Starting phenix.real_space_refine on Thu Jan 18 10:37:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8feg_29026/01_2024/8feg_29026_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8feg_29026/01_2024/8feg_29026.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8feg_29026/01_2024/8feg_29026_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8feg_29026/01_2024/8feg_29026_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8feg_29026/01_2024/8feg_29026_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8feg_29026/01_2024/8feg_29026.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8feg_29026/01_2024/8feg_29026.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8feg_29026/01_2024/8feg_29026_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8feg_29026/01_2024/8feg_29026_updated.pdb" } resolution = 2.54 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= 0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 64 5.16 5 C 5453 2.51 5 N 1418 2.21 5 O 1604 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 46": "OE1" <-> "OE2" Residue "F PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 8539 Number of models: 1 Model: "" Number of chains: 7 Chain: "C" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1507 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 2, 'TRANS': 193} Chain breaks: 3 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "D" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2600 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "F" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "B" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2129 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 9, 'TRANS': 268} Chain breaks: 2 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 1, 'ARG:plan': 6, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 53 Chain: "A" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 94 Unusual residues: {'ACE': 1, 'XT9': 1} Classifications: {'peptide': 8, 'undetermined': 2} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 3} Link IDs: {'ACE_C-N': 1, 'CIS': 3, 'TRANS': 4, None: 1} Not linked: pdbres="DPN A 9 " pdbres="XT9 A 101 " Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 5.31, per 1000 atoms: 0.62 Number of scatterers: 8539 At special positions: 0 Unit cell: (88.88, 123.2, 127.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 64 16.00 O 1604 8.00 N 1418 7.00 C 5453 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS F 147 " - pdb=" SG CYS F 217 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 210 " 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.50 Conformation dependent library (CDL) restraints added in 1.8 seconds 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTY A 4 " pdb=" CB DTH A 5 " pdb=" CB DPN A 9 " Number of C-beta restraints generated: 2076 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 13 sheets defined 34.1% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.97 Creating SS restraints... Processing helix chain 'C' and resid 7 through 32 removed outlier: 4.549A pdb=" N ARG C 32 " --> pdb=" O GLU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 214 Processing helix chain 'C' and resid 227 through 230 Processing helix chain 'C' and resid 242 through 254 Processing helix chain 'C' and resid 271 through 280 removed outlier: 3.659A pdb=" N LYS C 279 " --> pdb=" O GLU C 275 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LYS C 280 " --> pdb=" O GLU C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 285 No H-bonds generated for 'chain 'C' and resid 283 through 285' Processing helix chain 'C' and resid 296 through 310 removed outlier: 4.051A pdb=" N LEU C 310 " --> pdb=" O GLN C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 350 removed outlier: 4.273A pdb=" N VAL C 335 " --> pdb=" O ASN C 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 25 Processing helix chain 'D' and resid 30 through 36 removed outlier: 5.901A pdb=" N ASN D 36 " --> pdb=" O GLN D 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 17 Processing helix chain 'E' and resid 30 through 43 Processing helix chain 'E' and resid 45 through 47 No H-bonds generated for 'chain 'E' and resid 45 through 47' Processing helix chain 'F' and resid 29 through 31 No H-bonds generated for 'chain 'F' and resid 29 through 31' Processing helix chain 'F' and resid 53 through 55 No H-bonds generated for 'chain 'F' and