Starting phenix.real_space_refine on Wed Feb 14 02:02:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bya_16325/02_2024/8bya_16325_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bya_16325/02_2024/8bya_16325.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bya_16325/02_2024/8bya_16325.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bya_16325/02_2024/8bya_16325.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bya_16325/02_2024/8bya_16325_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bya_16325/02_2024/8bya_16325_updated.pdb" } resolution = 3.38 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= -0.000 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 35 5.16 5 C 5392 2.51 5 N 1432 2.21 5 O 1528 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 181": "OD1" <-> "OD2" Residue "B GLU 190": "OE1" <-> "OE2" Residue "B TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 277": "OE1" <-> "OE2" Residue "B TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 284": "OD1" <-> "OD2" Residue "B ASP 345": "OD1" <-> "OD2" Residue "B TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 75": "OE1" <-> "OE2" Residue "C TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1083": "OD1" <-> "OD2" Residue "D ASP 1089": "OD1" <-> "OD2" Residue "D PHE 1139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1148": "OE1" <-> "OE2" Residue "E TYR 2128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 2178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 2214": "OE1" <-> "OE2" Residue "E PHE 2243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 2271": "OE1" <-> "OE2" Residue "E ASP 2319": "OD1" <-> "OD2" Residue "E PHE 2328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 2355": "OE1" <-> "OE2" Residue "E PHE 2368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 3027": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8389 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2025 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 19, 'TRANS': 257} Chain breaks: 2 Unresolved non-hydrogen bonds: 206 Unresolved non-hydrogen angles: 258 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'TPO:plan-1': 1, 'ASN:plan1': 2, 'ASP:plan': 7, 'HIS:plan': 4, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 114 Chain: "B" Number of atoms: 1871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1871 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 242} Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 254 Unresolved non-hydrogen dihedrals: 168 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 6, 'GLU:plan': 8, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 115 Chain: "C" Number of atoms: 499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 499 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 6, 'TRANS': 62} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 80 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 69 Chain: "D" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 855 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain breaks: 2 Unresolved non-hydrogen bonds: 262 Unresolved non-hydrogen angles: 329 Unresolved non-hydrogen dihedrals: 212 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 9, 'PHE:plan': 4, 'GLU:plan': 12, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 157 Chain: "E" Number of atoms: 2481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2481 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 13, 'TRANS': 311} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "F" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 589 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 63} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "G" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 69 Classifications: {'peptide': 10} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Residues with excluded nonbonded symmetry interactions: 10 residue: pdb=" N LEU A 25 " occ=0.73 ... (3 atoms not shown) pdb=" CB LEU A 25 " occ=0.73 residue: pdb=" N ASP A 68 " occ=0.38 ... (3 atoms not shown) pdb=" CB ASP A 68 " occ=0.38 residue: pdb=" N PRO A 294 " occ=0.52 ... (5 atoms not shown) pdb=" CD PRO A 294 " occ=0.52 residue: pdb=" N HIS A 295 " occ=0.67 ... (8 atoms not shown) pdb=" NE2 HIS A 295 " occ=0.67 residue: pdb=" N LEU A 296 " occ=0.52 ... (6 atoms not shown) pdb=" CD2 LEU A 296 " occ=0.52 residue: pdb=" N THR D1082 " occ=0.22 ... (5 atoms not shown) pdb=" CG2 THR D1082 " occ=0.22 residue: pdb=" N ASP D1083 " occ=0.52 ... (6 atoms not shown) pdb=" OD2 ASP D1083 " occ=0.52 residue: pdb=" N ASP D1084 " occ=0.40 ... (3 atoms not shown) pdb=" CB ASP D1084 " occ=0.40 residue: pdb=" N ILE D1085 " occ=0.53 ... (6 atoms not shown) pdb=" CD1 ILE D1085 " occ=0.53 residue: pdb=" N PRO E2101 " occ=0.63 ... (5 atoms not shown) pdb=" CD PRO E2101 " occ=0.63 Time building chain proxies: 4.95, per 1000 atoms: 0.59 Number of scatterers: 8389 At special positions: 0 Unit cell: (82.39, 115.56, 115.