : 0.911 Fit side-chains REVERT: A 334 ARG cc_start: 0.5921 (pmt-80) cc_final: 0.5278 (pmt-80) REVERT: A 340 LYS cc_start: 0.7102 (ptmt) cc_final: 0.6263 (mmmt) REVERT: A 369 ASP cc_start: 0.8030 (t0) cc_final: 0.7493 (t0) REVERT: C 46 ARG cc_start: 0.7270 (ttt-90) cc_final: 0.6799 (mtp85) REVERT: C 59 TYR cc_start: 0.8460 (m-80) cc_final: 0.8096 (m-80) REVERT: C 204 CYS cc_start: 0.7303 (t) cc_final: 0.6843 (t) REVERT: D 52 THR cc_start: 0.8251 (OUTLIER) cc_final: 0.7920 (p) REVERT: D 62 ARG cc_start: 0.6191 (tpm170) cc_final: 0.5688 (ttp80) outliers start: 11 outliers final: 7 residues processed: 110 average time/residue: 0.2396 time to fit residues: 35.6178 Evaluate side-chains 104 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 96 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain R residue 277 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 6.9990 chunk 30 optimal weight: 0.0170 chunk 82 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 99 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 79 optimal weight: 0.4980 overall best weight: 0.8620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8923 Z= 0.187 Angle : 0.520 8.032 12083 Z= 0.272 Chirality : 0.041 0.139 1397 Planarity : 0.003 0.040 1519 Dihedral : 5.710 82.654 1224 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.77 % Allowed : 13.84 % Favored : 84.39 % 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: -2.00 (0.24), residues: 1099 helix: 0.74 (0.28), residues: 365 sheet: -2.23 (0.28), residues: 288 loop : -2.43 (0.26), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 211 HIS 0.005 0.001 HIS E 232 PHE 0.010 0.001 PHE A 234 TYR 0.012 0.001 TYR E 190 ARG 0.003 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 107 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.7041 (ptmt) cc_final: 0.6214 (mmmt) REVERT: A 369 ASP cc_start: 0.7930 (t0) cc_final: 0.7429 (t0) REVERT: C 46 ARG cc_start: 0.7273 (ttt-90) cc_final: 0.6757 (mtp85) REVERT: C 59 TYR cc_start: 0.8442 (m-80) cc_final: 0.8142 (m-80) REVERT: C 153 ASP cc_start: 0.7416 (m-30) cc_final: 0.7179 (m-30) REVERT: C 204 CYS cc_start: 0.7305 (t) cc_final: 0.6815 (t) REVERT: D 52 THR cc_start: 0.8251 (OUTLIER) cc_final: 0.7927 (p) REVERT: D 62 ARG cc_start: 0.6161 (tpm170) cc_final: 0.5715 (ttp80) REVERT: E 113 GLN cc_start: 0.7893 (mm-40) cc_final: 0.7691 (mm-40) REVERT: E 140 MET cc_start: 0.8537 (mtp) cc_final: 0.8175 (mtp) outliers start: 17 outliers final: 11 residues processed: 117 average time/residue: 0.2457 time to fit residues: 39.0413 Evaluate side-chains 108 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 96 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 ASN Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain R residue 167 ILE Chi-restraints excluded: chain R residue 277 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 10 optimal weight: 8.9990 chunk 47 optimal weight: 5.9990 chunk 66 optimal weight: 0.4980 chunk 99 optimal weight: 6.9990 chunk 105 optimal weight: 9.9990 chunk 94 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 87 optimal weight: 9.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8923 Z= 0.237 Angle : 0.533 7.841 12083 Z= 0.280 Chirality : 0.041 0.140 1397 Planarity : 0.004 0.042 1519 Dihedral : 5.709 83.964 1224 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.91 % Allowed : 15.71 % Favored : 81.37 % 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: -1.63 (0.25), residues: 1099 helix: 1.10 (0.28), residues: 364 sheet: -2.07 (0.28), residues: 284 loop : -2.21 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 211 HIS 0.006 0.001 HIS E 232 PHE 0.011 0.001 PHE C 241 TYR 0.013 0.001 TYR E 175 ARG 0.004 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 99 time to evaluate : 0.983 Fit side-chains revert: symmetry clash REVERT: A 340 LYS cc_start: 0.7071 (ptmt) cc_final: 0.6262 (mmmt) REVERT: C 46 ARG cc_start: 0.7211 (ttt-90) cc_final: 0.6721 (mtp85) REVERT: C 59 TYR cc_start: 0.8492 (m-80) cc_final: 0.8145 (m-80) REVERT: C 204 CYS cc_start: 0.7409 (t) cc_final: 