Starting phenix.real_space_refine on Mon Mar 11 13:36:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e9x_27967/03_2024/8e9x_27967_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e9x_27967/03_2024/8e9x_27967.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e9x_27967/03_2024/8e9x_27967_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e9x_27967/03_2024/8e9x_27967_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e9x_27967/03_2024/8e9x_27967_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e9x_27967/03_2024/8e9x_27967.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e9x_27967/03_2024/8e9x_27967.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e9x_27967/03_2024/8e9x_27967_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e9x_27967/03_2024/8e9x_27967_updated.pdb" } resolution = 2.7 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= 0.022 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 61 5.16 5 C 5364 2.51 5 N 1401 2.21 5 O 1554 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8380 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2124 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 263} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 1666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1666 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 210} Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "C" Number of atoms: 2485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2485 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'ARG:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 88 Chain: "D" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 353 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "E" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1730 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'WEC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.94, per 1000 atoms: 0.59 Number of scatterers: 8380 At special positions: 0 Unit cell: (91.52, 117.04, 128.48, 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 61 16.00 O 1554 8.00 N 1401 7.00 C 5364 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 105 " - pdb=" SG CYS A 185 " distance=2.03 Simple disulfide: pdb=" SG CYS A 426 " - pdb=" SG CYS A 429 " distance=2.02 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.79 Conformation dependent library (CDL) restraints added in 1.5 seconds 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2076 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 31 helices and 12 sheets defined 33.8% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 29 through 59 removed outlier: 3.652A pdb=" N THR A 46 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 47 " --> pdb=" O SER A 43 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE A 51 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU A 52 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL A 53 " --> pdb=" O GLY A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 83 removed outlier: 3.611A pdb=" N PHE A 70 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU A 71 " --> pdb=" O ASN A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 95 removed outlier: 3.880A pdb=" N THR A 90 " --> pdb=" O MET A 86 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL A 91 " --> pdb=" O ASN A 87 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 135 removed outlier: 4.162A pdb=" N ASN A 117 " --> pdb=" O CYS A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 143 No H-bonds generated for 'chain 'A' and resid 140 through 143' Processing helix chain 'A' and resid 146 through 169 removed outlier: 3.616A pdb=" N TRP A 157 " --> pdb=" O ILE A 153 " (cutoff:3.500A) Proline residue: A 166 - end of helix Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 188 through 191 removed outlier: 3.724A pdb=" N SER A 191 " --> pdb=" O GLN A 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 188 through 191' Processing helix chain 'A' and resid 193 through 203 Processing helix chain 'A' and resid 205 through 222 removed outlier: 3.561A pdb=" N MET A 211 " --> pdb=" O PRO A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 411 removed outlier: 4.038A pdb=" N LYS A 397 " --> pdb=" O ALA A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 425 removed outlier: 3.749A pdb=" N LEU A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR A 424 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N PHE A 425 " --> pdb=" O LEU A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 452 removed outlier: 3.530A pdb=" N SER A 436 " --> pdb=" O ASP A 432 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE A 437 " --> pdb=" O THR A 433 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N CYS A 442 " --> pdb=" O GLY A 438 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TYR A 443 " --> pdb=" O TYR A 439 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN A 445 