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 35 16.00 P 2 15.00 O 1528 8.00 N 1432 7.00 C 5392 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 3.11 Conformation dependent library (CDL) restraints added in 2.1 seconds 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2196 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 47 helices and 4 sheets defined 35.8% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.77 Creating SS restraints... Processing helix chain 'A' and resid 46 through 56 removed outlier: 4.207A pdb=" N LEU A 54 " --> pdb=" O ARG A 50 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS A 56 " --> pdb=" O ILE A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 104 No H-bonds generated for 'chain 'A' and resid 101 through 104' Processing helix chain 'A' and resid 109 through 121 Processing helix chain 'A' and resid 130 through 132 No H-bonds generated for 'chain 'A' and resid 130 through 132' Processing helix chain 'A' and resid 166 through 168 No H-bonds generated for 'chain 'A' and resid 166 through 168' Processing helix chain 'A' and resid 171 through 174 No H-bonds generated for 'chain 'A' and resid 171 through 174' Processing helix chain 'A' and resid 184 through 188 removed outlier: 3.722A pdb=" N SER A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 184 through 188' Processing helix chain 'A' and resid 194 through 197 No H-bonds generated for 'chain 'A' and resid 194 through 197' Processing helix chain 'A' and resid 208 through 219 removed outlier: 3.667A pdb=" N THR A 218 " --> pdb=" O ARG A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 232 No H-bonds generated for 'chain 'A' and resid 230 through 232' Processing helix chain 'A' and resid 258 through 261 No H-bonds generated for 'chain 'A' and resid 258 through 261' Processing helix chain 'B' and resid 179 through 192 removed outlier: 4.894A pdb=" N VAL B 191 " --> pdb=" O ARG B 187 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LYS B 192 " --> pdb=" O GLU B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 200 No H-bonds generated for 'chain 'B' and resid 198 through 200' Processing helix chain 'B' and resid 208 through 224 Processing helix chain 'B' and resid 229 through 245 removed outlier: 4.328A pdb=" N SER B 245 " --> pdb=" O ARG B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 268 Processing helix chain 'B' and resid 275 through 280 Processing helix chain 'B' and resid 288 through 301 Processing helix chain 'B' and resid 311 through 317 Processing helix chain 'B' and resid 330 through 342 removed outlier: 3.521A pdb=" N LEU B 341 " --> pdb=" O GLY B 337 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE B 342 " --> pdb=" O GLU B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 367 removed outlier: 3.835A pdb=" N LEU B 364 " --> pdb=" O PHE B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 380 removed outlier: 3.766A pdb=" N ARG B 378 " --> pdb=" O GLU B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 399 removed outlier: 3.526A pdb=" N ASP B 393 " --> pdb=" O PRO B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 413 removed outlier: 3.536A pdb=" N TYR B 413 " --> pdb=" O ILE B 409 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 409 through 413' Processing helix chain 'B' and resid 416 through 418 No H-bonds generated for 'chain 'B' and resid 416 through 418' Processing helix chain 'C' and resid 38 through 53 removed outlier: 5.341A pdb=" N GLU C 53 " --> pdb=" O CYS C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'D' and resid 1025 through 1030 Processing helix chain 'D' and resid 1046 through 1062 removed outlier: 3.898A pdb=" N ASN D1051 " --> pdb=" O LEU D1047 " (cutoff:3.500A) Processing helix chain 'D' and resid 1087 through 1091 Processing helix chain 'D' and resid 1097 through 1110 Processing helix chain 'D' and resid 1114 through 1127 Processing helix chain 'D' and resid 1132 through 1138 Processing helix chain 'D' and resid 1149 through 1159 removed outlier: 3.528A pdb=" N ASN D1157 " --> pdb=" O VAL D1153 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN D1158 " --> pdb=" O ARG D1154 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N TRP D1159 " --> pdb=" O LYS D1155 " (cutoff:3.500A) Processing helix chain 'E' and resid 2102 through 2110 Processing helix chain 'E' and resid 2114 through 2118 Processing helix chain 'E' and resid 2126 through 2132 removed outlier: 3.641A pdb=" N LEU E2130 " --> pdb=" O ARG E2126 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER E2132 " --> pdb=" O TYR E2128 " (cutoff:3.500A) Processing helix chain 'E' and resid 2152 through 2158 removed outlier: 3.597A pdb=" N GLN E2158 " --> pdb=" O ARG E2154 " (cutoff:3.500A) Processing helix chain 'E' and resid 2195 through 2202 Processing helix chain 'E' and resid 2220 through 2227 removed outlier: 3.901A pdb=" N ALA E2227 " --> pdb=" O VAL E2223 " (cutoff:3.500A) Processing helix chain 'E' and resid 2245 through 2254 Processing helix chain 'E' and resid 2271 through 2279 Processing helix chain 'E' and resid 2299 through 2308 Processing helix chain 'E' and resid 2328 through 2333 removed outlier: 3.529A pdb=" N GLN E2333 " --> pdb=" O GLN E2329 " (cutoff:3.500A) Processing helix chain 'E' and resid 2351 through 2358 Processing helix chain 'E' and resid 2375 through 2382 Processing helix chain 'F' and resid 3043 through 3046 No H-bonds generated for 'chain 'F' and resid 3043 through 3046' Processing sheet with id= A, first strand: chain 'A' and resid 30 through 32 Processing sheet with id= B, first strand: chain 'E' and resid 2162 through 2164 removed outlier: 6.811A pdb=" N HIS E2185 " --> pdb=" O PHE E2163 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'E' and resid 2210 through 2212 removed outlier: 6.253A pdb=" N ARG E2234 " --> pdb=" O LEU E2211 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'F' and resid 3017 through 3023 removed outlier: 4.252A pdb=" N LEU F3068 " --> pdb=" O MET F3058 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N MET F3058 " --> pdb=" O LEU F3068 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ARG F3070 " --> pdb=" O HIS F3056 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N HIS F3056 " --> pdb=" O ARG F3070 " (cutoff:3.500A) 213 hydrogen bonds defined for protein. 