Starting phenix.real_space_refine on Wed Feb 14 07:41:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eo2_31225/02_2024/7eo2_31225_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eo2_31225/02_2024/7eo2_31225.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eo2_31225/02_2024/7eo2_31225_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eo2_31225/02_2024/7eo2_31225_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eo2_31225/02_2024/7eo2_31225_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eo2_31225/02_2024/7eo2_31225.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eo2_31225/02_2024/7eo2_31225.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eo2_31225/02_2024/7eo2_31225_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eo2_31225/02_2024/7eo2_31225_neut_updated.pdb" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.106 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 63 5.16 5 C 5665 2.51 5 N 1498 2.21 5 O 1638 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 294": "OE1" <-> "OE2" Residue "A TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 317": "OE1" <-> "OE2" Residue "B PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 251": "OD1" <-> "OD2" Residue "B PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 226": "OE1" <-> "OE2" Residue "C PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 48": "OD1" <-> "OD2" Residue "D PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 62": "OD1" <-> "OD2" Residue "E PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8865 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2257 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 6, 'TRANS': 273} Chain breaks: 3 Chain: "B" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1769 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 2, 'TRANS': 217} Chain breaks: 2 Chain: "C" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2592 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain: "D" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "E" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1777 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'J89': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.95, per 1000 atoms: 0.56 Number of scatterers: 8865 At special positions: 0 Unit cell: (95.7, 121, 132, 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 63 16.00 P 1 15.00 O 1638 8.00 N 1498 7.00 C 5665 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 184 " - pdb=" SG CYS A 191 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 287 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 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: 3.03 Conformation dependent library (CDL) restraints added in 1.6 seconds 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2112 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 12 sheets defined 34.1% alpha, 21.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'A' and resid 22 through 32 Processing helix chain 'A' and resid 47 through 72 removed outlier: 3.763A pdb=" N LYS A 72 " --> pdb=" O LEU A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 103 Processing helix chain 'A' and resid 106 through 110 Processing helix chain 'A' and resid 114 through 145 removed outlier: 3.855A pdb=" N MET A 124 " --> pdb=" O ARG A 120 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL A 132 " --> pdb=" O LEU A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 180 removed outlier: 4.019A pdb=" N LEU A 177 " --> pdb=" O ILE A 173 " (cutoff:3.500A) Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 188 through 190 No H-bonds generated for 'chain 'A' and resid 188 through 190' Processing helix chain 'A' and resid 200 through 234 removed outlier: 4.297A pdb=" N ARG A 234 " --> pdb=" O THR A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 281 Proline residue: A 271 - end of helix removed outlier: 3.567A pdb=" N GLY A 281 " --> pdb=" O LEU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 305 removed outlier: 3.507A pdb=" N ALA A 293 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N GLU A 294 " --> pdb=" O PHE A 291 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU A 297 " --> pdb=" O GLU A 294 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N VAL A 298 " --> pdb=" O TYR A 295 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL A 301 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASN A 303 " --> pdb=" O ALA A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 310 No H-bonds generated for 'chain 'A' and resid 307 through 310' Processing helix chain 'A' and resid 316 through 323 removed outlier: 4.364A pdb=" N ILE A 323 " --> pdb=" O ARG A 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 32 removed outlier: 4.123A pdb=" N ALA B 11 " --> pdb=" O ALA B 7 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ARG B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 52 Processing helix chain 'B' and resid 208 through 210 No H-bonds generated for 'chain 'B' and resid 208 through 210' Processing helix chain 'B' and resid 212 through 215 Processing helix chain 'B' and resid 242 through 254 Processing helix chain 'B' and resid 271 through 278 Processing helix chain 'B' and resid 283 through 285 No H-bonds generated for 'chain 'B' and resid 283 through 285' Processing helix chain 'B' and resid 296 through 310 removed outlier: 4.464A pdb=" N LEU B 310 " --> pdb=" O GLN B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 350 Processing helix chain 'C' and resid 5 through 24 Processing helix chain 'C' and resid 30 through 33 No H-bonds generated for 'chain 'C' and resid 30 through 33' Processing helix chain 'D' and resid 6 through 23 Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'D' and resid 45 through 47 No H-bonds generated for 'chain 'D' and resid 45 through 47' Processing helix chain 'D' and resid 56 through 58 No H-bonds generated for 'chain 'D' and resid 56 through 58' 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 sheet with id= A, first strand: chain 'B' and resid 319 through 323 removed outlier: 6.747A pdb=" N ILE B 264 " --> pdb=" O TYR B 320 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N HIS B 322 " --> pdb=" O ILE B 264 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU B 266 " --> pdb=" O HIS B 322 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA B 220 " --> pdb=" O LYS B 35 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.954A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.924A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 5.830A 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: 7.024A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 187 through 192 removed outlier: 7.152A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 229 through 232 removed outlier: 7.038A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N THR C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 276 through 278 Processing sheet with id= H, first strand: chain 'C' and resid 47 through 51 removed outlier: 7.059A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.683A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 128 through 130 Processing sheet with id= L, first strand: chain 'E' and resid 213 through 219 removed outlier: 6.120A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ARG E 168 " --> pdb=" O PRO E 173 " (cutoff:3.500A) 401 hydrogen bonds defined for protein. 1131 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: 2.49 Time building geometry restraints manager: 3.32 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: 2817 1.35 - 1.48: 2296 1.48 - 1.61: 3835 1.61 - 1.74: 1 1.74 - 1.87: 91 Bond restraints: 9040 Sorted by residual: bond pdb=" O21 J89 A 401 " pdb=" P22 J89 A 401 " ideal model delta sigma weight residual 1.648 1.866 -0.218 2.00e-02 2.50e+03 1.19e+02 bond pdb=" C17 J89 A 401 " pdb=" C20 J89 A 401 " ideal model delta sigma weight residual 1.527 1.640 -0.113 2.00e-02 2.50e+03 3.20e+01 bond pdb=" C16 J89 A 401 " pdb=" C17 J89 A 401 " ideal model delta sigma weight residual 1.527 1.603 -0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C GLU E 222 " pdb=" N TYR E 223 " ideal model delta sigma weight residual 1.328 1.273 0.055 1.44e-02 4.82e+03 1.45e+01 bond pdb=" N TRP C 82 " pdb=" CA TRP C 82 " ideal model delta sigma weight residual 1.455 1.499 -0.043 1.23e-02 6.61e+03 1.24e+01 ... (remaining 9035 not shown) Histogram of bond angle deviations from ideal: 99.11 - 106.08: 145 106.08 - 113.06: 4940 113.06 - 120.03: 3168 120.03 - 127.00: 3881 127.00 - 133.98: 98 Bond angle restraints: 12232 Sorted by residual: angle pdb=" N MET E 180 " pdb=" CA MET E 180 " pdb=" CB MET E 180 " ideal