0.6979 (t) REVERT: D 62 ARG cc_start: 0.6206 (tpm170) cc_final: 0.5655 (ttp80) outliers start: 28 outliers final: 15 residues processed: 119 average time/residue: 0.2408 time to fit residues: 38.8678 Evaluate side-chains 109 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 94 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 ASN Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 175 TYR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain R residue 167 ILE Chi-restraints excluded: chain R residue 277 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 0.0970 chunk 1 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8923 Z= 0.170 Angle : 0.500 7.739 12083 Z= 0.262 Chirality : 0.040 0.133 1397 Planarity : 0.003 0.041 1519 Dihedral : 5.432 83.187 1224 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.08 % Allowed : 17.38 % Favored : 80.54 % 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: -1.30 (0.25), residues: 1099 helix: 1.36 (0.28), residues: 364 sheet: -1.90 (0.29), residues: 284 loop : -1.99 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 211 HIS 0.004 0.001 HIS E 232 PHE 0.010 0.001 PHE C 292 TYR 0.011 0.001 TYR E 190 ARG 0.003 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 102 time to evaluate : 0.961 Fit side-chains revert: symmetry clash REVERT: A 340 LYS cc_start: 0.7017 (ptmt) cc_final: 0.6220 (mmmt) REVERT: C 46 ARG cc_start: 0.7219 (ttt-90) cc_final: 0.6731 (mtp85) REVERT: C 59 TYR cc_start: 0.8460 (m-80) cc_final: 0.8153 (m-80) REVERT: C 204 CYS cc_start: 0.7314 (t) cc_final: 0.6835 (t) REVERT: C 234 PHE cc_start: 0.9123 (OUTLIER) cc_final: 0.8712 (m-80) REVERT: D 62 ARG cc_start: 0.6146 (tpm170) cc_final: 0.5716 (ttp80) outliers start: 20 outliers final: 11 residues processed: 114 average time/residue: 0.2397 time to fit residues: 37.0310 Evaluate side-chains 113 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 101 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain R residue 167 ILE Chi-restraints excluded: chain R residue 277 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 105 optimal weight: 9.9990 chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 55 optimal weight: 8.9990 chunk 101 optimal weight: 0.9980 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8923 Z= 0.266 Angle : 0.543 8.967 12083 Z= 0.284 Chirality : 0.042 0.135 1397 Planarity : 0.004 0.042 1519 Dihedral : 5.614 84.158 1224 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.60 % Allowed : 17.17 % Favored : 80.23 % 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: -1.29 (0.25), residues: 1099 helix: 1.31 (0.28), residues: 368 sheet: -1.88 (0.29), residues: 284 loop : -1.96 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 211 HIS 0.009 0.001 HIS A 344 PHE 0.013 0.001 PHE C 241 TYR 0.015 0.002 TYR E 175 ARG 0.003 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 98 time to evaluate : 0.993 Fit side-chains revert: symmetry clash REVERT: A 320 ARG cc_start: 0.7608 (mtp180) cc_final: 0.7315 (mtp180) REVERT: A 340 LYS cc_start: 0.7065 (ptmt) cc_final: 0.6275 (mmmt) REVERT: C 46 ARG cc_start: 0.7213 (ttt-90) cc_final: 0.6712 (mtp85) REVERT: C 59 TYR cc_start: 0.8498 (m-80) cc_final: 0.8115 (m-80) REVERT: C 204 CYS cc_start: 0.7498 (t) cc_final: 0.7056 (t) REVERT: C 234 PHE cc_start: 0.9153 (OUTLIER) cc_final: 0.8758 (m-80) REVERT: D 62 ARG cc_start: 0.6259 (tpm170) cc_final: 0.5642 (ttp80) outliers start: 25 outliers final: 18 residues processed: 116 average time/residue: 0.2462 time to fit residues: 38.2761 Evaluate side-chains 115 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 96 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 175 TYR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 167 ILE Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 277 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 77 optimal weight: 0.0870 chunk 59 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 105 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8923 Z= 0.204 Angle : 0.516 9.003 12083 Z= 0.268 Chirality : 0.041 