624 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: 2.16 Time building geometry restraints manager: 3.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1487 1.33 - 1.45: 2137 1.45 - 1.57: 4911 1.57 - 1.69: 2 1.69 - 1.81: 47 Bond restraints: 8584 Sorted by residual: bond pdb=" OG1 TPO G4187 " pdb=" P TPO G4187 " ideal model delta sigma weight residual 1.717 1.593 0.124 2.00e-02 2.50e+03 3.86e+01 bond pdb=" OG1 TPO A 159 " pdb=" P TPO A 159 " ideal model delta sigma weight residual 1.717 1.621 0.096 2.00e-02 2.50e+03 2.28e+01 bond pdb=" C PRO B 426 " pdb=" O PRO B 426 " ideal model delta sigma weight residual 1.243 1.213 0.031 8.50e-03 1.38e+04 1.29e+01 bond pdb=" CB TPO A 159 " pdb=" OG1 TPO A 159 " ideal model delta sigma weight residual 1.406 1.469 -0.063 2.00e-02 2.50e+03 9.94e+00 bond pdb=" N ILE F3006 " pdb=" CA ILE F3006 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.32e-02 5.74e+03 8.73e+00 ... (remaining 8579 not shown) Histogram of bond angle deviations from ideal: 99.89 - 106.78: 323 106.78 - 113.66: 4802 113.66 - 120.55: 3256 120.55 - 127.43: 3267 127.43 - 134.32: 103 Bond angle restraints: 11751 Sorted by residual: angle pdb=" N ILE F3028 " pdb=" CA ILE F3028 " pdb=" C ILE F3028 " ideal model delta sigma weight residual 113.53 107.69 5.84 9.80e-01 1.04e+00 3.55e+01 angle pdb=" N VAL E2233 " pdb=" CA VAL E2233 " pdb=" C VAL E2233 " ideal model delta sigma weight residual 113.47 108.68 4.79 1.01e+00 9.80e-01 2.25e+01 angle pdb=" C PRO B 426 " pdb=" CA PRO B 426 " pdb=" CB PRO B 426 " ideal model delta sigma weight residual 111.17 106.89 4.28 9.40e-01 1.13e+00 2.08e+01 angle pdb=" N MET B 210 " pdb=" CA MET B 210 " pdb=" C MET B 210 " ideal model delta sigma weight residual 111.07 106.73 4.34 1.07e+00 8.73e-01 1.64e+01 angle pdb=" C LYS D1130 " pdb=" CA LYS D1130 " pdb=" CB LYS D1130 " ideal model delta sigma weight residual 116.34 111.13 5.21 1.40e+00 5.10e-01 1.38e+01 ... (remaining 11746 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 4503 17.53 - 35.06: 458 35.06 - 52.60: 109 52.60 - 70.13: 21 70.13 - 87.66: 9 Dihedral angle restraints: 5100 sinusoidal: 1735 harmonic: 3365 Sorted by residual: dihedral pdb=" CA ASP B 345 " pdb=" C ASP B 345 " pdb=" N PRO B 346 " pdb=" CA PRO B 346 " ideal model delta harmonic sigma weight residual 0.00 -20.57 20.57 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA LEU A 267 " pdb=" C LEU A 267 " pdb=" N HIS A 268 " pdb=" CA HIS A 268 " ideal model delta harmonic sigma weight residual 180.00 159.82 20.18 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA GLN E2158 " pdb=" C GLN E2158 " pdb=" N GLY E2159 " pdb=" CA GLY E2159 " ideal model delta harmonic sigma weight residual 180.00 160.50 19.50 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 5097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 948 0.042 - 0.084: 328 0.084 - 0.126: 94 0.126 - 0.168: 15 0.168 - 0.210: 9 Chirality restraints: 1394 Sorted by residual: chirality pdb=" CA ARG E2344 " pdb=" N ARG E2344 " pdb=" C ARG E2344 " pdb=" CB ARG E2344 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA GLU C 75 " pdb=" N GLU C 75 " pdb=" C GLU C 75 " pdb=" CB GLU C 75 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.58e-01 chirality pdb=" CA MET B 392 " pdb=" N MET B 392 " pdb=" C MET B 392 " pdb=" CB MET B 392 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.85e-01 ... (remaining 1391 not shown) Planarity restraints: 1503 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN C 31 " 0.011 2.00e-02 2.50e+03 2.21e-02 4.90e+00 pdb=" C ASN C 31 " -0.038 2.00e-02 2.50e+03 pdb=" O ASN C 31 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU C 32 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B 323 " -0.033 5.00e-02 4.00e+02 5.01e-02 4.01e+00 pdb=" N PRO B 324 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 324 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 324 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D1045 " 0.032 5.00e-02 4.00e+02 4.83e-02 3.73e+00 pdb=" N PRO D1046 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO D1046 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO D1046 " 0.027 5.00e-02 4.00e+02 ... (remaining 1500 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.14: 3 2.14 - 2.83: 2732 2.83 - 3.52: 11468 3.52 - 4.21: 18556 4.21 - 4.90: 32058 Nonbonded interactions: 64817 Sorted by model distance: nonbonded pdb=" CD ARG D1136 " pdb=" OD2 ASP D1144 " model vdw 1.446 3.440 nonbonded pdb=" NE2 GLN A 85 " pdb=" OH TYR A 107 " model vdw 1.977 2.520 nonbonded pdb=" OE1 GLN A 85 " pdb=" CE2 TYR A 107 " model vdw 2.049 3.340 nonbonded pdb=" OD1 ASP F3014 " pdb=" N GLU F3015 " model vdw 2.158 2.520 nonbonded pdb=" OD1 ASP A 86 " pdb=" CD2 LEU A 134 " model vdw 2.182 3.460 ... (remaining 64812 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 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: 1.930 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: 6.080 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 27.610 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.080 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:3.