Starting phenix.real_space_refine on Sat Apr 6 14:10:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jxw_36715/04_2024/8jxw_36715_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jxw_36715/04_2024/8jxw_36715.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jxw_36715/04_2024/8jxw_36715_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jxw_36715/04_2024/8jxw_36715_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jxw_36715/04_2024/8jxw_36715_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jxw_36715/04_2024/8jxw_36715.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jxw_36715/04_2024/8jxw_36715.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jxw_36715/04_2024/8jxw_36715_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jxw_36715/04_2024/8jxw_36715_neut_updated.pdb" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.118 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 S 57 5.16 5 Cl 1 4.86 5 C 5390 2.51 5 N 1374 2.21 5 O 1567 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 33": "OE1" <-> "OE2" Residue "D GLU 58": "OE1" <-> "OE2" Residue "E GLU 46": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 8389 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1727 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 2, 'TRANS': 217} Chain breaks: 2 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "C" Number of atoms: 2432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2432 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 152 Unresolved non-hydrogen angles: 181 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 4, 'ARG:plan': 13, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 118 Chain: "D" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 363 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "E" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1691 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 217} Chain breaks: 1 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 49 Chain: "R" Number of atoms: 2153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2153 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 9, 'TRANS': 261} Chain breaks: 2 Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'TRP:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 61 Chain: "R" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'VCF': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.86, per 1000 atoms: 0.58 Number of scatterers: 8389 At special positions: 0 Unit cell: (91.3, 121, 129.8, 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) Cl 1 17.00 S 57 16.00 O 1567 8.00 N 1374 7.00 C 5390 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 160 " - pdb=" SG CYS E 230 " distance=2.05 Simple disulfide: pdb=" SG CYS R 87 " - pdb=" SG CYS R 164 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.18 Conformation dependent library (CDL) restraints added in 1.4 seconds 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2080 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 12 sheets defined 34.7% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'B' and resid 7 through 31 removed outlier: 3.861A pdb=" N ALA B 31 " --> pdb=" O GLY B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 52 Processing helix chain 'B' and resid 213 through 215 No H-bonds generated for 'chain 'B' and resid 213 through 215' Processing helix chain 'B' and resid 228 through 231 removed outlier: 4.508A pdb=" N ASP B 231 " --> pdb=" O SER B 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 228 through 231' Processing helix chain 'B' and resid 242 through 254 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 271 through 279 removed outlier: 3.650A pdb=" N LYS B 279 " --> pdb=" O GLU B 275 " (cutoff:3.500A) 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: 4.117A pdb=" N LEU B 310 " --> pdb=" O GLN B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 350 removed outlier: 4.417A pdb=" N PHE B 334 " --> pdb=" O ASN B 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 25 removed outlier: 3.862A pdb=" N CYS C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 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 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'R' and