resid 53 through 55' Processing helix chain 'F' and resid 88 through 90 No H-bonds generated for 'chain 'F' and resid 88 through 90' Processing helix chain 'F' and resid 209 through 211 No H-bonds generated for 'chain 'F' and resid 209 through 211' Processing helix chain 'B' and resid 61 through 86 Processing helix chain 'B' and resid 93 through 120 removed outlier: 3.912A pdb=" N THR B 111 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET B 112 " --> pdb=" O VAL B 108 " (cutoff:3.500A) Proline residue: B 113 - end of helix Processing helix chain 'B' and resid 128 through 161 Processing helix chain 'B' and resid 163 through 168 removed outlier: 3.861A pdb=" N LEU B 167 " --> pdb=" O PRO B 163 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ASP B 168 " --> pdb=" O VAL B 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 163 through 168' Processing helix chain 'B' and resid 172 through 196 removed outlier: 4.483A pdb=" N VAL B 189 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU B 196 " --> pdb=" O SER B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 234 Processing helix chain 'B' and resid 236 through 255 removed outlier: 4.092A pdb=" N SER B 255 " --> pdb=" O LEU B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 259 No H-bonds generated for 'chain 'B' and resid 257 through 259' Processing helix chain 'B' and resid 264 through 298 removed outlier: 3.774A pdb=" N LEU B 275 " --> pdb=" O ARG B 271 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU B 277 " --> pdb=" O THR B 273 " (cutoff:3.500A) Proline residue: B 289 - end of helix Processing helix chain 'B' and resid 306 through 323 removed outlier: 5.110A pdb=" N SER B 311 " --> pdb=" O ALA B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 330 Processing sheet with id= A, first strand: chain 'C' and resid 319 through 323 removed outlier: 6.392A pdb=" N ILE C 264 " --> pdb=" O TYR C 320 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N HIS C 322 " --> pdb=" O ILE C 264 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEU C 266 " --> pdb=" O HIS C 322 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA C 220 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N HIS C 195 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N LEU C 36 " --> pdb=" O HIS C 195 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LYS C 197 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LEU C 38 " --> pdb=" O LYS C 197 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N PHE C 199 " --> pdb=" O LEU C 38 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 61 through 63 removed outlier: 3.776A pdb=" N LYS D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ASP D 83 " --> pdb=" O LYS D 89 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LYS D 89 " --> pdb=" O ASP D 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 100 through 105 removed outlier: 6.728A pdb=" N GLY D 115 " --> pdb=" O MET D 101 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N CYS D 103 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ALA D 113 " --> pdb=" O CYS D 103 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N TYR D 105 " --> pdb=" O TYR D 111 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N TYR D 111 " --> pdb=" O TYR D 105 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLY D 116 " --> pdb=" O ILE D 120 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ILE D 120 " --> pdb=" O GLY D 116 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ASN D 125 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N VAL D 135 " --> pdb=" O ASN D 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 146 through 151 removed outlier: 6.600A pdb=" N SER D 160 " --> pdb=" O SER D 147 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N CYS D 149 " --> pdb=" O VAL D 158 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL D 158 " --> pdb=" O CYS D 149 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N PHE D 151 " --> pdb=" O GLN D 156 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N GLN D 156 " --> pdb=" O PHE D 151 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THR D 165 " --> pdb=" O SER D 161 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ASP D 170 " --> pdb=" O GLN D 176 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N GLN D 176 " --> pdb=" O ASP D 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 187 through 