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.124 8584 Z= 0.334 Angle : 0.800 7.514 11751 Z= 0.511 Chirality : 0.047 0.210 1394 Planarity : 0.005 0.050 1503 Dihedral : 15.658 87.660 2904 Min Nonbonded Distance : 1.446 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.01 % Favored : 94.90 % Rotamer: Outliers : 0.88 % Allowed : 21.83 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.25), residues: 1117 helix: -0.01 (0.26), residues: 422 sheet: -2.53 (0.71), residues: 59 loop : -1.79 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 217 HIS 0.003 0.001 HIS E2185 PHE 0.010 0.001 PHE A 152 TYR 0.018 0.001 TYR B 280 ARG 0.004 0.000 ARG D1136 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 152 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 180 GLU cc_start: 0.6614 (pt0) cc_final: 0.5986 (mm-30) REVERT: D 1161 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7676 (tt0) REVERT: E 2134 GLU cc_start: 0.8358 (pt0) cc_final: 0.8153 (pt0) REVERT: E 2332 PHE cc_start: 0.7487 (OUTLIER) cc_final: 0.5999 (m-80) REVERT: E 2355 GLU cc_start: 0.7652 (tp30) cc_final: 0.7300 (tp30) outliers start: 7 outliers final: 1 residues processed: 154 average time/residue: 0.1826 time to fit residues: 39.9713 Evaluate side-chains 137 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 135 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 2332 PHE Chi-restraints excluded: chain E residue 2344 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 44 optimal weight: 0.0570 chunk 86 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 overall best weight: 1.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 HIS C 48 HIS D1157 ASN F3052 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8584 Z= 0.271 Angle : 0.606 8.041 11751 Z= 0.311 Chirality : 0.043 0.157 1394 Planarity : 0.005 0.046 1503 Dihedral : 5.379 56.436 1212 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.16 % Favored : 92.75 % Rotamer: Outliers : 5.52 % Allowed : 18.44 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.25), residues: 1117 helix: 0.15 (0.26), residues: 431 sheet: -2.51 (0.69), residues: 61 loop : -1.76 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP F3043 HIS 0.010 0.001 HIS A 84 PHE 0.020 0.002 PHE A 152 TYR 0.015 0.002 TYR F3057 ARG 0.003 0.000 ARG E2217 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 142 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 180 GLU cc_start: 0.6944 (pt0) cc_final: 0.6325 (mm-30) REVERT: D 1126 MET cc_start: 0.7445 (tmm) cc_final: 0.7219 (tmm) REVERT: D 1161 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7695 (tt0) REVERT: E 2127 TRP cc_start: 0.8122 (m-10) cc_final: 0.7851 (m-10) REVERT: E 2269 PHE cc_start: 0.8551 (OUTLIER) cc_final: 0.7277 (m-10) REVERT: E 2273 HIS cc_start: 0.8646 (OUTLIER) cc_final: 0.7760 (m170) outliers start: 44 outliers final: 24 residues processed: 173 average time/residue: 0.1827 time to fit residues: 46.2332 Evaluate side-chains 162 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 135 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 121 HIS Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain D residue 1059 ILE Chi-restraints excluded: chain D residue 1095 VAL Chi-restraints excluded: chain D residue 1116 LEU Chi-restraints excluded: chain D residue 1153 VAL Chi-restraints excluded: chain D residue 1161 GLU Chi-restraints excluded: chain E residue 2142 LEU Chi-restraints excluded: chain E residue 2151 VAL Chi-restraints excluded: chain E residue 2168 SER Chi-restraints excluded: chain E residue 2220 ASP Chi-restraints excluded: chain E residue 2223 VAL Chi-restraints excluded: chain E residue 2269 PHE Chi-restraints excluded: chain E residue 2273 HIS Chi-restraints excluded: chain E residue 2337 LEU Chi-restraints excluded: chain E residue 2344 ARG Chi-restraints excluded: chain E residue 2364 THR Chi-restraints excluded: chain F residue 3012 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 0.3980 chunk 31 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 chunk 34 optimal weight: 9.9990 chunk 80 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8584 Z= 0.189 Angle : 0.533 6.705 11751 Z= 0.272 Chirality : 0.041 0.155 1394 Planarity : 0.004 0.044 1503 Dihedral : 4.868 57.329 1210 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 5.27 % Allowed : 20.45 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.26), residues: 1117 helix: 0.35 (0.26), residues: 439 sheet: -2.63 (0.74), residues: 50 loop : -1.60 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D1088 HIS 0.005 0.001 HIS F3021 PHE 0.017 0.001 PHE E2267 TYR 0.009 0.001 TYR C 88 ARG 0.002 0.000 ARG E2217 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 144 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 180 GLU cc_start: 0.6882 (pt0) cc_final: 0.6316 (mm-30) REVERT: D 1126 MET cc_start: 0.7586 (tmm) cc_final: 0.7103 (tmm) REVERT: D 1161 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7760 (tt0) REVERT: E 2126 ARG cc_start: 0.7235 (OUTLIER) cc_final: 0.7024 (tmm160) REVERT: E 2127 TRP cc_start: 0.8046 (m-10) cc_final: 0.7674 (m-10) REVERT: E 2217 ARG cc_start: 0.8076 (ttm-80) cc_final: 0.7548 (ttm-80) REVERT: E 2269 PHE cc_start: 0.8512 (OUTLIER) cc_final: 0.7298 (m-10) REVERT: G 4185 GLU cc_start: 0.7022 (mp0) cc_final: 0.6344 (mp0) outliers start: 42 outliers final: 25 residues processed: 169 average time/residue: 0.1846 time to fit residues: 44.0353 Evaluate side-chains 167 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 139 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 121 HIS Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain D residue 1116 LEU Chi-restraints excluded: chain D residue 1153 VAL