resid 15 through 42 removed outlier: 3.746A pdb=" N ALA R 19 " --> pdb=" O ARG R 15 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE R 20 " --> pdb=" O VAL R 16 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE R 21 " --> pdb=" O THR R 17 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 77 removed outlier: 3.693A pdb=" N VAL R 64 " --> pdb=" O SER R 60 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER R 68 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ILE R 69 " --> pdb=" O GLY R 65 " (cutoff:3.500A) Proline residue: R 70 - end of helix removed outlier: 3.703A pdb=" N ILE R 73 " --> pdb=" O ILE R 69 " (cutoff:3.500A) Proline residue: R 74 - end of helix Processing helix chain 'R' and resid 84 through 117 removed outlier: 3.862A pdb=" N VAL R 116 " --> pdb=" O ARG R 112 " (cutoff:3.500A) Processing helix chain 'R' and resid 119 through 123 Processing helix chain 'R' and resid 131 through 153 removed outlier: 3.974A pdb=" N ASN R 147 " --> pdb=" O ALA R 143 " (cutoff:3.500A) Proline residue: R 149 - end of helix Processing helix chain 'R' and resid 167 through 170 Processing helix chain 'R' and resid 172 through 204 removed outlier: 5.733A pdb=" N ILE R 185 " --> pdb=" O LEU R 181 " (cutoff:3.500A) Proline residue: R 186 - end of helix removed outlier: 4.108A pdb=" N ARG R 204 " --> pdb=" O SER R 200 " (cutoff:3.500A) Processing helix chain 'R' and resid 294 through 329 Proline residue: R 318 - end of helix removed outlier: 3.829A pdb=" N TYR R 329 " --> pdb=" O VAL R 325 " (cutoff:3.500A) Processing helix chain 'R' and resid 338 through 361 removed outlier: 3.715A pdb=" N TRP R 348 " --> pdb=" O PHE R 344 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN R 350 " --> pdb=" O LEU R 346 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N SER R 351 " --> pdb=" O GLN R 347 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE R 352 " --> pdb=" O TRP R 348 " (cutoff:3.500A) Proline residue: R 355 - end of helix removed outlier: 3.665A pdb=" N TYR R 358 " --> pdb=" O ASN R 354 " (cutoff:3.500A) Proline residue: R 359 - end of helix Processing helix chain 'R' and resid 363 through 371 Processing sheet with id= A, first strand: chain 'B' and resid 319 through 323 removed outlier: 6.835A pdb=" N ILE B 264 " --> pdb=" O TYR B 320 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N HIS B 322 " --> pdb=" O ILE B 264 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LEU B 266 " --> pdb=" O HIS B 322 " (cutoff:3.500A) removed outlier: 3.775A 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: 7.043A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 5.655A 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: 6.955A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.835A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.070A 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: 6.855A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.312A 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 234 removed outlier: 7.005A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 275 through 278 removed outlier: 4.486A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.941A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.802A 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 115 through 117 removed outlier: 5.593A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 156 through 161 Processing sheet with id= L, first strand: chain 'E' and resid 244 through 246 removed outlier: 6.178A pdb=" N LEU E 179 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N LEU E 188 " --> pdb=" O LEU E 179 " (cutoff:3.500A) 389 hydrogen bonds defined for protein. 1059 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: 2.17 Time building geometry restraints manager: 3.