192 removed outlier: 6.850A pdb=" N GLY D 202 " --> pdb=" O MET D 188 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LEU D 190 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL D 200 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N LEU D 192 " --> pdb=" O LEU D 198 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU D 198 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N SER D 207 " --> pdb=" O ALA D 203 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ASP D 212 " --> pdb=" O CYS D 218 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N CYS D 218 " --> pdb=" O ASP D 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 229 through 234 removed outlier: 6.719A pdb=" N GLY D 244 " --> pdb=" O ASN D 230 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ILE D 232 " --> pdb=" O ALA D 242 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ALA D 242 " --> pdb=" O ILE D 232 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N PHE D 234 " --> pdb=" O ALA D 240 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ALA D 240 " --> pdb=" O PHE D 234 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ASP D 254 " --> pdb=" O GLU D 260 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N GLU D 260 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 294 through 297 removed outlier: 3.819A pdb=" N SER D 275 " --> pdb=" O GLY D 288 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 46 through 51 removed outlier: 6.832A pdb=" N ILE D 338 " --> pdb=" O ARG D 48 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N THR D 50 " --> pdb=" O LEU D 336 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LEU D 336 " --> pdb=" O THR D 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'F' and resid 10 through 12 removed outlier: 5.731A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N ALA F 40 " --> pdb=" O LEU F 45 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LEU F 45 " --> pdb=" O ALA F 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 143 through 148 Processing sheet with id= L, first strand: chain 'F' and resid 231 through 233 removed outlier: 6.244A pdb=" N LEU F 166 " --> pdb=" O LEU F 175 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N LEU F 175 " --> pdb=" O LEU F 166 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 199 through 201 403 hydrogen bonds defined for protein. 1110 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: 2.53 Time building geometry restraints manager: 3.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1382 1.31 - 1.44: 2390 1.44 - 1.57: 4843 1.57 - 1.70: 4 1.70 - 1.83: 94 Bond restraints: 8713 Sorted by residual: bond pdb=" C39 XT9 A 101 " pdb=" N40 XT9 A 101 " ideal model delta sigma weight residual 2.071 1.365 0.706 2.00e-02 2.50e+03 1.25e+03 bond pdb=" C33 XT9 A 101 " pdb=" C38 XT9 A 101 " ideal model delta sigma weight residual 1.158 1.642 -0.484 2.00e-02 2.50e+03 5.87e+02 bond pdb=" C38 XT9 A 101 " pdb=" C39 XT9 A 101 " ideal model delta sigma weight residual 1.970 1.648 0.322 2.00e-02 2.50e+03 2.59e+02 bond pdb=" C34 XT9 A 101 " pdb=" C36 XT9 A 101 " ideal model delta sigma weight residual 1.329 1.638 -0.309 2.00e-02 2.50e+03 2.39e+02 bond pdb=" C31 XT9 A 101 " pdb=" C34 XT9 A 101 " ideal model delta sigma weight residual 1.799 1.540 0.259 2.00e-02 2.50e+03 1.68e+02 ... (remaining 8708 not shown) Histogram of bond angle deviations from ideal: 98.75 - 105.84: 145 105.84 - 112.94: 4712 112.94 - 120.03: 3072 120.03 - 127.12: 3819 127.12 - 134.22: 89 Bond angle restraints: 11837 Sorted by residual: angle pdb=" CA DPN A 9 " pdb=" CB DPN A 9 " pdb=" CG DPN A 9 " ideal model delta sigma weight residual 113.80 105.17 8.63 1.00e+00 1.00e+00 7.45e+01 angle pdb=" C48 XT9 A 101 " pdb=" C50 XT9 A 101 " pdb=" O51 XT9 A 101 " ideal model delta sigma weight residual 108.25 133.57 -25.32 3.00e+00 1.11e-01 7.12e+01 angle pdb=" C PRO B 59 " pdb=" N VAL B 60 " pdb=" CA VAL B 60 " ideal model delta sigma weight residual 122.09 110.85 11.24 1.49e+00 4.50e-01 5.70e+01 angle pdb=" N LYS B 338 " pdb=" CA LYS B 338 " pdb=" C LYS B 338 " ideal model delta sigma weight residual 113.21 105.23 7.98 1.15e+00 7.56e-01 4.81e+01 angle pdb=" N VAL C 201 " pdb=" CA VAL C 201 " pdb=" C VAL C 201 " ideal model delta sigma weight residual 113.71 108.29 5.42 9.50e-01 1.11e+00 3.26e+01 ... (remaining 11832 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 4603 17.40 - 