Chi-restraints excluded: chain D residue 1161 GLU Chi-restraints excluded: chain E residue 2126 ARG Chi-restraints excluded: chain E residue 2142 LEU Chi-restraints excluded: chain E residue 2143 THR Chi-restraints excluded: chain E residue 2151 VAL Chi-restraints excluded: chain E residue 2168 SER Chi-restraints excluded: chain E residue 2220 ASP Chi-restraints excluded: chain E residue 2269 PHE Chi-restraints excluded: chain E residue 2344 ARG Chi-restraints excluded: chain E residue 2364 THR Chi-restraints excluded: chain E residue 2401 ILE Chi-restraints excluded: chain F residue 3012 TYR Chi-restraints excluded: chain F residue 3016 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 11 optimal weight: 0.6980 chunk 47 optimal weight: 7.9990 chunk 67 optimal weight: 8.9990 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 0.0970 chunk 52 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2273 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8584 Z= 0.169 Angle : 0.523 7.971 11751 Z= 0.264 Chirality : 0.041 0.153 1394 Planarity : 0.004 0.046 1503 Dihedral : 4.698 58.299 1210 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 5.90 % Allowed : 20.45 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.26), residues: 1117 helix: 0.54 (0.27), residues: 432 sheet: -2.67 (0.67), residues: 60 loop : -1.42 (0.26), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D1088 HIS 0.008 0.001 HIS C 48 PHE 0.017 0.001 PHE E2267 TYR 0.009 0.001 TYR C 88 ARG 0.002 0.000 ARG E2217 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 148 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 PHE cc_start: 0.8230 (t80) cc_final: 0.7590 (t80) REVERT: B 180 GLU cc_start: 0.6797 (pt0) cc_final: 0.6329 (mm-30) REVERT: B 290 GLN cc_start: 0.7324 (mt0) cc_final: 0.6624 (mt0) REVERT: D 1126 MET cc_start: 0.7617 (tmm) cc_final: 0.7141 (tmm) REVERT: D 1161 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7690 (tt0) REVERT: E 2126 ARG cc_start: 0.7084 (OUTLIER) cc_final: 0.6670 (tmm-80) REVERT: E 2217 ARG cc_start: 0.8072 (ttm-80) cc_final: 0.7544 (ttm-80) REVERT: E 2269 PHE cc_start: 0.8517 (OUTLIER) cc_final: 0.7278 (m-10) REVERT: E 2332 PHE cc_start: 0.7650 (OUTLIER) cc_final: 0.7148 (t80) REVERT: E 2348 ILE cc_start: 0.6802 (mm) cc_final: 0.6547 (mm) REVERT: G 4185 GLU cc_start: 0.7110 (mp0) cc_final: 0.6577 (mp0) outliers start: 47 outliers final: 27 residues processed: 175 average time/residue: 0.1729 time to fit residues: 43.3814 Evaluate side-chains 173 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 142 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 121 HIS Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain D residue 1095 VAL Chi-restraints excluded: chain D residue 1116 LEU Chi-restraints excluded: chain D residue 1153 VAL Chi-restraints excluded: chain D residue 1161 GLU Chi-restraints excluded: chain E residue 2126 ARG Chi-restraints excluded: chain E residue 2142 LEU Chi-restraints excluded: chain E residue 2143 THR Chi-restraints excluded: chain E residue 2151 VAL Chi-restraints excluded: chain E residue 2168 SER Chi-restraints excluded: chain E residue 2220 ASP Chi-restraints excluded: chain E residue 2269 PHE Chi-restraints excluded: chain E residue 2323 LEU Chi-restraints excluded: chain E residue 2332 PHE Chi-restraints excluded: chain E residue 2344 ARG Chi-restraints excluded: chain F residue 3012 TYR Chi-restraints excluded: chain F residue 3016 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 90 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 132 ASN ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 8584 Z= 0.439 Angle : 0.719 8.021 11751 Z= 0.366 Chirality : 0.048 0.188 1394 Planarity : 0.005 0.050 1503 Dihedral : 5.677 58.686 1210 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 5.90 % Allowed : 21.83 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.26), residues: 1117 helix: 0.20 (0.26), residues: 433 sheet: -2.50 (0.67), residues: 62 loop : -1.75 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP F3043 HIS 0.011 0.002 HIS F3021 PHE 0.026 0.003 PHE A 193 TYR 0.020 0.002 TYR F3057 ARG 0.005 0.001 ARG A 122 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 137 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 180 GLU cc_start: 0.7084 (pt0) cc_final: 0.6635 (mm-30) REVERT: D 1126 MET cc_start: 0.7717 (tmm) cc_final: 0.7262 (tmm) REVERT: D 1161 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7856 (tt0) REVERT: E 2126 ARG cc_start: 0.7248 (OUTLIER) cc_final: 0.6815 (tmm-80) REVERT: E 2130 LEU cc_start: 0.8331 (tt) cc_final: 0.8127 (tp) REVERT: E 2164 ARG cc_start: 0.7808 (OUTLIER) cc_final: 0.7603 (ttt180) REVERT: E 2332 PHE cc_start: 0.7638 (OUTLIER) cc_final: 0.7136 (t80) REVERT: E 2344 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.8072 (ttp-110) REVERT: E 2396 ILE cc_start: 0.8588 (OUTLIER) cc_final: 0.8333 (mm) outliers start: 47 outliers final: 31 residues processed: 169 average time/residue: 0.1875 time to fit residues: 44.9175 Evaluate side-chains 171 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 134 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 121 HIS Chi-restraints excluded: chain A residue 132 ASN Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain D residue 1095 VAL Chi-restraints excluded: chain D residue 1116 LEU Chi-restraints excluded: chain D residue 1153 VAL Chi-restraints excluded: chain D residue 1161 GLU Chi-restraints excluded: chain E residue 2126 ARG Chi-restraints excluded: chain E residue 2142 LEU