model delta sigma weight residual 114.17 108.88 5.29 1.14e+00 7.69e-01 2.15e+01 angle pdb=" N LEU A 151 " pdb=" CA LEU A 151 " pdb=" C LEU A 151 " ideal model delta sigma weight residual 111.14 116.03 -4.89 1.08e+00 8.57e-01 2.05e+01 angle pdb=" C LEU A 147 " pdb=" CA LEU A 147 " pdb=" CB LEU A 147 " ideal model delta sigma weight residual 110.45 103.07 7.38 1.73e+00 3.34e-01 1.82e+01 angle pdb=" C15 J89 A 401 " pdb=" C16 J89 A 401 " pdb=" C17 J89 A 401 " ideal model delta sigma weight residual 109.47 121.32 -11.85 3.00e+00 1.11e-01 1.56e+01 angle pdb=" C SER E 52 " pdb=" CA SER E 52 " pdb=" CB SER E 52 " ideal model delta sigma weight residual 110.36 103.50 6.86 1.78e+00 3.16e-01 1.49e+01 ... (remaining 12227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.95: 5195 26.95 - 53.90: 157 53.90 - 80.84: 17 80.84 - 107.79: 4 107.79 - 134.74: 1 Dihedral angle restraints: 5374 sinusoidal: 2104 harmonic: 3270 Sorted by residual: dihedral pdb=" C05 J89 A 401 " pdb=" C06 J89 A 401 " pdb=" C07 J89 A 401 " pdb=" C08 J89 A 401 " ideal model delta sinusoidal sigma weight residual 234.39 99.65 134.74 1 3.00e+01 1.11e-03 1.82e+01 dihedral pdb=" CA TRP C 82 " pdb=" C TRP C 82 " pdb=" N ASP C 83 " pdb=" CA ASP C 83 " ideal model delta harmonic sigma weight residual 180.00 160.33 19.67 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA PHE C 235 " pdb=" C PHE C 235 " pdb=" N PRO C 236 " pdb=" CA PRO C 236 " ideal model delta harmonic sigma weight residual 180.00 -160.36 -19.64 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 5371 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1203 0.059 - 0.118: 172 0.118 - 0.177: 28 0.177 - 0.236: 3 0.236 - 0.295: 2 Chirality restraints: 1408 Sorted by residual: chirality pdb=" CA TRP C 82 " pdb=" N TRP C 82 " pdb=" C TRP C 82 " pdb=" CB TRP C 82 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CA ALA A 253 " pdb=" N ALA A 253 " pdb=" C ALA A 253 " pdb=" CB ALA A 253 " both_signs ideal model delta sigma weight residual False 2.48 2.73 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" C17 J89 A 401 " pdb=" C16 J89 A 401 " pdb=" C20 J89 A 401 " pdb=" N26 J89 A 401 " both_signs ideal model delta sigma weight residual False 2.61 2.83 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 1405 not shown) Planarity restraints: 1520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 177 " 0.046 5.00e-02 4.00e+02 6.97e-02 7.78e+00 pdb=" N PRO A 178 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO A 178 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 178 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 74 " 0.043 5.00e-02 4.00e+02 6.48e-02 6.73e+00 pdb=" N PRO E 75 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO E 75 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO E 75 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER E 106 " -0.036 5.00e-02 4.00e+02 5.39e-02 4.64e+00 pdb=" N PRO E 107 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO E 107 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO E 107 " -0.030 5.00e-02 4.00e+02 ... (remaining 1517 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 236 2.70 - 3.25: 8558 3.25 - 3.80: 12788 3.80 - 4.35: 16649 4.35 - 4.90: 29164 Nonbonded interactions: 67395 Sorted by model distance: nonbonded pdb=" N GLY C 144 " pdb=" OD2 ASP C 163 " model vdw 2.152 2.520 nonbonded pdb=" OD1 ASN B 269 " pdb=" OG1 THR B 324 " model vdw 2.187 2.440 nonbonded pdb=" OG1 THR C 86 " pdb=" OD1 ASN C 88 " model vdw 2.229 2.440 nonbonded pdb=" OG SER A 192 " pdb=" O LEU A 195 " model vdw 2.291 2.440 nonbonded pdb=" OE2 GLU B 318 " pdb=" OH TYR B 320 " model vdw 2.296 2.440 ... (remaining 67390 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.670 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.940 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 25.940 Find NCS groups from input model: 0.240 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:12.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 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 0.218 9040 Z= 0.283 Angle : 0.773 11.854 12232 Z= 0.437 Chirality : 0.045 0.295 1408 Planarity : 0.004 0.070 1520 Dihedral : 13.291 134.739 3253 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 0.