34.80: 417 34.80 - 52.20: 94 52.20 - 69.60: 17 69.60 - 87.00: 6 Dihedral angle restraints: 5137 sinusoidal: 1924 harmonic: 3213 Sorted by residual: dihedral pdb=" CB CYS B 131 " pdb=" SG CYS B 131 " pdb=" SG CYS B 210 " pdb=" CB CYS B 210 " ideal model delta sinusoidal sigma weight residual 93.00 133.89 -40.89 1 1.00e+01 1.00e-02 2.34e+01 dihedral pdb=" CA GLY D 306 " pdb=" C GLY D 306 " pdb=" N VAL D 307 " pdb=" CA VAL D 307 " ideal model delta harmonic sigma weight residual -180.00 -159.96 -20.04 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA PHE F 32 " pdb=" C PHE F 32 " pdb=" N GLY F 33 " pdb=" CA GLY F 33 " ideal model delta harmonic sigma weight residual 180.00 160.20 19.80 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 5134 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.034: 1382 1.034 - 2.067: 0 2.067 - 3.101: 0 3.101 - 4.135: 0 4.135 - 5.169: 1 Chirality restraints: 1383 Sorted by residual: chirality pdb=" C34 XT9 A 101 " pdb=" C31 XT9 A 101 " pdb=" C33 XT9 A 101 " pdb=" C36 XT9 A 101 " both_signs ideal model delta sigma weight residual False -2.68 2.49 -5.17 2.00e-01 2.50e+01 6.68e+02 chirality pdb=" CB ILE B 290 " pdb=" CA ILE B 290 " pdb=" CG1 ILE B 290 " pdb=" CG2 ILE B 290 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.08e+00 chirality pdb=" C29 XT9 A 101 " pdb=" C30 XT9 A 101 " pdb=" C32 XT9 A 101 " pdb=" N28 XT9 A 101 " both_signs ideal model delta sigma weight residual False 2.40 2.76 -0.36 2.00e-01 2.50e+01 3.20e+00 ... (remaining 1380 not shown) Planarity restraints: 1480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 332 " 0.031 2.00e-02 2.50e+03 2.74e-02 1.88e+01 pdb=" CG TRP D 332 " -0.072 2.00e-02 2.50e+03 pdb=" CD1 TRP D 332 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP D 332 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP D 332 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 332 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 332 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 332 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 332 " 0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP D 332 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 299 " -0.017 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C LEU B 299 " 0.061 2.00e-02 2.50e+03 pdb=" O LEU B 299 " -0.023 2.00e-02 2.50e+03 pdb=" N GLY B 300 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 83 " 0.016 2.00e-02 2.50e+03 3.19e-02 1.01e+01 pdb=" C VAL B 83 " -0.055 2.00e-02 2.50e+03 pdb=" O VAL B 83 " 0.021 2.00e-02 2.50e+03 pdb=" N ILE B 84 " 0.018 2.00e-02 2.50e+03 ... (remaining 1477 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1021 2.75 - 3.29: 8003 3.29 - 3.83: 14554 3.83 - 4.36: 16799 4.36 - 4.90: 29258 Nonbonded interactions: 69635 Sorted by model distance: nonbonded pdb=" CG1 VAL B 69 " pdb=" SG CYS B 324 " model vdw 2.217 3.820 nonbonded pdb=" OG SER D 331 " pdb=" OD1 ASP D 333 " model vdw 2.245 2.440 nonbonded pdb=" OG1 THR D 128 " pdb=" O GLU D 130 " model vdw 2.263 2.440 nonbonded pdb=" OE2 GLU C 8 " pdb=" OH TYR F 163 " model vdw 2.281 2.440 nonbonded pdb=" OH TYR D 85 " pdb=" OE1 GLU E 58 " model vdw 2.291 2.440 ... (remaining 69630 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.170 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 27.960 Find NCS groups from input model: 0.260 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: 0.010 Load rotamer database and sin/cos tables:12.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 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 : 0.014 0.706 8713 Z= 0.967 Angle : 0.960 25.319 11837 Z= 0.514 Chirality : 0.150 5.169 1383 Planarity : 0.006 0.065 1480 Dihedral : 14.295 87.003 3055 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 1.11 % Allowed : 5.00 % Favored : 93.88 % Rotamer: Outliers : 1.52 % Allowed : 1.31 % Favored : 97.