Chi-restraints excluded: chain E residue 2143 THR Chi-restraints excluded: chain E residue 2151 VAL Chi-restraints excluded: chain E residue 2164 ARG Chi-restraints excluded: chain E residue 2168 SER Chi-restraints excluded: chain E residue 2190 ASN Chi-restraints excluded: chain E residue 2208 LEU Chi-restraints excluded: chain E residue 2220 ASP Chi-restraints excluded: chain E residue 2297 LEU Chi-restraints excluded: chain E residue 2332 PHE Chi-restraints excluded: chain E residue 2344 ARG Chi-restraints excluded: chain E residue 2361 THR Chi-restraints excluded: chain E residue 2364 THR Chi-restraints excluded: chain E residue 2396 ILE Chi-restraints excluded: chain E residue 2417 THR Chi-restraints excluded: chain F residue 3012 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 62 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 55 optimal weight: 0.0030 chunk 102 optimal weight: 0.0870 overall best weight: 0.5168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8584 Z= 0.170 Angle : 0.550 8.764 11751 Z= 0.279 Chirality : 0.041 0.173 1394 Planarity : 0.004 0.048 1503 Dihedral : 4.948 59.536 1210 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 4.39 % Allowed : 24.47 % Favored : 71.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.26), residues: 1117 helix: 0.46 (0.26), residues: 436 sheet: -2.84 (0.68), residues: 54 loop : -1.51 (0.26), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D1088 HIS 0.007 0.001 HIS C 48 PHE 0.011 0.001 PHE A 193 TYR 0.009 0.001 TYR D1109 ARG 0.005 0.000 ARG B 378 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 145 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 PHE cc_start: 0.8269 (t80) cc_final: 0.7631 (t80) REVERT: B 180 GLU cc_start: 0.6889 (pt0) cc_final: 0.6463 (mm-30) REVERT: B 190 GLU cc_start: 0.6028 (pm20) cc_final: 0.5729 (pm20) REVERT: D 1126 MET cc_start: 0.7743 (tmm) cc_final: 0.7276 (tmm) REVERT: E 2105 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7029 (tp) REVERT: E 2126 ARG cc_start: 0.7107 (OUTLIER) cc_final: 0.6807 (tmm160) REVERT: E 2130 LEU cc_start: 0.8304 (tt) cc_final: 0.8094 (tp) REVERT: E 2269 PHE cc_start: 0.8708 (OUTLIER) cc_final: 0.7522 (m-10) REVERT: E 2332 PHE cc_start: 0.7731 (OUTLIER) cc_final: 0.7180 (t80) REVERT: E 2348 ILE cc_start: 0.7087 (mm) cc_final: 0.6872 (mm) outliers start: 35 outliers final: 23 residues processed: 166 average time/residue: 0.1801 time to fit residues: 42.7994 Evaluate side-chains 168 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 141 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 121 HIS Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 415 ASN Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain D residue 1116 LEU Chi-restraints excluded: chain D residue 1153 VAL Chi-restraints excluded: chain E residue 2105 LEU Chi-restraints excluded: chain E residue 2126 ARG Chi-restraints excluded: chain E residue 2142 LEU Chi-restraints excluded: chain E residue 2151 VAL Chi-restraints excluded: chain E residue 2168 SER Chi-restraints excluded: chain E residue 2220 ASP Chi-restraints excluded: chain E residue 2269 PHE Chi-restraints excluded: chain E residue 2332 PHE Chi-restraints excluded: chain E residue 2344 ARG Chi-restraints excluded: chain F residue 3012 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.0980 chunk 60 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 64 optimal weight: 9.9990 chunk 48 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 overall best weight: 3.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 119 HIS A 132 ASN ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3060 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.071 8584 Z= 0.573 Angle : 0.810 8.371 11751 Z= 0.415 Chirality : 0.051 0.240 1394 Planarity : 0.006 0.063 1503 Dihedral : 6.140 57.646 1210 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.10 % Favored : 88.90 % Rotamer: Outliers : 6.27 % Allowed : 21.71 % Favored : 72.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.25), residues: 1117 helix: -0.13 (0.25), residues: 430 sheet: -2.74 (0.66), residues: 62 loop : -1.99 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP F3043 HIS 0.013 0.002 HIS F3021 PHE 0.030 0.003 PHE A 193 TYR 0.021 0.002 TYR F3057 ARG 0.004 0.001 ARG F3020 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 135 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 ASP cc_start: 0.8078 (t0) cc_final: 0.7853 (t0) REVERT: B 180 GLU cc_start: 0.7287 (pt0) cc_final: 0.6829 (mm-30) REVERT: B 290 GLN cc_start: 0.7681 (mt0) cc_final: 0.7059 (mt0) REVERT: D 1126 MET cc_start: 0.7739 (tmm) cc_final: 0.7297 (tmm) REVERT: D 1128 LYS cc_start: 0.8272 (mmtt) cc_final: 0.7872 (mttt) REVERT: E 2126 ARG cc_start: 0.7315 (OUTLIER) cc_final: 0.6964 (tmm160) REVERT: E 2130 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8146 (tp) REVERT: E 2273 HIS cc_start: 0.8767 (OUTLIER) cc_final: 0.8003 (m170) REVERT: E 2332 PHE cc_start: 0.7685 (OUTLIER) cc_final: 0.7055 (t80) REVERT: E 2344 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8165 (ttp-110) REVERT: E 2396 ILE cc_start: 0.8271 (OUTLIER) cc_final: 0.8060 (mm) outliers start: 50 outliers final: 32 residues processed: 171 average time/residue: 0.1803 time to fit residues: 43.6258 Evaluate side-chains 171 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 133 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 121 HIS Chi-restraints excluded: chain A residue 132 ASN Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain D residue 