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.60 (0.25), residues: 1104 helix: 1.47 (0.27), residues: 367 sheet: -0.52 (0.31), residues: 265 loop : -1.86 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 164 HIS 0.007 0.001 HIS C 91 PHE 0.016 0.001 PHE C 199 TYR 0.013 0.001 TYR C 124 ARG 0.005 0.001 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 HIS cc_start: 0.6461 (m-70) cc_final: 0.5869 (m90) REVERT: E 18 ARG cc_start: 0.8095 (tpp80) cc_final: 0.7810 (mmt90) REVERT: E 218 MET cc_start: 0.8204 (ttp) cc_final: 0.7561 (ttt) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 1.1202 time to fit residues: 149.6841 Evaluate side-chains 94 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 2.9990 chunk 84 optimal weight: 9.9990 chunk 46 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 10.0000 chunk 87 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 52 optimal weight: 0.0020 chunk 64 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 HIS E 171 GLN E 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9040 Z= 0.176 Angle : 0.558 8.403 12232 Z= 0.298 Chirality : 0.042 0.146 1408 Planarity : 0.004 0.059 1520 Dihedral : 6.829 90.523 1231 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.96 % Allowed : 8.03 % Favored : 90.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.34 (0.26), residues: 1104 helix: 2.30 (0.27), residues: 366 sheet: -0.13 (0.31), residues: 268 loop : -1.26 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 82 HIS 0.007 0.001 HIS B 188 PHE 0.023 0.002 PHE A 273 TYR 0.019 0.002 TYR A 98 ARG 0.005 0.000 ARG E 148 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 112 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 HIS cc_start: 0.6474 (m-70) cc_final: 0.6122 (m90) REVERT: A 188 LEU cc_start: 0.7036 (pt) cc_final: 0.6794 (pp) REVERT: E 130 GLN cc_start: 0.6496 (mm110) cc_final: 0.6240 (mm-40) REVERT: E 218 MET cc_start: 0.8210 (ttp) cc_final: 0.7534 (ttt) outliers start: 19 outliers final: 7 residues processed: 120 average time/residue: 1.0738 time to fit residues: 139.1744 Evaluate side-chains 104 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 97 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 258 ASP Chi-restraints excluded: chain E residue 2 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.3980 chunk 31 optimal weight: 0.9990 chunk 83 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 109 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 34 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 HIS E 113 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9040 Z= 0.159 Angle : 0.510 5.769 12232 Z= 0.275 Chirality : 0.041 0.142 1408 Planarity : 0.004 0.062 1520 Dihedral : 6.273 88.256 1231 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.85 % Allowed : 10.92 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.76 (0.26), residues: 1104 helix: 2.67 (0.27), residues: 367 sheet: 0.15 (0.31), residues: 268 loop : -1.08 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 82 HIS 0.006 0.001 HIS B 188 PHE 0.022 0.002 PHE A 273 TYR 0.014 0.001 TYR A 202 ARG 0.007 0.000 ARG C 304 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 100 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 HIS cc_start: 0.6481 (m90) cc_final: 0.5800 (m90) REVERT: A 275 LEU cc_start: 0.7285 (OUTLIER) cc_final: 0.7027 (tm) REVERT: E 90 ASP cc_start: 0.7906 (OUTLIER) cc_final: 0.7575 (m-30) REVERT: E 211 ASP cc_start: 0.7748 (m-30) cc_final: 0.7448 (t0) REVERT: E 218 MET cc_start: 0.8198 (ttp) cc_final: 0.7672 (ttt) outliers start: 18 outliers final: 13 residues processed: 113 average time/residue: 1.0742 time to fit residues: 131.0384 Evaluate side-chains 109 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 94 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 103 CYS Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 258 ASP Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 90 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 0.8980 chunk 52 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 HIS ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9040 Z= 0.210 Angle : 0.549 7.083 12232 Z= 0.293 Chirality : 0.042 0.138 1408 Planarity : 0.004 0.062 1520 Dihedral : 6.244 84.433 1231 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.57 % Allowed : 12.46 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1104 helix: 2.67 (0.27), residues: 367 sheet: 0.14 (0.31), residues: 273 loop : -0.99 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 211 HIS 0.006 0.001 HIS B 188 PHE 0.022 0.002 PHE A 273 TYR 0.014 0.002 TYR A 202 ARG 0.003 0.000 ARG C 150 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 101 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 LEU cc_start: 0.7340 (OUTLIER) cc_final: 0.7077 (tm) REVERT: C 207 SER cc_start: 0.7531 (m) cc_final: 0.6901 (p) REVERT: C 262 MET cc_start: 0.5738 (mpp) cc_final: 0.5331 (mpt) REVERT: E 90 ASP cc_start: 0.7969 (OUTLIER) cc_final: 0.7645 (m-30) REVERT: E 130 GLN cc_start: 0.6654 (mm-40) cc_final: 0.6179 (mt0) REVERT: E 211 ASP cc_start: 0.7647 (m-30) cc_final: 0.7421 (t0) REVERT: E 218 MET cc_start: 0.8122 (ttp) cc_final: 0.7551 (ttt) outliers start: 25 outliers final: 14 residues processed: 117 average time/residue: 0.9989 time to fit residues: 126.2289 Evaluate side-chains 114 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 98 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 103 CYS Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 258 ASP Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 90 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 chunk 44 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 54 optimal weight: 0.8980 chunk 96 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 113 GLN ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9040 Z= 0.191 Angle : 0.535 6.927 12232 Z= 0.282 Chirality : 0.041 0.151 1408 Planarity : 0.004 0.061 1520 Dihedral : 6.145 86.355 1231 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.57 % Allowed : 14.11 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.92 (0.26), residues: 1104 helix: 2.75 (0.27), residues: 368 sheet: 0.20 (0.31), residues: 273 loop : -0.93 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 82 HIS 0.006 0.001 HIS B 188 PHE 0.022 0.002 PHE A 273 TYR 0.014 0.001 TYR A 31 ARG 0.002 0.000 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 98 time to evaluate : 0.955 Fit side-chains revert: symmetry clash REVERT: A 28 HIS cc_start: 0.6285 (m90) cc_final: 0.5754 (m90) REVERT: A 275 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.7084 (tm) REVERT: C 207 SER cc_start: 0.7496 (m) cc_final: 0.6864 (p) REVERT: C 262 MET cc_start: 0.5889 (mpp) cc_final: 0.5621 (mpt) REVERT: E 90 ASP cc_start: 0.7951 (OUTLIER) cc_final: 0.7584 (m-30) REVERT: E 130 GLN cc_start: 0.6714 (mm-40) cc_final: 0.6243 (mt0) REVERT: E 218 MET cc_start: 0.8119 (ttp) cc_final: 0.7444 (ttt) REVERT: E 222 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7676 (pt0) outliers start: 25 outliers final: 17 residues processed: 117 average time/residue: 0.9861 time to fit residues: 124.8848 Evaluate side-chains 115 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 95 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 103 CYS Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 258 ASP Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain E residue 222 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.0010 chunk 26 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 56 optimal weight: 0.0670 chunk 103 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.0130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9040 Z= 0.199 Angle : 0.551 6.538 12232 Z= 0.290 Chirality : 0.041 0.141 1408 Planarity : 0.004 0.060 1520 Dihedral : 6.076 84.411 1231 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.09 % Allowed : 14.83 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.91 (0.26), residues: 1104 helix: 2.74 (0.27), residues: 368 sheet: 0.26 (0.31), residues: 268 loop : -0.97 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 82 HIS 0.006 0.001 HIS B 188 PHE 0.022 0.002 PHE A 273 TYR 0.012 0.001 TYR A 202 ARG 0.002 0.000 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 96 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.7191 (tm) REVERT: B 270 LYS cc_start: 0.7534 (mttm) cc_final: 0.7262 (ttmm) REVERT: C 207 SER cc_start: 0.7367 (m) cc_final: 0.6754 (p) REVERT: C 262 MET cc_start: 0.5836 (mpp) cc_final: 0.5625 (mpt) REVERT: E 90 ASP cc_start: 0.7977 (OUTLIER) cc_final: 0.7541 (m-30) REVERT: E 130 GLN cc_start: 0.6558 (OUTLIER) cc_final: 0.6003 (mt0) REVERT: E 218 MET cc_start: 0.8126 (ttp) cc_final: 0.7466 (ttt) REVERT: E 222 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7681 (pt0) outliers start: 30 outliers final: 18 residues processed: 116 average time/residue: 1.0324 time to fit residues: 129.5122 Evaluate side-chains 114 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 92 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 258 ASP Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 130 GLN Chi-restraints excluded: chain E residue 222 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 106 optimal weight: 0.3980 chunk 66 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 32 optimal weight: 0.0470 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 183 HIS E 113 GLN ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9040 Z= 0.146 Angle : 0.500 6.837 12232 Z= 0.263 Chirality : 0.040 0.139 1408 Planarity : 0.003 0.060 1520 Dihedral : 5.694 86.647 1231 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.47 % Allowed : 15.76 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1.04 (0.26), residues: 1104 helix: 2.78 (0.27), residues: 374 sheet: 0.39 (0.31), residues: 268 loop : -0.93 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 82 HIS 0.006 0.001 HIS B 188 PHE 0.023 0.001 PHE A 273 TYR 0.010 0.001 TYR C 124 ARG 0.004 0.000 ARG B 208 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 99 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 LEU cc_start: 0.7396 (OUTLIER) cc_final: 0.7086 (tm) REVERT: B 270 LYS cc_start: 0.7499 (mttm) cc_final: 0.7259 (ttmm) REVERT: C 207 SER cc_start: 0.7316 (m) cc_final: 0.6677 (p) REVERT: E 130 GLN cc_start: 0.6672 (OUTLIER) cc_final: 0.6062 (mt0) REVERT: E 218 MET cc_start: 0.8077 (ttp) cc_final: 0.7555 (ttt) REVERT: E 222 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7689 (pt0) outliers start: 24 outliers final: 13 residues processed: 113 average time/residue: 1.0078 time to fit residues: 123.4913 Evaluate side-chains 108 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 92 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 258 ASP Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 128 MET Chi-restraints excluded: chain E residue 130 GLN Chi-restraints excluded: chain E residue 222 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 68 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 chunk 52 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 97 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9040 Z= 0.181 Angle : 0.539 8.709 12232 Z= 0.282 Chirality : 0.041 0.144 1408 Planarity : 0.004 0.060 1520 Dihedral : 5.481 81.227 1231 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.57 % Allowed : 16.68 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1.01 (0.26), residues: 1104 helix: 2.73 (0.27), residues: 374 sheet: 0.37 (0.32), residues: 270 loop : -0.93 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 117 HIS 0.005 0.001 HIS B 188 PHE 0.024 0.002 PHE A 273 TYR 0.012 0.001 TYR A 202 ARG 0.003 0.000 ARG B 208 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 96 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.7207 (tm) REVERT: B 270 LYS cc_start: 0.7511 (mttm) cc_final: 0.7280 (ttmm) REVERT: C 207 SER cc_start: 0.7264 (m) cc_final: 0.6641 (p) REVERT: C 266 HIS cc_start: 0.5414 (OUTLIER) cc_final: 0.4374 (t-90) REVERT: C 336 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7590 (mt) REVERT: E 90 ASP cc_start: 0.8012 (OUTLIER) cc_final: 0.7520 (m-30) REVERT: E 130 GLN cc_start: 0.6741 (OUTLIER) cc_final: 0.6155 (mt0) REVERT: E 218 MET cc_start: 0.8125 (ttp) cc_final: 0.7651 (ttt) outliers start: 25 outliers final: 14 residues processed: 112 average time/residue: 1.0889 time to fit residues: 132.3221 Evaluate side-chains 111 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 92 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 258 ASP Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 130 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 chunk 43 optimal weight: 10.0000 chunk 78 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 99 optimal weight: 7.9990 chunk 65 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN B 204 GLN E 113 GLN ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9040 Z= 0.215 Angle : 0.561 6.584 12232 Z= 0.294 Chirality : 0.042 0.144 1408 Planarity : 0.004 0.060 1520 Dihedral : 5.370 74.537 1231 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.47 % Allowed : 16.68 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1.01 (0.26), residues: 1104 helix: 2.79 (0.27), residues: 368 sheet: 0.40 (0.32), residues: 268 loop : -0.94 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 117 HIS 0.005 0.001 HIS E 35 PHE 0.025 0.002 PHE A 273 TYR 0.013 0.002 TYR A 31 ARG 0.003 0.000 ARG B 208 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 90 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7341 (tm) REVERT: B 270 LYS cc_start: 0.7506 (mttm) cc_final: 0.7275 (ttmm) REVERT: C 207 SER cc_start: 0.7341 (m) cc_final: 0.6735 (p) REVERT: C 266 HIS cc_start: 0.5455 (OUTLIER) cc_final: 0.4394 (t-90) REVERT: C 336 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7595 (mt) REVERT: E 130 GLN cc_start: 0.6715 (OUTLIER) cc_final: 0.6277 (mt0) REVERT: E 218 MET cc_start: 0.8161 (ttp) cc_final: 0.7690 (ttt) outliers start: 24 outliers final: 14 residues processed: 105 average time/residue: 1.1424 time to fit residues: 128.8627 Evaluate side-chains 102 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 84 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 258 ASP Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 130 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 7.9990 chunk 73 optimal weight: 0.6980 chunk 110 optimal weight: 0.9990 chunk 101 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 68 optimal weight: 0.4980 chunk 53 optimal weight: 7.9990 chunk 69 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9040 Z= 0.169 Angle : 0.529 8.201 12232 Z= 0.277 Chirality : 0.041 0.145 1408 Planarity : 0.004 0.060 1520 Dihedral : 5.013 71.250 1231 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.06 % Allowed : 17.20 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1.12 (0.26), residues: 1104 helix: 2.88 (0.27), residues: 368 sheet: 0.47 (0.32), residues: 273 loop : -0.89 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 117 HIS 0.005 0.001 HIS B 188 PHE 0.024 0.001 PHE A 273 TYR 0.011 0.001 TYR A 202 ARG 0.005 0.000 ARG E 148 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 92 time to evaluate : 1.061 Fit side-chains revert: symmetry clash REVERT: A 275 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7362 (tm) REVERT: B 270 LYS cc_start: 0.7464 (mttm) cc_final: 0.7229 (ttmm) REVERT: C 207 SER cc_start: 0.7310 (m) cc_final: 0.6672 (p) REVERT: C 234 PHE cc_start: 0.7188 (OUTLIER) cc_final: 0.6817 (t80) REVERT: C 266 HIS cc_start: 0.5437 (OUTLIER) cc_final: 0.4439 (t-90) REVERT: C 336 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7567 (mt) REVERT: D 38 MET cc_start: 0.6670 (tpt) cc_final: 0.6098 (ptp) REVERT: E 130 GLN cc_start: 0.6584 (OUTLIER) cc_final: 0.6132 (mt0) REVERT: E 218 MET cc_start: 0.8125 (ttp) cc_final: 0.7636 (ttt) outliers start: 20 outliers final: 15 residues processed: 107 average time/residue: 1.1042 time to fit residues: 127.4846 Evaluate side-chains 109 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 89 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 258 ASP Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 130 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 0.0770 chunk 77 optimal weight: 0.0020 chunk 5 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 overall best weight: 0.5746 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN E 113 GLN ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.213489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.155875 restraints weight = 10621.607| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 3.34 r_work: 0.3751 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6376 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9040 Z= 0.150 Angle : 0.517 7.459 12232 Z= 0.270 Chirality : 0.040 0.161 1408 Planarity : 0.004 0.060 1520 Dihedral : 4.763 68.108 1231 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.96 % Allowed : 17.40 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 (0.26), residues: 1104 helix: 2.93 (0.27), residues: 369 sheet: 0.53 (0.32), residues: 273 loop : -0.88 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 168 HIS 0.004 0.001 HIS B 188 PHE 0.024 0.001 PHE A 273 TYR 0.011 0.001 TYR A 202 ARG 0.006 0.000 ARG E 148 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3060.57 seconds wall clock time: 55 minutes 23.45 seconds (3323.45 seconds total)