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % 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: -0.96 (0.24), residues: 1079 helix: 0.26 (0.25), residues: 359 sheet: -0.13 (0.30), residues: 269 loop : -1.64 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.003 TRP D 332 HIS 0.006 0.001 HIS D 54 PHE 0.029 0.002 PHE F 200 TYR 0.020 0.002 TYR F 178 ARG 0.005 0.000 ARG D 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 173 time to evaluate : 0.840 Fit side-chains revert: symmetry clash REVERT: B 302 THR cc_start: 0.7425 (OUTLIER) cc_final: 0.7070 (m) REVERT: B 305 SER cc_start: 0.8180 (m) cc_final: 0.7736 (p) outliers start: 14 outliers final: 9 residues processed: 184 average time/residue: 1.0229 time to fit residues: 201.7758 Evaluate side-chains 171 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 161 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 257 ARG Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain A residue 2 TYR Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 7 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 63 optimal weight: 0.6980 chunk 98 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 313 ASN F 130 GLN B 95 ASN B 115 GLN B 304 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.0945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 8713 Z= 0.247 Angle : 0.779 26.642 11837 Z= 0.349 Chirality : 0.061 1.599 1383 Planarity : 0.004 0.055 1480 Dihedral : 7.592 56.620 1226 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.83 % Allowed : 11.21 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % 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: -0.35 (0.25), residues: 1079 helix: 1.20 (0.27), residues: 361 sheet: -0.15 (0.30), residues: 257 loop : -1.44 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 332 HIS 0.004 0.001 HIS D 91 PHE 0.022 0.001 PHE B 293 TYR 0.018 0.002 TYR F 178 ARG 0.006 0.000 ARG D 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 174 time to evaluate : 0.974 Fit side-chains REVERT: D 219 ARG cc_start: 0.7164 (ttm-80) cc_final: 0.6865 (ttm-80) REVERT: B 257 ARG cc_start: 0.7411 (OUTLIER) cc_final: 0.6766 (mtm110) REVERT: B 305 SER cc_start: 0.7911 (m) cc_final: 0.7126 (p) REVERT: A 2 TYR cc_start: 0.2130 (OUTLIER) cc_final: 0.0765 (t80) outliers start: 26 outliers final: 15 residues processed: 183 average time/residue: 1.0425 time to fit residues: 204.9750 Evaluate side-chains 191 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 174 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 313 ASN Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain E residue 58 GLU Chi-restraints excluded: chain F residue 211 ASP Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 257 ARG Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain B residue 304 HIS Chi-restraints excluded: chain A residue 2 TYR Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 7 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 98 optimal weight: 0.5980 chunk 106 optimal weight: 0.9980 chunk 87 optimal weight: 0.1980 chunk 97 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 88 ASN D 110 ASN D 125 ASN D 239 ASN ** D 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 293 ASN D 313 ASN ** D 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 304 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8713 Z= 0.200 Angle : 0.749 26.093 11837 Z= 0.331 Chirality : 0.060 1.621 1383 Planarity : 0.004 0.052 1480 Dihedral : 7.277 57.175 1224 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.94 % Allowed : 14.25 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % 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: -0.01 (0.25), residues: 1079 helix: 1.69 (0.28), residues: 358 sheet: -0.06 (0.30), residues: 260 loop : -1.35 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 332 HIS 0.006 0.001 HIS B 304 PHE 0.013 0.001 PHE F 200 TYR 0.019 0.001 TYR B 140 ARG 0.004 0.000 ARG D 314 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 172 time to evaluate : 0.982 Fit side-chains revert: symmetry clash REVERT: F 19 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.8143 (tptp) REVERT: B 257 ARG cc_start: 0.7400 (OUTLIER) cc_final: 0.6825 (mtm110) REVERT: B 305 SER cc_start: 0.7982 (m) cc_final: 0.7459 (p) outliers start: 27 outliers final: 16 residues processed: 184 average time/residue: 1.0127 time to fit residues: 200.2924 Evaluate side-chains 188 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 170 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 58 GLU Chi-restraints excluded: chain F residue 19 LYS Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain F residue 211 ASP Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 257 ARG Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain A residue 2 TYR Chi-restraints excluded: chain A residue 7 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 0.0770 chunk 73 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 