1095 VAL Chi-restraints excluded: chain D residue 1116 LEU Chi-restraints excluded: chain D residue 1144 ASP Chi-restraints excluded: chain E residue 2105 LEU Chi-restraints excluded: chain E residue 2126 ARG Chi-restraints excluded: chain E residue 2130 LEU Chi-restraints excluded: chain E residue 2142 LEU Chi-restraints excluded: chain E residue 2143 THR Chi-restraints excluded: chain E residue 2151 VAL Chi-restraints excluded: chain E residue 2168 SER Chi-restraints excluded: chain E residue 2197 THR Chi-restraints excluded: chain E residue 2208 LEU Chi-restraints excluded: chain E residue 2220 ASP Chi-restraints excluded: chain E residue 2223 VAL Chi-restraints excluded: chain E residue 2273 HIS Chi-restraints excluded: chain E residue 2297 LEU Chi-restraints excluded: chain E residue 2332 PHE Chi-restraints excluded: chain E residue 2344 ARG Chi-restraints excluded: chain E residue 2361 THR Chi-restraints excluded: chain E residue 2364 THR Chi-restraints excluded: chain E residue 2396 ILE Chi-restraints excluded: chain E residue 2417 THR Chi-restraints excluded: chain F residue 3012 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 20.0000 chunk 31 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 83 optimal weight: 0.5980 chunk 96 optimal weight: 0.7980 chunk 101 optimal weight: 0.6980 chunk 92 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 132 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8584 Z= 0.191 Angle : 0.581 9.181 11751 Z= 0.294 Chirality : 0.042 0.153 1394 Planarity : 0.005 0.055 1503 Dihedral : 5.264 58.492 1210 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 4.14 % Allowed : 23.96 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.26), residues: 1117 helix: 0.25 (0.26), residues: 440 sheet: -2.54 (0.72), residues: 49 loop : -1.71 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP D1088 HIS 0.009 0.001 HIS C 48 PHE 0.012 0.001 PHE F3017 TYR 0.015 0.001 TYR C 89 ARG 0.005 0.000 ARG B 378 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 143 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 180 GLU cc_start: 0.6941 (pt0) cc_final: 0.6539 (mm-30) REVERT: B 190 GLU cc_start: 0.6129 (pm20) cc_final: 0.5737 (pm20) REVERT: D 1126 MET cc_start: 0.7638 (tmm) cc_final: 0.7237 (tmm) REVERT: D 1128 LYS cc_start: 0.8300 (mmtt) cc_final: 0.7841 (mttt) REVERT: E 2126 ARG cc_start: 0.7282 (OUTLIER) cc_final: 0.6967 (tmm160) REVERT: E 2130 LEU cc_start: 0.8345 (tt) cc_final: 0.8113 (tp) REVERT: E 2217 ARG cc_start: 0.8080 (ttm-80) cc_final: 0.7544 (ttm-80) REVERT: E 2269 PHE cc_start: 0.8814 (OUTLIER) cc_final: 0.7667 (m-10) REVERT: E 2332 PHE cc_start: 0.7714 (OUTLIER) cc_final: 0.6983 (t80) REVERT: E 2344 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.8213 (ttp-110) outliers start: 33 outliers final: 23 residues processed: 166 average time/residue: 0.1890 time to fit residues: 44.7011 Evaluate side-chains 167 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 140 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 121 HIS Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain D residue 1116 LEU Chi-restraints excluded: chain E residue 2105 LEU Chi-restraints excluded: chain E residue 2126 ARG Chi-restraints excluded: chain E residue 2143 THR Chi-restraints excluded: chain E residue 2151 VAL Chi-restraints excluded: chain E residue 2168 SER Chi-restraints excluded: chain E residue 2220 ASP Chi-restraints excluded: chain E residue 2269 PHE Chi-restraints excluded: chain E residue 2332 PHE Chi-restraints excluded: chain E residue 2337 LEU Chi-restraints excluded: chain E residue 2344 ARG Chi-restraints excluded: chain F residue 3012 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 59 optimal weight: 0.1980 chunk 43 optimal weight: 10.0000 chunk 77 optimal weight: 0.8980 chunk 30 optimal weight: 9.9990 chunk 89 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 104 optimal weight: 0.6980 chunk 63 optimal weight: 9.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8584 Z= 0.232 Angle : 0.591 8.340 11751 Z= 0.298 Chirality : 0.043 0.160 1394 Planarity : 0.005 0.047 1503 Dihedral : 5.082 57.287 1210 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 4.14 % Allowed : 24.09 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.26), residues: 1117 helix: 0.36 (0.26), residues: 439 sheet: -2.49 (0.67), residues: 57 loop : -1.64 (0.26), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP D1088 HIS 0.010 0.001 HIS C 48 PHE 0.017 0.002 PHE A 152 TYR 0.015 0.001 TYR A 180 ARG 0.003 0.000 ARG B 378 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 143 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 MET cc_start: 0.8491 (mmm) cc_final: 0.8200 (tpt) REVERT: A 117 PHE cc_start: 0.8300 (t80) cc_final: 0.7671 (t80) REVERT: B 180 GLU cc_start: 0.7019 (pt0) cc_final: 0.6636 (mm-30) REVERT: B 190 GLU cc_start: 0.6167 (pm20) cc_final: 0.5804 (pm20) REVERT: D 1126 MET cc_start: 0.7719 (tmm) cc_final: 0.7307 (tmm) REVERT: D 1128 LYS cc_start: 0.8280 (mmtt) cc_final: 0.7833 (mttt) REVERT: E 2105 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7179 (tp) REVERT: E 2126 ARG cc_start: 0.7296 (OUTLIER) cc_final: 0.6981 (tmm160) REVERT: E 2130 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8116 (tp) REVERT: E 2269 PHE cc_start: 0.8799 (OUTLIER) cc_final: 0.7623 (m-10) REVERT: E 2332 PHE cc_start: 0.7708 (OUTLIER) cc_final: 0.7059 (t80) REVERT: E 2344 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.8028 (ttp-110) outliers start: 33 outliers final: 22 residues