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2652 1.34 - 1.46: 2161 1.46 - 1.58: 3684 1.58 - 1.70: 1 1.70 - 1.83: 83 Bond restraints: 8581 Sorted by residual: bond pdb=" C08 VCF R 401 " pdb=" N09 VCF R 401 " ideal model delta sigma weight residual 1.453 1.313 0.140 2.00e-02 2.50e+03 4.93e+01 bond pdb=" N VAL B 233 " pdb=" CA VAL B 233 " ideal model delta sigma weight residual 1.457 1.494 -0.036 1.25e-02 6.40e+03 8.39e+00 bond pdb=" C13 VCF R 401 " pdb="CL1 VCF R 401 " ideal model delta sigma weight residual 1.785 1.730 0.055 2.00e-02 2.50e+03 7.57e+00 bond pdb=" C11 VCF R 401 " pdb=" O17 VCF R 401 " ideal model delta sigma weight residual 1.418 1.365 0.053 2.00e-02 2.50e+03 7.12e+00 bond pdb=" C10 VCF R 401 " pdb=" N09 VCF R 401 " ideal model delta sigma weight residual 1.472 1.420 0.052 2.00e-02 2.50e+03 6.85e+00 ... (remaining 8576 not shown) Histogram of bond angle deviations from ideal: 99.17 - 106.16: 167 106.16 - 113.14: 4636 113.14 - 120.12: 3123 120.12 - 127.11: 3660 127.11 - 134.09: 102 Bond angle restraints: 11688 Sorted by residual: angle pdb=" CA PRO R 355 " pdb=" N PRO R 355 " pdb=" CD PRO R 355 " ideal model delta sigma weight residual 112.00 102.45 9.55 1.40e+00 5.10e-01 4.66e+01 angle pdb=" CA PRO C 39 " pdb=" N PRO C 39 " pdb=" CD PRO C 39 " ideal model delta sigma weight residual 112.00 102.87 9.13 1.40e+00 5.10e-01 4.25e+01 angle pdb=" C19 VCF R 401 " pdb=" C18 VCF R 401 " pdb=" O17 VCF R 401 " ideal model delta sigma weight residual 129.02 112.34 16.68 3.00e+00 1.11e-01 3.09e+01 angle pdb=" C11 VCF R 401 " pdb=" C10 VCF R 401 " pdb=" N09 VCF R 401 " ideal model delta sigma weight residual 110.98 125.10 -14.12 3.00e+00 1.11e-01 2.22e+01 angle pdb=" N ALA E 92 " pdb=" CA ALA E 92 " pdb=" C ALA E 92 " ideal model delta sigma weight residual 107.88 113.70 -5.82 1.41e+00 5.03e-01 1.70e+01 ... (remaining 11683 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.99: 4377 13.99 - 27.98: 445 27.98 - 41.96: 118 41.96 - 55.95: 26 55.95 - 69.94: 12 Dihedral angle restraints: 4978 sinusoidal: 1758 harmonic: 3220 Sorted by residual: dihedral pdb=" CB CYS E 160 " pdb=" SG CYS E 160 " pdb=" SG CYS E 230 " pdb=" CB CYS E 230 " ideal model delta sinusoidal sigma weight residual 93.00 138.07 -45.07 1 1.00e+01 1.00e-02 2.82e+01 dihedral pdb=" CA ILE R 67 " pdb=" C ILE R 67 " pdb=" N SER R 68 " pdb=" CA SER R 68 " ideal model delta harmonic sigma weight residual -180.00 -155.30 -24.70 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA GLU R 182 " pdb=" C GLU R 182 " pdb=" N PHE R 183 " pdb=" CA PHE R 183 " ideal model delta harmonic sigma weight residual -180.00 -156.83 -23.17 0 5.00e+00 4.00e-02 2.15e+01 ... (remaining 4975 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 833 0.039 - 0.078: 382 0.078 - 0.118: 103 0.118 - 0.157: 38 0.157 - 0.196: 3 Chirality restraints: 1359 Sorted by residual: chirality pdb=" CA PRO R 355 " pdb=" N PRO R 355 " pdb=" C PRO R 355 " pdb=" CB PRO R 355 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 9.59e-01 chirality pdb=" CA VAL R 16 " pdb=" N VAL R 16 " pdb=" C VAL R 16 " pdb=" CB VAL R 16 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.55e-01 chirality pdb=" CA VAL B 233 " pdb=" N VAL B 233 " pdb=" C VAL B 233 " pdb=" CB VAL B 233 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.49e-01 ... (remaining 1356 not shown) Planarity restraints: 1465 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN R 354 " 0.068 5.00e-02 4.00e+02 9.69e-02 1.50e+01 pdb=" N PRO R 355 " -0.167 5.00e-02 4.00e+02 pdb=" CA PRO R 355 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO R 355 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 38 " -0.063 5.00e-02 4.00e+02 8.98e-02 1.29e+01 pdb=" N PRO C 39 " 0.155 5.00e-02 4.00e+02 pdb=" CA PRO C 39 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 39 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 48 " -0.043 5.00e-02 4.00e+02 6.50e-02 6.76e+00 pdb=" N PRO D 49 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO D 49 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 49 " -0.036 5.00e-02 4.00e+02 ... (remaining 1462 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 81 2.65 - 3.22: 7431 3.22 - 3.78: 11784 3.78 - 4.34: 15890 4.34 - 4.90: 27582 Nonbonded interactions: 62768 Sorted by model distance: nonbonded pdb=" O HIS C 54 " pdb=" OG SER C 334 " model vdw 2.092 2.440 nonbonded pdb=" OG SER C 331 " pdb=" OD1 ASP C 333 " model vdw 2.130 2.440 nonbonded pdb=" OD1 ASP C 247 " pdb=" OG1 THR C 249 " model vdw 2.185 2.440 nonbonded pdb=" O ASP C 163 " pdb=" OG1 THR C 164 " model vdw 2.218 2.440 nonbonded pdb=" OG SER R 179 " pdb=" OG SER R 320 " model vdw 2.243 2.440 ... (remaining 62763 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: 0.700 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: 3.930 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 24.950 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 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 : 0.006 0.140 8581 Z= 0.403 Angle : 0.865 16.683 11688 Z= 0.472 Chirality : 0.048 0.196 1359 Planarity : 0.006 0.097 1465 Dihedral : 13.113 69.938 2892 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.80 % Allowed : 1.03 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.59 (0.24), residues: 1088 helix: 1.24 (0.26), residues: 374 sheet: 0.09 (0.30), residues: 280 loop : -2.25 (0.25), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 211 HIS 0.010 0.002 HIS C 183 PHE 0.017 0.002 PHE R 349 TYR 0.014 0.002 TYR R 329 ARG 0.008 0.001 ARG C 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 112 time to evaluate : 0.868 Fit side-chains REVERT: C 101 MET cc_start: 0.8642 (mtt) cc_final: 0.8392 (mtt) outliers start: 7 outliers final: 4 residues processed: 119 average time/residue: 0.2303 time to fit residues: 37.2072 Evaluate side-chains 98 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 94 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 293 ASN Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 15 ARG Chi-restraints excluded: chain R residue 16 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.9980 chunk 82 optimal weight: 0.0170 chunk 45 optimal weight: 0.3980 chunk 28 optimal weight: 0.6980 chunk 55 optimal weight: 20.0000 chunk 44 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 331 ASN C 110 ASN C 119 ASN ** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 33 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 8581 Z= 0.158 Angle : 0.553 7.034 11688 Z= 0.293 Chirality : 0.041 0.139 1359 Planarity : 0.004 0.046 1465 Dihedral : 5.418 53.170 1188 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.38 % Allowed : 7.00 % Favored : 91.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.09 (0.25), residues: 1088 helix: 1.93 (0.26), residues: 374 sheet: 0.21 (0.31), residues: 278 loop : -1.78 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 82 HIS 0.005 0.001 HIS C 183 PHE 0.020 0.001 PHE R 322 TYR 0.012 0.001 TYR R 329 ARG 0.005 0.000 ARG C 304 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 112 time to evaluate : 0.919 Fit side-chains REVERT: B 349 LYS cc_start: 0.6678 (mmtt) cc_final: 0.6354 (mmtm) REVERT: C 101 MET cc_start: 0.8610 (mtt) cc_final: 0.8337 (mtt) outliers start: 12 outliers final: 9 residues processed: 114 average time/residue: 0.1989 time to fit residues: 31.6613 Evaluate side-chains 111 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 102 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain E residue 160 CYS Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain R residue 15 ARG Chi-restraints excluded: chain R residue 16 VAL Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain R residue 321 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 0.0030 chunk 30 optimal weight: 0.9990 chunk 82 optimal weight: 6.9990 chunk 67 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 99 optimal weight: 0.0980 chunk 107 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 8581 Z= 0.148 Angle : 0.531 8.987 11688 Z= 0.279 Chirality : 0.041 0.133 1359 Planarity : 0.004 0.041 1465 Dihedral : 4.773 48.361 1185 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.41 % Allowed : 8.37 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.35 (0.25), residues: 1088 helix: 1.98 (0.27), residues: 382 sheet: 0.38 (0.31), residues: 277 loop : -1.54 (0.27), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 82 HIS 0.004 0.001 HIS C 183 PHE 0.012 0.001 PHE R 168 TYR 0.011 0.001 TYR R 329 ARG 0.005 0.000 ARG C 304 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 104 time to evaluate : 0.903 Fit side-chains REVERT: C 101 MET cc_start: 0.8599 (mtt) cc_final: 0.8351 (mtt) REVERT: C 237 ASN cc_start: 0.8594 (t0) cc_final: 0.8378 (t0) REVERT: E 83 MET cc_start: 0.6767 (mtp) cc_final: 0.6549 (mtm) REVERT: R 15 ARG cc_start: 0.6490 (OUTLIER) cc_final: 0.6255 (mmt180) outliers start: 21 