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N SER A 446 " --> pdb=" O CYS A 442 " (cutoff:3.500A) Proline residue: A 450 - end of helix Processing helix chain 'A' and resid 454 through 456 No H-bonds generated for 'chain 'A' and resid 454 through 456' Processing helix chain 'A' and resid 458 through 464 Processing helix chain 'B' and resid 4 through 28 Processing helix chain 'B' and resid 43 through 45 No H-bonds generated for 'chain 'B' and resid 43 through 45' Processing helix chain 'B' and resid 90 through 92 No H-bonds generated for 'chain 'B' and resid 90 through 92' Processing helix chain 'B' and resid 94 through 97 Processing helix chain 'B' and resid 112 through 126 removed outlier: 4.168A pdb=" N HIS B 116 " --> pdb=" O TYR B 112 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLU B 117 " --> pdb=" O ASN B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 152 removed outlier: 3.600A pdb=" N GLU B 148 " --> pdb=" O ASP B 144 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS B 151 " --> pdb=" O GLY B 147 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYS B 152 " --> pdb=" O GLU B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 182 removed outlier: 3.810A pdb=" N LYS B 182 " --> pdb=" O GLN B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 222 Processing helix chain 'C' and resid 4 through 24 removed outlier: 3.558A pdb=" N GLU C 10 " --> pdb=" O GLN C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 33 No H-bonds generated for 'chain 'C' and resid 30 through 33' Processing helix chain 'D' and resid 13 through 22 Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'D' and resid 45 through 47 No H-bonds generated for 'chain 'D' and resid 45 through 47' Processing helix chain 'D' and resid 56 through 58 No H-bonds generated for 'chain 'D' and resid 56 through 58' Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'B' and resid 191 through 194 removed outlier: 3.931A pdb=" N ALA B 102 " --> pdb=" O LYS B 32 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.910A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.116A 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: 6.986A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.208A 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: 6.661A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.204A 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: 6.844A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.702A 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: 6.649A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 273 through 278 removed outlier: 6.516A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N PHE C 278 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LEU C 284 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY C 306 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 327 through 330 removed outlier: 3.676A pdb=" N LEU C 336 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.540A pdb=" N THR E 78 " --> pdb=" O ASP E 73 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 95 through 99 removed outlier: 3.622A pdb=" N ALA E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.537A pdb=" N LYS E 232 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY E 213 " --> pdb=" O LEU E 233 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE E 177 " --> pdb=" O TRP E 164 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 143 through 147 357 hydrogen bonds defined for protein. 1023 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: 2.18 Time building geometry restraints manager: 3.08 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: 2673 1.34 - 1.46: 2103 1.46 - 1.58: 3703 1.58 - 1.70: 0 1.70 - 1.82: 86 Bond restraints: 8565 Sorted by residual: bond pdb=" C01 WEC A 501 " pdb=" N02 WEC A 501 " ideal model delta sigma weight residual 1.446 1.286 0.160 2.00e-02 2.50e+03 6.41e+01 bond pdb=" N TRP A 440 " pdb=" CA TRP A 440 " ideal model delta sigma weight residual 1.459 1.511 -0.052 1.23e-02 6.61e+03 1.78e+01 bond pdb=" C03 WEC A 501 " pdb=" N02 WEC A 501 " ideal model delta sigma weight residual 1.431 1.371 0.060 2.00e-02 2.50e+03 9.04e+00 bond pdb=" C22 WEC A 501 " pdb=" N02 WEC A 501 " ideal model delta sigma weight residual 1.432 1.372 0.060 2.00e-02 2.50e+03 8.89e+00 bond pdb=" N TYR A 439 " pdb=" CA TYR A 439 " ideal model delta sigma weight residual 1.458 1.495 -0.038 1.27e-02 6.20e+03 8.88e+00 ... (remaining 8560 not shown) Histogram of bond angle deviations from ideal: 99.84 - 106.71: 195 106.71 - 113.59: 4732 113.59 - 120.46: 3198 120.46 - 127.34: 3454 127.34 - 134.21: 91 Bond angle restraints: 11670 Sorted by residual: angle pdb=" N TRP A 440 " pdb=" CA TRP A 440 " pdb=" C TRP A 440 " ideal model delta sigma weight residual 111.33 117.20 -5.87 1.21e+00 6.83e-01 2.35e+01 angle pdb=" C TYR A 439 " pdb=" CA TYR A 439 " pdb=" CB TYR A 439 " ideal model delta sigma weight