0.145 1397 Planarity : 0.003 0.040 1519 Dihedral : 5.391 82.747 1224 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.60 % Allowed : 17.59 % Favored : 79.81 % 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: -1.13 (0.26), residues: 1099 helix: 1.44 (0.28), residues: 368 sheet: -1.76 (0.29), residues: 284 loop : -1.90 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 63 HIS 0.010 0.001 HIS A 344 PHE 0.011 0.001 PHE C 292 TYR 0.011 0.001 TYR E 190 ARG 0.003 0.000 ARG E 87 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 100 time to evaluate : 1.014 Fit side-chains revert: symmetry clash REVERT: A 340 LYS cc_start: 0.7021 (ptmt) cc_final: 0.6234 (mmmt) REVERT: C 46 ARG cc_start: 0.7229 (ttt-90) cc_final: 0.6716 (mtp85) REVERT: C 59 TYR cc_start: 0.8457 (m-80) cc_final: 0.8150 (m-80) REVERT: C 204 CYS cc_start: 0.7395 (t) cc_final: 0.6951 (t) REVERT: C 234 PHE cc_start: 0.9137 (OUTLIER) cc_final: 0.8754 (m-80) REVERT: C 262 MET cc_start: 0.7729 (mmm) cc_final: 0.7524 (tpp) REVERT: D 62 ARG cc_start: 0.6231 (tpm170) cc_final: 0.5684 (ttp80) REVERT: E 60 TYR cc_start: 0.8954 (m-80) cc_final: 0.8536 (m-80) REVERT: R 126 ILE cc_start: 0.7136 (OUTLIER) cc_final: 0.6836 (mt) outliers start: 25 outliers final: 17 residues processed: 116 average time/residue: 0.2394 time to fit residues: 37.6194 Evaluate side-chains 114 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 95 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain R residue 126 ILE Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 167 ILE Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 277 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 9 optimal weight: 0.3980 chunk 82 optimal weight: 0.0470 chunk 95 optimal weight: 0.7980 chunk 100 optimal weight: 0.7980 chunk 91 optimal weight: 6.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 ASN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8923 Z= 0.134 Angle : 0.478 9.050 12083 Z= 0.248 Chirality : 0.040 0.152 1397 Planarity : 0.003 0.038 1519 Dihedral : 5.044 82.582 1224 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.87 % Allowed : 18.21 % Favored : 79.92 % 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: -0.84 (0.26), residues: 1099 helix: 1.60 (0.29), residues: 368 sheet: -1.49 (0.29), residues: 288 loop : -1.73 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 233 HIS 0.010 0.001 HIS A 344 PHE 0.011 0.001 PHE C 292 TYR 0.010 0.001 TYR E 190 ARG 0.003 0.000 ARG E 87 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 107 time to evaluate : 0.995 Fit side-chains revert: symmetry clash REVERT: A 340 LYS cc_start: 0.6977 (ptmt) cc_final: 0.6209 (mmmt) REVERT: C 46 ARG cc_start: 0.7262 (ttt-90) cc_final: 0.6737 (mtp85) REVERT: C 59 TYR cc_start: 0.8391 (m-80) cc_final: 0.8178 (m-80) REVERT: C 204 CYS cc_start: 0.7204 (t) cc_final: 0.6672 (t) REVERT: C 234 PHE cc_start: 0.9122 (OUTLIER) cc_final: 0.8744 (m-80) REVERT: D 62 ARG cc_start: 0.6043 (tpm170) cc_final: 0.5671 (ttp80) outliers start: 18 outliers final: 11 residues processed: 119 average time/residue: 0.2197 time to fit residues: 35.9744 Evaluate side-chains 116 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 104 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain R residue 167 ILE Chi-restraints excluded: chain R residue 277 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8923 Z= 0.198 Angle : 0.515 9.258 12083 Z= 0.267 Chirality : 0.041 0.144 1397 Planarity : 0.003 0.036 1519 Dihedral : 5.194 82.726 1224 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.77 % Allowed : 18.73 % Favored : 79.50 % 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: -0.85 (0.26), residues: 1099 helix: 1.59 (0.29), residues: 368 sheet: -1.47 (0.29), residues: 288 loop : -1.75 (0.27), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 233 HIS 0.011 0.001 HIS A 344 PHE 0.013 0.001 PHE C 292 TYR 0.012 0.001 TYR E 190 ARG 0.005 0.000 ARG E 87 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 101 time to evaluate : 1.000 Fit side-chains revert: symmetry clash REVERT: A 234 PHE cc_start: 0.8099 (OUTLIER) cc_final: 0.7609 (t80) REVERT: A 340 LYS cc_start: 0.7045 (ptmt) cc_final: 0.6230 (mmmt) REVERT: C 46 ARG cc_start: 0.7226 (ttt-90) cc_final: 0.6717 (mtp85) REVERT: C 59 TYR cc_start: 0.8458 (m-80) cc_final: 0.8233 (m-80) REVERT: C 204 CYS cc_start: 0.7277 (t) cc_final: 0.6835 (t) REVERT: C 234 PHE cc_start: 0.9118 (OUTLIER) cc_final: 0.8735 (m-80) REVERT: D 62 ARG cc_start: 0.6123 (tpm170) cc_final: 0.5651 (ttp80) REVERT: R 126 ILE cc_start: 0.7134 (OUTLIER) cc_final: 0.6831 (mt) outliers start: 17 outliers final: 12 residues processed: 113 average time/residue: 0.2363 time to fit residues: 36.2265 Evaluate side-chains 113 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 98 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 126 ILE Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 167 ILE Chi-restraints excluded: chain R residue 277 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 92 optimal weight: 0.3980 chunk 26 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8923 Z= 0.202 Angle : 0.518 9.148 12083 Z= 0.269 Chirality : 0.041 0.156 1397 Planarity : 0.003 0.038 1519 Dihedral : 5.227 82.452 1224 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.66 % Allowed : 19.04 % Favored : 79.29 % 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: -0.81 (0.26), residues: 1099 helix: 1.58 (0.28), residues: 368 sheet: -1.41 (0.29), residues: 287 loop : -1.71 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 105 HIS 0.011 0.001 HIS A 344 PHE 0.014 0.001 PHE C 292 TYR 0.012 0.001 TYR E 190 ARG 0.006 0.000 ARG E 87 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 97 time to evaluate : 1.003 Fit side-chains revert: symmetry clash REVERT: A 234 PHE cc_start: 0.8097 (OUTLIER) cc_final: 0.7598 (t80) REVERT: A 340 LYS cc_start: 0.7023 (ptmt) cc_final: 0.6215 (mmmt) REVERT: C 46 ARG cc_start: 0.7223 (ttt-90) cc_final: 0.6717 (mtp85) REVERT: C 59 TYR cc_start: 0.8451 (m-80) cc_final: 0.8235 (m-80) REVERT: C 130 GLU cc_start: 0.8314 (mp0) cc_final: 0.8089 (mp0) REVERT: C 204 CYS cc_start: 0.7379 (t) cc_final: 0.6926 (t) REVERT: C 234 PHE cc_start: 0.9129 (OUTLIER) cc_final: 0.8739 (m-80) REVERT: D 62 ARG cc_start: 0.6190 (tpm170) cc_final: 0.5673 (ttp80) REVERT: R 126 ILE cc_start: 0.7133 (OUTLIER) cc_final: 0.6829 (mt) outliers start: 16 outliers final: 13 residues processed: 109 average time/residue: 0.2241 time to fit residues: 33.4555 Evaluate side-chains 112 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 96 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 126 ILE Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 167 ILE Chi-restraints excluded: chain R residue 277 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 88 optimal weight: 0.8980 chunk 10 optimal weight: 9.9990 chunk 15 optimal weight: 0.0070 chunk 76 optimal weight: 1.9990 chunk 4 optimal weight: 0.0470 chunk 62 optimal weight: 0.5980 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 ASN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.193490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.124045 restraints weight = 8996.207| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.38 r_work: 0.3263 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3035 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3035 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8923 Z= 0.132 Angle : 0.480 9.251 12083 Z= 0.249 Chirality : 0.040 0.153 1397 Planarity : 0.003 0.037 1519 Dihedral : 4.949 81.910 1224 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.87 % Allowed : 18.83 % Favored : 79.29 % 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: -0.61 (0.26), residues: 1099 helix: 1.69 (0.28), residues: 368 sheet: -1.28 (0.29), residues: 288 loop : -1.58 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 233 HIS 0.010 0.001 HIS A 344 PHE 0.012 0.001 PHE C 292 TYR 0.008 0.001 TYR E 190 ARG 0.005 0.000 ARG C 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2320.47 seconds wall clock time: 43 minutes 5.37 seconds (2585.37 seconds total)