outliers final: 16 residues processed: 111 average time/residue: 0.1996 time to fit residues: 30.8503 Evaluate side-chains 119 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 102 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 160 CYS Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain R residue 15 ARG Chi-restraints excluded: chain R residue 151 ILE Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain R residue 325 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 47 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 94 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8581 Z= 0.196 Angle : 0.554 7.424 11688 Z= 0.292 Chirality : 0.042 0.133 1359 Planarity : 0.004 0.042 1465 Dihedral : 4.608 42.360 1184 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.98 % Allowed : 8.94 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.41 (0.25), residues: 1088 helix: 2.01 (0.27), residues: 383 sheet: 0.43 (0.31), residues: 277 loop : -1.50 (0.27), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 82 HIS 0.004 0.001 HIS C 183 PHE 0.014 0.002 PHE B 189 TYR 0.013 0.001 TYR R 329 ARG 0.006 0.000 ARG C 304 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 102 time to evaluate : 0.926 Fit side-chains REVERT: C 101 MET cc_start: 0.8619 (mtt) cc_final: 0.8347 (mtt) REVERT: C 336 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8685 (tt) REVERT: E 83 MET cc_start: 0.6908 (mtp) cc_final: 0.6598 (mtm) REVERT: R 15 ARG cc_start: 0.6728 (OUTLIER) cc_final: 0.5773 (mmp-170) REVERT: R 30 MET cc_start: 0.7547 (ptm) cc_final: 0.7338 (ptp) outliers start: 26 outliers final: 19 residues processed: 113 average time/residue: 0.1911 time to fit residues: 30.3365 Evaluate side-chains 117 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 96 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 160 CYS Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain R residue 15 ARG Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 151 ILE Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain R residue 325 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 0.0980 chunk 1 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 43 optimal weight: 0.0980 chunk 89 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 94 optimal weight: 0.7980 chunk 26 optimal weight: 0.4980 chunk 35 optimal weight: 2.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 331 ASN C 119 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8581 Z= 0.120 Angle : 0.488 6.686 11688 Z= 0.257 Chirality : 0.040 0.133 1359 Planarity : 0.004 0.041 1465 Dihedral : 4.247 38.371 1184 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.83 % Allowed : 10.89 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.62 (0.26), residues: 1088 helix: 2.20 (0.28), residues: 381 sheet: 0.53 (0.31), residues: 277 loop : -1.36 (0.27), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 82 HIS 0.003 0.001 HIS C 183 PHE 0.011 0.001 PHE R 168 TYR 0.009 0.001 TYR R 329 ARG 0.005 0.000 ARG C 304 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 105 time to evaluate : 0.863 Fit side-chains REVERT: C 101 MET cc_start: 0.8517 (mtt) cc_final: 0.8267 (mtt) REVERT: C 336 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8553 (tt) REVERT: E 83 MET cc_start: 0.6789 (mtp) cc_final: 0.6516 (mtm) REVERT: E 93 MET cc_start: 0.6959 (OUTLIER) cc_final: 0.6474 (mmm) REVERT: R 30 MET cc_start: 0.7441 (ptm) cc_final: 0.7212 (ptp) outliers start: 16 outliers final: 13 residues processed: 113 average time/residue: 0.1991 time to fit residues: 31.5323 Evaluate side-chains 114 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 99 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 160 CYS Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain R residue 321 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 105 optimal weight: 8.9990 chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 0.0020 chunk 8 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 chunk 101 optimal weight: 0.0980 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8581 Z= 0.125 Angle : 0.484 9.474 11688 Z= 0.253 Chirality : 0.040 0.134 1359 Planarity : 0.004 0.041 1465 Dihedral : 3.879 18.791 1180 