residual 110.56 102.09 8.47 1.83e+00 2.99e-01 2.14e+01 angle pdb=" C06 WEC A 501 " pdb=" N07 WEC A 501 " pdb=" C08 WEC A 501 " ideal model delta sigma weight residual 120.02 133.22 -13.20 3.00e+00 1.11e-01 1.94e+01 angle pdb=" N ASN B 202 " pdb=" CA ASN B 202 " pdb=" C ASN B 202 " ideal model delta sigma weight residual 114.12 108.45 5.67 1.39e+00 5.18e-01 1.66e+01 angle pdb=" C09 WEC A 501 " pdb=" N14 WEC A 501 " pdb=" C15 WEC A 501 " ideal model delta sigma weight residual 111.01 122.28 -11.27 3.00e+00 1.11e-01 1.41e+01 ... (remaining 11665 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.42: 4665 19.42 - 38.84: 297 38.84 - 58.27: 31 58.27 - 77.69: 7 77.69 - 97.11: 2 Dihedral angle restraints: 5002 sinusoidal: 1783 harmonic: 3219 Sorted by residual: dihedral pdb=" CA THR E 160 " pdb=" C THR E 160 " pdb=" N TYR E 161 " pdb=" CA TYR E 161 " ideal model delta harmonic sigma weight residual -180.00 -160.77 -19.23 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA CYS A 426 " pdb=" C CYS A 426 " pdb=" N GLN A 427 " pdb=" CA GLN A 427 " ideal model delta harmonic sigma weight residual 180.00 -160.90 -19.10 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CB CYS A 105 " pdb=" SG CYS A 105 " pdb=" SG CYS A 185 " pdb=" CB CYS A 185 " ideal model delta sinusoidal sigma weight residual -86.00 -117.07 31.07 1 1.00e+01 1.00e-02 1.38e+01 ... (remaining 4999 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1135 0.054 - 0.108: 189 0.108 - 0.161: 31 0.161 - 0.215: 6 0.215 - 0.269: 1 Chirality restraints: 1362 Sorted by residual: chirality pdb=" CA LEU A 52 " pdb=" N LEU A 52 " pdb=" C LEU A 52 " pdb=" CB LEU A 52 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA TRP A 440 " pdb=" N TRP A 440 " pdb=" C TRP A 440 " pdb=" CB TRP A 440 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA ASN A 50 " pdb=" N ASN A 50 " pdb=" C ASN A 50 " pdb=" CB ASN A 50 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.21 2.00e-01 2.50e+01 1.05e+00 ... (remaining 1359 not shown) Planarity restraints: 1470 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG E 179 " 0.016 2.00e-02 2.50e+03 3.28e-02 1.07e+01 pdb=" C ARG E 179 " -0.057 2.00e-02 2.50e+03 pdb=" O ARG E 179 " 0.021 2.00e-02 2.50e+03 pdb=" N MET E 180 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 202 " -0.007 2.00e-02 2.50e+03 1.40e-02 1.97e+00 pdb=" C ASN B 202 " 0.024 2.00e-02 2.50e+03 pdb=" O ASN B 202 " -0.009 2.00e-02 2.50e+03 pdb=" N ALA B 203 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 153 " 0.022 5.00e-02 4.00e+02 3.35e-02 1.80e+00 pdb=" N PRO B 154 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO B 154 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 154 " 0.019 5.00e-02 4.00e+02 ... (remaining 1467 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 568 2.74 - 3.28: 8306 3.28 - 3.82: 13839 3.82 - 4.36: 16998 4.36 - 4.90: 29224 Nonbonded interactions: 68935 Sorted by model distance: nonbonded pdb=" O ILE C 58 " pdb=" OG SER C 316 " model vdw 2.200 2.440 nonbonded pdb=" OG SER B 88 " pdb=" OD2 ASP C 186 " model vdw 2.225 2.440 nonbonded pdb=" OG1 THR C 274 " pdb=" O VAL C 315 " model vdw 2.271 2.440 nonbonded pdb=" ND2 ASN C 340 " pdb=" OD1 ASN D 59 " model vdw 2.319 2.520 nonbonded pdb=" O SER E 30 " pdb=" OG SER E 53 " model vdw 2.328 2.440 ... (remaining 68930 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: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.130 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 24.430 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 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 : 0.004 0.160 8565 Z= 0.220 Angle : 0.602 13.200 11670 Z= 0.321 Chirality : 0.044 0.269 1362 Planarity : 0.003 0.034 1470 Dihedral : 12.623 97.111 2917 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.15 (0.26), residues: 1093 helix: 0.51 (0.28), residues: 359 sheet: 0.59 (0.31), residues: 286 loop : -1.00 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 339 HIS 0.002 0.001 HIS E 35 PHE 0.012 0.001 PHE A 189 TYR 0.023 0.001 TYR E 178 ARG 0.003 0.000 ARG E 179 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 0.975 Fit side-chains REVERT: A 410 ILE cc_start: 0.7951 (mm) cc_final: 0.7667 (mm) REVERT: B 29 LYS cc_start: 0.7759 (mppt) cc_final: 0.7504 (mppt) REVERT: B 81 PHE cc_start: 0.8308 (m-80) cc_final: 0.7896 (m-80) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.7920 time to fit residues: 163.7880 Evaluate side-chains 168 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 45 optimal weight: 0.2980 chunk 28 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 85 optimal weight: 0.0270 chunk 33 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 overall best weight: 0.6240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 ASN B 128 ASN B 202 ASN B 217 ASN C 88 ASN C 110 ASN C 259 GLN C 293 ASN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8565 Z= 