10 optimal weight: 0.0020 chunk 46 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 98 optimal weight: 0.5980 chunk 104 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 266 HIS D 293 ASN ** D 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 130 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8713 Z= 0.172 Angle : 0.735 26.586 11837 Z= 0.321 Chirality : 0.059 1.583 1383 Planarity : 0.004 0.050 1480 Dihedral : 6.716 55.625 1221 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.59 % Allowed : 15.23 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % 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: 0.17 (0.25), residues: 1079 helix: 1.87 (0.28), residues: 358 sheet: -0.04 (0.30), residues: 261 loop : -1.22 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 332 HIS 0.004 0.001 HIS D 54 PHE 0.012 0.001 PHE D 253 TYR 0.021 0.001 TYR B 140 ARG 0.004 0.000 ARG D 49 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 165 time to evaluate : 0.985 Fit side-chains outliers start: 33 outliers final: 21 residues processed: 178 average time/residue: 1.0285 time to fit residues: 196.7359 Evaluate side-chains 182 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 161 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 58 GLU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain F residue 211 ASP Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 304 HIS Chi-restraints excluded: chain A residue 2 TYR Chi-restraints excluded: chain A residue 7 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 1.9990 chunk 59 optimal weight: 0.4980 chunk 1 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 72 optimal weight: 0.3980 chunk 0 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 26 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 293 ASN ** D 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 130 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8713 Z= 0.219 Angle : 0.751 26.436 11837 Z= 0.332 Chirality : 0.060 1.581 1383 Planarity : 0.004 0.050 1480 Dihedral : 6.477 55.082 1217 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.24 % Allowed : 15.56 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % 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: 0.21 (0.25), residues: 1079 helix: 1.83 (0.28), residues: 363 sheet: -0.07 (0.30), residues: 262 loop : -1.12 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 332 HIS 0.004 0.001 HIS D 54 PHE 0.015 0.001 PHE B 293 TYR 0.018 0.002 TYR B 140 ARG 0.004 0.000 ARG D 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 158 time to evaluate : 0.943 Fit side-chains revert: symmetry clash REVERT: D 217 MET cc_start: 0.6620 (OUTLIER) cc_final: 0.6034 (pmt) REVERT: D 325 MET cc_start: 0.7272 (OUTLIER) cc_final: 0.6952 (mmt) outliers start: 39 outliers final: 22 residues processed: 175 average time/residue: 0.9734 time to fit residues: 183.5281 Evaluate side-chains 183 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 159 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 58 GLU Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain F residue 211 ASP Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain A residue 2 TYR Chi-restraints excluded: chain A residue 7 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.1980 chunk 94 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 104 optimal weight: 0.0980 chunk 86 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 8 optimal weight: 0.0470 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 333 GLN D 293 ASN ** D 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 130 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8713 Z= 0.178 Angle : 0.736 26.729 11837 Z= 0.322 Chirality : 0.059 1.575 1383 Planarity : 0.004 0.050 1480 Dihedral : 6.089 55.463 1213 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.48 % Allowed : 17.19 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % 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: 0.24 (0.26), residues: 1079 helix: 1.84 (0.28), residues: 368 sheet: -0.05 (0.30), residues: 262 loop : -1.13 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 332 HIS 0.004 0.001 HIS D 54 PHE 0.019 0.001 PHE B 293 TYR 0.016 0.001 TYR B 140 ARG 0.006 0.000 ARG B 271 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 165 time to evaluate : 0.939 Fit side-chains revert: symmetry clash REVERT: C 243 MET cc_start: 0.6309 (mmm) cc_final: 0.5998 (mmm) REVERT: D 217 MET cc_start: 0.6570 (OUTLIER) cc_final: 0.6090 (pmt) REVERT: A 2 TYR cc_start: 0.2132 (OUTLIER) cc_final: 0.0901 (t80) outliers start: 32 outliers final: 23 residues processed: 178 average time/residue: 0.9362 time to fit residues: 180.0965 Evaluate side-chains 184 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 159 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 333 GLN Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 58 GLU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain F residue 211 ASP Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain A residue 2 TYR Chi-restraints excluded: chain A residue 7 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 104 optimal weight: 9.9990 chunk 65 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 333 GLN D 293 ASN ** D 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 130 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8713 Z= 0.275 Angle : 0.780 26.339 11837 Z= 0.348 Chirality : 0.061 1.581 1383 Planarity : 0.004 0.049 1480 Dihedral : 6.226 55.771 1213 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.70 % Allowed : 17.41 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % 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: 0.16 (0.25), residues: 1079 helix: 1.71 (0.28), residues: 372 sheet: -0.07 (0.30), residues: 262 loop : -1.16 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 332 HIS 0.003 0.001 HIS D 54 PHE 0.027 0.002 PHE B 293 TYR 0.018 0.002 TYR B 140 ARG 0.005 0.000 ARG B 271 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 158 time to evaluate : 1.039 Fit side-chains revert: symmetry clash REVERT: C 243 MET cc_start: 0.6332 (mmm) cc_final: 0.6037 (mmm) REVERT: D 217 MET cc_start: 0.6606 (OUTLIER) cc_final: 0.6131 (pmt) REVERT: D 325 MET cc_start: 0.7308 (OUTLIER) cc_final: 0.6972 (mmt) REVERT: A 2 TYR cc_start: 0.2284 (OUTLIER) cc_final: 0.0949 (t80) outliers start: 34 outliers final: 24 residues processed: 171 average time/residue: 1.0028 time to fit residues: 185.4945 Evaluate side-chains 189 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 162 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 101 MET Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 58 GLU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain F residue 211 ASP Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain A residue 2 TYR Chi-restraints excluded: chain A residue 7 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 94 optimal weight: 0.8980 chunk 99 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 130 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8713 Z= 0.254 Angle : 0.774 26.394 11837 Z= 0.345 Chirality : 0.060 1.581 1383 Planarity : 0.004 0.049 1480 Dihedral : 6.214 56.730 1213 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.70 % Allowed : 18.17 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % 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: 0.20 (0.25), residues: 1079 helix: 1.77 (0.28), residues: 369 sheet: -0.05 (0.30), residues: 262 loop : -1.13 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP D 332 HIS 0.004 0.001 HIS D 54 PHE 0.028 0.001 PHE B 293 TYR 0.017 0.002 TYR F 178 ARG 0.005 0.000 ARG B 271 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 160 time to evaluate : 1.056 Fit side-chains revert: symmetry clash REVERT: C 243 MET cc_start: 0.6323 (mmm) cc_final: 0.6038 (mmm) REVERT: D 325 MET cc_start: 0.7315 (OUTLIER) cc_final: 0.6998 (mmt) REVERT: A 2 TYR cc_start: 0.2720 (OUTLIER) cc_final: 0.1478 (t80) outliers start: 34 outliers final: 24 residues processed: 175 average time/residue: 1.1116 time to fit residues: 209.1194 Evaluate side-chains 184 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 158 time to evaluate : 1.