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.18 % Allowed : 11.12 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.73 (0.26), residues: 1088 helix: 2.25 (0.28), residues: 382 sheet: 0.56 (0.31), residues: 276 loop : -1.26 (0.27), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 82 HIS 0.002 0.001 HIS E 35 PHE 0.011 0.001 PHE B 189 TYR 0.010 0.001 TYR R 329 ARG 0.007 0.000 ARG C 304 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 101 time to evaluate : 0.940 Fit side-chains REVERT: C 101 MET cc_start: 0.8525 (mtt) cc_final: 0.8268 (mtt) REVERT: E 83 MET cc_start: 0.6807 (mtp) cc_final: 0.6533 (mtm) REVERT: E 93 MET cc_start: 0.6950 (OUTLIER) cc_final: 0.6642 (mmm) REVERT: R 30 MET cc_start: 0.7459 (ptm) cc_final: 0.7218 (ptp) outliers start: 19 outliers final: 12 residues processed: 110 average time/residue: 0.1918 time to fit residues: 29.9998 Evaluate side-chains 109 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 96 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 160 CYS Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain R residue 60 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 88 optimal weight: 0.0870 chunk 58 optimal weight: 2.9990 chunk 105 optimal weight: 0.1980 chunk 65 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 48 optimal weight: 0.0060 chunk 41 optimal weight: 1.9990 overall best weight: 0.4174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8581 Z= 0.116 Angle : 0.473 8.972 11688 Z= 0.247 Chirality : 0.040 0.133 1359 Planarity : 0.004 0.040 1465 Dihedral : 3.769 18.308 1180 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.52 % Allowed : 11.12 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.79 (0.26), residues: 1088 helix: 2.31 (0.28), residues: 383 sheet: 0.48 (0.31), residues: 282 loop : -1.16 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 82 HIS 0.002 0.001 HIS E 35 PHE 0.010 0.001 PHE B 189 TYR 0.008 0.001 TYR R 192 ARG 0.006 0.000 ARG C 304 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 107 time to evaluate : 0.975 Fit side-chains REVERT: B 211 TRP cc_start: 0.6931 (OUTLIER) cc_final: 0.6644 (p-90) REVERT: C 101 MET cc_start: 0.8510 (mtt) cc_final: 0.8286 (mtt) REVERT: E 93 MET cc_start: 0.6902 (OUTLIER) cc_final: 0.6534 (mmm) REVERT: R 30 MET cc_start: 0.7402 (ptm) cc_final: 0.7157 (ptp) outliers start: 22 outliers final: 12 residues processed: 116 average time/residue: 0.2007 time to fit residues: 33.1037 Evaluate side-chains 115 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 101 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 160 CYS Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 151 ILE Chi-restraints excluded: chain R residue 178 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 66 optimal weight: 0.3980 chunk 71 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 82 optimal weight: 0.2980 chunk 95 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8581 Z= 0.145 Angle : 0.493 8.595 11688 Z= 0.258 Chirality : 0.040 0.133 1359 Planarity : 0.004 0.041 1465 Dihedral : 3.834 18.356 1180 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.06 % Allowed : 12.27 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.75 (0.26), residues: 1088 helix: 2.21 (0.28), residues: 389 sheet: 0.46 (0.31), residues: 282 loop : -1.16 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 82 HIS 0.003 0.001 HIS E 35 PHE 0.011 0.001 PHE C 199 TYR 0.009 0.001 TYR E 191 ARG 0.008 0.000 ARG C 304 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 99 time to evaluate : 0.969 Fit side-chains revert: symmetry clash REVERT: C 101 MET cc_start: 0.8531 (mtt) cc_final: 0.8284 (mtt) REVERT: E 93 MET cc_start: 0.6966 (OUTLIER) cc_final: 0.6612 (mmm) REVERT: R 30 MET cc_start: 0.7465 (ptm) cc_final: 0.7233 (ptp) outliers start: 18 outliers final: 14 residues processed: 107 average time/residue: 0.1945 time to fit residues: 29.6764 Evaluate side-chains 113 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 98 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 160 CYS Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 151 ILE Chi-restraints excluded: chain R residue 182 GLU Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain R residue 362 