0.226 Angle : 0.521 6.411 11670 Z= 0.272 Chirality : 0.042 0.163 1362 Planarity : 0.004 0.042 1470 Dihedral : 5.937 107.743 1192 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.07 % Allowed : 10.33 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.46 (0.26), residues: 1093 helix: 1.55 (0.28), residues: 357 sheet: 0.53 (0.30), residues: 289 loop : -0.85 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 169 HIS 0.004 0.001 HIS E 35 PHE 0.013 0.002 PHE A 189 TYR 0.014 0.001 TYR A 92 ARG 0.007 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 180 time to evaluate : 0.911 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 10 residues processed: 185 average time/residue: 0.7734 time to fit residues: 156.9400 Evaluate side-chains 177 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 167 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 439 TYR Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 201 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 98 optimal weight: 0.0040 chunk 33 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 GLN B 128 ASN B 217 ASN C 293 ASN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8565 Z= 0.233 Angle : 0.506 6.414 11670 Z= 0.263 Chirality : 0.041 0.148 1362 Planarity : 0.003 0.041 1470 Dihedral : 5.936 107.398 1192 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.33 % Allowed : 12.40 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.54 (0.26), residues: 1093 helix: 1.84 (0.29), residues: 356 sheet: 0.35 (0.29), residues: 297 loop : -0.84 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 169 HIS 0.003 0.001 HIS E 35 PHE 0.015 0.001 PHE A 189 TYR 0.015 0.001 TYR A 92 ARG 0.008 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 171 time to evaluate : 0.925 Fit side-chains revert: symmetry clash REVERT: A 73 SER cc_start: 0.8028 (p) cc_final: 0.7810 (t) REVERT: A 439 TYR cc_start: 0.8158 (OUTLIER) cc_final: 0.7841 (m-80) REVERT: B 29 LYS cc_start: 0.8050 (mppt) cc_final: 0.7602 (mppt) outliers start: 29 outliers final: 17 residues processed: 181 average time/residue: 0.8051 time to fit residues: 159.4444 Evaluate side-chains 186 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 168 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 426 CYS Chi-restraints excluded: chain A residue 439 TYR Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 201 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 2.9990 chunk 74 optimal weight: 0.0970 chunk 51 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 ASN B 217 ASN C 88 ASN C 293 ASN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8565 Z= 0.244 Angle : 0.507 7.938 11670 Z= 0.262 Chirality : 0.042 0.134 1362 Planarity : 0.003 0.041 1470 Dihedral : 5.963 107.614 1192 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.36 % Allowed : 13.20 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.53 (0.26), residues: 1093 helix: 1.89 (0.29), residues: 356 sheet: 0.30 (0.29), residues: 295 loop : -0.87 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 169 HIS 0.003 0.001 HIS E 35 PHE 0.015 0.001 PHE A 189 TYR 0.015 0.001 TYR A 92 ARG 0.009 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 173 time to evaluate : 0.932 Fit side-chains revert: symmetry clash REVERT: A 32 MET cc_start: 0.5667 (ppp) cc_final: 0.5431 (ppp) REVERT: A 439 TYR cc_start: 0.8125 (OUTLIER) cc_final: 0.7912 (m-80) REVERT: B 7 LYS cc_start: 0.8545 (mttp) cc_final: 0.8305 (mttm) REVERT: B 29 LYS cc_start: 0.8066 (mppt) cc_final: 0.7684 (mppt) outliers start: 38 outliers final: 23 residues processed: 187 average time/residue: 0.8032 time to fit residues: 165.1359 Evaluate side-chains 193 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 169 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 426 CYS Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 439 TYR Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 235 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 53 optimal weight: 0.0370 chunk 94 optimal weight: 2.9990 chunk 26 optimal weight: 0.2980 chunk 35 optimal weight: 1.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 ASN B 217 ASN C 293 ASN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8565 Z= 0.207 Angle : 0.487 7.005 11670 Z= 0.253 Chirality : 0.041 0.168 1362 Planarity : 0.003 0.037 1470 Dihedral : 5.894 107.732 1192 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.02 % Allowed : 14.47 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.57 (0.26), residues: 1093 helix: 1.98 (0.29), residues: 358 sheet: 0.37 (0.30), residues: 288 loop : -0.94 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 169 HIS 0.003 0.001 HIS E 35 PHE 0.013 0.001 PHE A 189 TYR 0.012 0.001 TYR A 92 ARG 0.008 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 169 time to evaluate : 1.073 Fit side-chains revert: symmetry clash REVERT: A 32 MET cc_start: 0.5591 (ppp) cc_final: 0.5348 (ppp) REVERT: A 439 TYR cc_start: 0.8103 (OUTLIER) cc_final: 0.7869 (m-80) REVERT: B 7 LYS cc_start: 0.8533 (mttp) cc_final: 0.8294 (mttm) REVERT: B 29 LYS cc_start: 0.8062 (mppt) cc_final: 0.7699 (mppt) REVERT: B 194 MET cc_start: 0.7835 (OUTLIER) cc_final: 0.7615 (mtp) outliers start: 35 outliers final: 24 residues processed: 182 average time/residue: 0.7868 time to fit residues: 157.3664 Evaluate side-chains 193 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 167 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 426 CYS Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 439 TYR Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 194 MET Chi-restraints excluded: chain B residue 202 ASN Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 235 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 26 optimal weight: 0.0000 chunk 105 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 ASN B 128 ASN B 217 ASN C 293 ASN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8565 Z= 0.230 Angle : 0.501 6.816 11670 Z= 0.259 Chirality : 0.042 0.145 1362 Planarity : 0.003 0.038 1470 Dihedral : 5.939 107.816 1192 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.02 % Allowed : 14.47 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.57 (0.26), residues: 1093 helix: 1.99 (0.29), residues: 359 sheet: 0.37 (0.29), residues: 288 loop : -0.97 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 169 HIS 0.003 0.001 HIS E 35 PHE 0.014 0.001 PHE A 189 TYR 0.012 0.001 TYR A 92 ARG 0.009 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 172 time to evaluate : 0.952 Fit side-chains revert: symmetry clash REVERT: A 32 MET cc_start: 0.5582 (ppp) cc_final: 0.5331 (ppp) REVERT: B 7 LYS cc_start: 0.8542 (mttp) cc_final: 0.8301 (mttm) REVERT: B 194 MET cc_start: 0.7837 (OUTLIER) cc_final: 0.7601 (mtp) outliers start: 35 outliers final: 25 residues processed: 184 average time/residue: 0.7941 time to fit residues: 160.4917 Evaluate side-chains 196 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 170 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 426 CYS Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 194 MET Chi-restraints excluded: chain B residue 202 ASN Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 235 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 88 optimal weight: 0.3980 chunk 58 optimal weight: 0.9990 chunk 105 optimal weight: 0.4980 chunk 65 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 ASN B 217 ASN C 293 ASN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 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 : 0.004 0.028 8565 Z= 0.255 Angle : 0.511 7.125 11670 Z= 0.266 Chirality : 0.042 0.134 1362 Planarity : 0.003 0.038 1470 Dihedral : 5.977 107.542 1192 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.79 % Allowed : 16.07 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.54 (0.26), residues: 1093 helix: 2.01 (0.29), residues: 357 sheet: 0.34 (0.29), residues: 288 loop : -0.99 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 169 HIS 0.003 0.001 HIS E 220 PHE 0.015 0.002 PHE A 189 TYR 0.014 0.001 TYR A 92 ARG 0.008 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 174 time to evaluate : 0.845 Fit side-chains revert: symmetry clash REVERT: A 32 MET cc_start: 0.5582 (ppp) cc_final: 0.5344 (ppp) REVERT: B 7 LYS cc_start: 0.8551 (mttp) cc_final: 0.8309 (mttm) REVERT: B 194 MET cc_start: 0.7838 (OUTLIER) cc_final: 0.7592 (mtp) outliers start: 33 outliers final: 25 residues processed: 185 average time/residue: 0.7516 time to fit residues: 152.5630 Evaluate side-chains 196 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 170 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 426 CYS Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 194 MET Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 235 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 71 optimal weight: 0.0970 chunk 51 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 82 optimal weight: 0.5980 chunk 95 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 ASN B 217 ASN C 293 ASN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8565 Z= 0.231 Angle : 0.516 9.674 11670 Z= 0.264 Chirality : 0.042 0.132 1362 Planarity : 0.003 0.034 1470 Dihedral : 5.963 107.701 1192 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.90 % Allowed : 16.19 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.55 (0.26), residues: 1093 helix: 2.03 (0.28), residues: 357 sheet: 0.34 (0.30), residues: 288 loop : -0.99 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 169 HIS 0.003 0.001 HIS E 35 PHE 0.014 0.001 PHE A 189 TYR 0.012 0.001 TYR A 92 ARG 0.008 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 169 time to evaluate : 1.031 Fit side-chains revert: symmetry clash REVERT: A 32 MET cc_start: 0.5593 (ppp) cc_final: 0.5364 (ppp) REVERT: B 7 LYS cc_start: 0.8540 (mttp) cc_final: 0.8301 (mttm) REVERT: B 194 MET cc_start: 0.7812 (OUTLIER) cc_final: 0.7588 (mtp) outliers start: 34 outliers final: 26 residues processed: 178 average time/residue: 0.8038 time to fit residues: 156.7458 Evaluate side-chains 198 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 171 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 426 CYS Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 194 MET Chi-restraints excluded: chain B residue 202 ASN Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 235 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 92 optimal weight: 0.0050 chunk 64 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 ASN B 217 ASN C 293 ASN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8565 Z= 0.219 Angle : 0.504 8.874 11670 Z= 0.260 Chirality : 0.041 0.131 1362 Planarity : 0.003 0.033 1470 Dihedral : 5.940 107.783 1192 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.10 % Allowed : 17.11 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.58 (0.26), residues: 1093 helix: 2.10 (0.29), residues: 357 sheet: 0.33 (0.29), residues: 288 loop : -0.99 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 169 HIS 0.003 0.001 HIS E 35 PHE 0.013 0.001 PHE A 189 TYR 0.011 0.001 TYR A 92 ARG 0.007 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 173 time to evaluate : 0.939 Fit side-chains revert: symmetry clash REVERT: A 32 MET cc_start: 0.5606 (ppp) cc_final: 0.5379 (ppp) REVERT: B 7 LYS cc_start: 0.8536 (mttp) cc_final: 0.8301 (mttm) REVERT: B 194 MET cc_start: 0.7811 (OUTLIER) cc_final: 0.7588 (mtp) REVERT: C 45 MET cc_start: 0.8345 (mtp) cc_final: 0.8106 (mtt) outliers start: 27 outliers final: 24 residues processed: 182 average time/residue: 0.7906 time to fit residues: 157.7076 Evaluate side-chains 202 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 177 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 426 CYS Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 194 MET Chi-restraints excluded: chain B residue 202 ASN Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 235 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 1.9990 chunk 71 optimal weight: 0.4980 chunk 108 optimal weight: 0.0970 chunk 99 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 53 optimal weight: 0.0980 chunk 68 optimal weight: 0.9980 chunk 92 optimal weight: 0.0020 chunk 26 optimal weight: 0.0030 overall best weight: 0.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 ASN ** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 ASN C 293 ASN D 59 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8565 Z= 0.112 Angle : 0.453 8.958 11670 Z= 0.232 Chirality : 0.039 0.133 1362 Planarity : 0.003 0.034 1470 Dihedral : 5.629 108.401 1192 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.41 % Allowed : 18.37 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1093 helix: 2.31 (0.29), residues: 359 sheet: 0.49 (0.30), residues: 285 loop : -0.95 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 169 HIS 0.002 0.000 HIS E 35 PHE 0.008 0.001 PHE B 122 TYR 0.013 0.001 TYR C 124 ARG 0.007 0.000 ARG C 219 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 184 time to evaluate : 0.919 Fit side-chains revert: symmetry clash REVERT: A 81 ILE cc_start: 0.7642 (OUTLIER) cc_final: 0.7321 (tp) REVERT: B 141 ASN cc_start: 0.7717 (m-40) cc_final: 0.7422 (m110) REVERT: D 38 MET cc_start: 0.7462 (ttm) cc_final: 0.7134 (ttp) outliers start: 21 outliers final: 12 residues processed: 190 average time/residue: 0.7242 time to fit residues: 151.5521 Evaluate side-chains 187 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 174 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 426 CYS Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain E residue 160 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 88 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 76 optimal weight: 0.0010 chunk 4 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 ASN B 217 ASN C 239 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.127097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.110830 restraints weight = 11864.541| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.73 r_work: 0.3357 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8565 Z= 0.194 Angle : 0.505 8.712 11670 Z= 0.257 Chirality : 0.041 0.138 1362 Planarity : 0.003 0.035 1470 Dihedral : 5.778 107.846 1192 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.30 % Allowed : 18.94 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.78 (0.26), residues: 1093 helix: 2.33 (0.29), residues: 356 sheet: 0.36 (0.29), residues: 295 loop : -0.89 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 169 HIS 0.003 0.001 HIS E 35 PHE 0.013 0.001 PHE C 151 TYR 0.010 0.001 TYR E 178 ARG 0.009 0.000 ARG C 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3412.81 seconds wall clock time: 61 minutes 27.59 seconds (3687.59 seconds total)