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 101 MET Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 58 GLU Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain F residue 211 ASP Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain A residue 2 TYR Chi-restraints excluded: chain A residue 7 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 0.7980 chunk 97 optimal weight: 0.0570 chunk 99 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 130 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8713 Z= 0.234 Angle : 0.770 26.545 11837 Z= 0.343 Chirality : 0.060 1.580 1383 Planarity : 0.004 0.049 1480 Dihedral : 6.176 58.427 1213 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.48 % Allowed : 18.50 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.25), residues: 1079 helix: 1.78 (0.28), residues: 369 sheet: -0.05 (0.30), residues: 262 loop : -1.09 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP D 332 HIS 0.004 0.001 HIS D 54 PHE 0.030 0.001 PHE B 293 TYR 0.017 0.001 TYR F 178 ARG 0.005 0.000 ARG D 314 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 161 time to evaluate : 0.953 Fit side-chains revert: symmetry clash REVERT: C 243 MET cc_start: 0.6314 (mmm) cc_final: 0.6036 (mmm) REVERT: D 325 MET cc_start: 0.7314 (OUTLIER) cc_final: 0.7001 (mmt) REVERT: E 37 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7643 (mp) REVERT: A 2 TYR cc_start: 0.2628 (OUTLIER) cc_final: 0.1373 (t80) outliers start: 32 outliers final: 22 residues processed: 174 average time/residue: 0.9841 time to fit residues: 184.4993 Evaluate side-chains 183 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 158 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 58 GLU Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain F residue 211 ASP Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain A residue 2 TYR Chi-restraints excluded: chain A residue 7 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 48 optimal weight: 0.4980 chunk 71 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 99 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 130 GLN B 322 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8713 Z= 0.230 Angle : 0.768 26.569 11837 Z= 0.342 Chirality : 0.060 1.579 1383 Planarity : 0.004 0.049 1480 Dihedral : 6.164 59.917 1213 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 3.16 % Allowed : 19.15 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.25), residues: 1079 helix: 1.82 (0.28), residues: 367 sheet: -0.04 (0.30), residues: 262 loop : -1.14 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP D 332 HIS 0.005 0.001 HIS D 54 PHE 0.034 0.001 PHE B 293 TYR 0.017 0.001 TYR F 178 ARG 0.005 0.000 ARG D 314 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 159 time to evaluate : 1.019 Fit side-chains revert: symmetry clash REVERT: C 243 MET cc_start: 0.6311 (mmm) cc_final: 0.6028 (mmm) REVERT: D 325 MET cc_start: 0.7313 (OUTLIER) cc_final: 0.7004 (mmt) REVERT: E 37 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7642 (mp) REVERT: B 90 MET cc_start: 0.4991 (mmt) cc_final: 0.4587 (mmt) REVERT: A 2 TYR cc_start: 0.2553 (OUTLIER) cc_final: 0.1317 (t80) outliers start: 29 outliers final: 23 residues processed: 173 average time/residue: 0.9912 time to fit residues: 184.6315 Evaluate side-chains 184 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 158 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 293 ASN Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 58 GLU Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain F residue 211 ASP Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain A residue 2 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 12 optimal weight: 0.2980 chunk 23 optimal weight: 0.7980 chunk 85 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 88 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 75 optimal weight: 0.0870 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 130 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.166308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.137021 restraints weight = 11736.902| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 1.90 r_work: 0.3655 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3514 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8713 Z= 0.202 Angle : 0.758 26.726 11837 Z= 0.336 Chirality : 0.060 1.576 1383 Planarity : 0.004 0.050 1480 Dihedral : 5.983 58.103 1212 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.72 % Allowed : 19.80 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % 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: 0.28 (0.25), residues: 1079 helix: 1.88 (0.28), residues: 367 sheet: -0.04 (0.30), residues: 262 loop : -1.11 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP D 332 HIS 0.004 0.001 HIS D 54 PHE 0.037 0.001 PHE B 293 TYR 0.016 0.001 TYR F 178 ARG 0.006 0.000 ARG D 314 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3926.93 seconds wall clock time: 70 minutes 34.77 seconds (4234.77 seconds total)