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.0470 chunk 100 optimal weight: 0.0970 chunk 58 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 88 optimal weight: 0.0000 chunk 92 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 overall best weight: 0.3280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8581 Z= 0.109 Angle : 0.463 8.643 11688 Z= 0.242 Chirality : 0.039 0.133 1359 Planarity : 0.004 0.040 1465 Dihedral : 3.697 18.153 1180 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.49 % Allowed : 13.07 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.83 (0.26), residues: 1088 helix: 2.27 (0.28), residues: 389 sheet: 0.52 (0.31), residues: 279 loop : -1.10 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 82 HIS 0.002 0.000 HIS E 35 PHE 0.010 0.001 PHE R 168 TYR 0.009 0.001 TYR R 192 ARG 0.007 0.000 ARG C 304 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 104 time to evaluate : 0.958 Fit side-chains REVERT: C 101 MET cc_start: 0.8557 (mtt) cc_final: 0.8305 (mtt) REVERT: C 303 ASP cc_start: 0.7742 (p0) cc_final: 0.7496 (p0) REVERT: E 93 MET cc_start: 0.6881 (OUTLIER) cc_final: 0.6417 (mmm) REVERT: R 30 MET cc_start: 0.7451 (ptm) cc_final: 0.7218 (ptp) outliers start: 13 outliers final: 9 residues processed: 111 average time/residue: 0.2071 time to fit residues: 32.0149 Evaluate side-chains 105 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 95 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 160 CYS Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 362 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 0.7980 chunk 71 optimal weight: 10.0000 chunk 108 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 92 optimal weight: 0.4980 chunk 26 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8581 Z= 0.156 Angle : 0.500 8.948 11688 Z= 0.261 Chirality : 0.040 0.133 1359 Planarity : 0.004 0.037 1465 Dihedral : 3.834 24.177 1180 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.26 % Allowed : 13.42 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.77 (0.26), residues: 1088 helix: 2.23 (0.27), residues: 389 sheet: 0.45 (0.31), residues: 282 loop : -1.13 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 82 HIS 0.003 0.001 HIS E 35 PHE 0.011 0.001 PHE C 199 TYR 0.009 0.001 TYR E 103 ARG 0.007 0.000 ARG C 304 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 98 time to evaluate : 1.076 Fit side-chains REVERT: C 101 MET cc_start: 0.8537 (mtt) cc_final: 0.8315 (mtt) REVERT: E 93 MET cc_start: 0.6927 (OUTLIER) cc_final: 0.6577 (mmm) REVERT: R 30 MET cc_start: 0.7472 (ptm) cc_final: 0.7247 (ptp) REVERT: R 316 TRP cc_start: 0.8220 (m100) cc_final: 0.8007 (m100) outliers start: 11 outliers final: 8 residues processed: 103 average time/residue: 0.1912 time to fit residues: 28.2870 Evaluate side-chains 103 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 94 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 160 CYS Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 362 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 6.9990 chunk 12 optimal weight: 0.4980 chunk 24 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 88 optimal weight: 0.0010 chunk 10 optimal weight: 0.0070 chunk 15 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 overall best weight: 0.4804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.183472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.138955 restraints weight = 9962.525| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.90 r_work: 0.3441 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8581 Z= 0.124 Angle : 0.471 8.987 11688 Z= 0.246 Chirality : 0.040 0.133 1359 Planarity : 0.004 0.037 1465 Dihedral : 3.753 22.515 1180 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.26 % Allowed : 13.76 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.26), residues: 1088 helix: 2.16 (0.28), residues: 395 sheet: 0.50 (0.31), residues: 279 loop : -1.00 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 82 HIS 0.003 0.001 HIS E 35 PHE 0.010 0.001 PHE B 189 TYR 0.009 0.001 TYR R 192 ARG 0.004 0.000 ARG C 304 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1967.99 seconds wall clock time: 36 minutes 41.63 seconds (2201.63 seconds total)