processed: 161 average time/residue: 0.1836 time to fit residues: 42.2845 Evaluate side-chains 168 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 140 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 121 HIS Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain D residue 1095 VAL Chi-restraints excluded: chain D residue 1116 LEU Chi-restraints excluded: chain E residue 2105 LEU Chi-restraints excluded: chain E residue 2126 ARG Chi-restraints excluded: chain E residue 2130 LEU Chi-restraints excluded: chain E residue 2143 THR Chi-restraints excluded: chain E residue 2151 VAL Chi-restraints excluded: chain E residue 2168 SER Chi-restraints excluded: chain E residue 2220 ASP Chi-restraints excluded: chain E residue 2269 PHE Chi-restraints excluded: chain E residue 2332 PHE Chi-restraints excluded: chain E residue 2337 LEU Chi-restraints excluded: chain E residue 2344 ARG Chi-restraints excluded: chain F residue 3012 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.9980 chunk 72 optimal weight: 0.0770 chunk 109 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 69 optimal weight: 0.0770 chunk 92 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.7698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 HIS E2273 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8584 Z= 0.202 Angle : 0.572 8.569 11751 Z= 0.288 Chirality : 0.042 0.206 1394 Planarity : 0.005 0.062 1503 Dihedral : 4.897 56.679 1210 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 4.02 % Allowed : 25.22 % Favored : 70.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.26), residues: 1117 helix: 0.45 (0.26), residues: 439 sheet: -2.57 (0.72), residues: 49 loop : -1.60 (0.26), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP D1088 HIS 0.011 0.001 HIS C 48 PHE 0.013 0.001 PHE A 152 TYR 0.013 0.001 TYR C 89 ARG 0.002 0.000 ARG B 378 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 141 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 MET cc_start: 0.8568 (mmm) cc_final: 0.8222 (tpt) REVERT: A 111 LEU cc_start: 0.7376 (OUTLIER) cc_final: 0.7158 (mt) REVERT: A 117 PHE cc_start: 0.8254 (t80) cc_final: 0.7606 (t80) REVERT: B 180 GLU cc_start: 0.6967 (pt0) cc_final: 0.6606 (mm-30) REVERT: B 190 GLU cc_start: 0.6127 (pm20) cc_final: 0.5773 (pm20) REVERT: D 1126 MET cc_start: 0.7689 (tmm) cc_final: 0.7283 (tmm) REVERT: D 1128 LYS cc_start: 0.8294 (mmtt) cc_final: 0.7941 (mttt) REVERT: E 2105 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.7236 (tp) REVERT: E 2126 ARG cc_start: 0.7336 (OUTLIER) cc_final: 0.6987 (tmm160) REVERT: E 2130 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8085 (tp) REVERT: E 2269 PHE cc_start: 0.8740 (OUTLIER) cc_final: 0.7532 (m-10) REVERT: E 2332 PHE cc_start: 0.7653 (OUTLIER) cc_final: 0.6994 (t80) REVERT: E 2344 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.8224 (ttp-110) REVERT: E 2348 ILE cc_start: 0.6606 (mm) cc_final: 0.6210 (mm) outliers start: 32 outliers final: 21 residues processed: 158 average time/residue: 0.1829 time to fit residues: 41.2731 Evaluate side-chains 165 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 137 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 121 HIS Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 415 ASN Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain D residue 1095 VAL Chi-restraints excluded: chain D residue 1116 LEU Chi-restraints excluded: chain E residue 2105 LEU Chi-restraints excluded: chain E residue 2126 ARG Chi-restraints excluded: chain E residue 2130 LEU Chi-restraints excluded: chain E residue 2143 THR Chi-restraints excluded: chain E residue 2151 VAL Chi-restraints excluded: chain E residue 2168 SER Chi-restraints excluded: chain E residue 2220 ASP Chi-restraints excluded: chain E residue 2269 PHE Chi-restraints excluded: chain E residue 2297 LEU Chi-restraints excluded: chain E residue 2332 PHE Chi-restraints excluded: chain E residue 2344 ARG Chi-restraints excluded: chain F residue 3012 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 36 optimal weight: 0.0870 chunk 89 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 4 optimal weight: 0.6980 chunk 63 optimal weight: 8.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 HIS E2273 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.208985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.173162 restraints weight = 11033.376| |-----------------------------------------------------------------------------| r_work (start): 0.4149 rms_B_bonded: 3.33 r_work: 0.3835 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3873 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3873 r_free = 0.3873 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3871 r_free = 0.3871 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3871 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8584 Z= 0.187 Angle : 0.552 8.409 11751 Z= 0.280 Chirality : 0.042 0.206 1394 Planarity : 0.005 0.059 1503 Dihedral : 4.739 55.761 1210 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 3.64 % Allowed : 25.60 % Favored : 70.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.26), residues: 1117 helix: 0.52 (0.26), residues: 440 sheet: -2.53 (0.72), residues: 49 loop : -1.52 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP D1088 HIS 0.011 0.001 HIS C 48 PHE 0.014 0.001 PHE A 152 TYR 0.012 0.001 TYR A 180 ARG 0.002 0.000 ARG B 378 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1979.48 seconds wall clock time: 36 minutes 32.11 seconds (2192.11 seconds total)