Starting phenix.real_space_refine on Sat Apr 6 09:01:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhn_36280/04_2024/8jhn_36280_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhn_36280/04_2024/8jhn_36280.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhn_36280/04_2024/8jhn_36280_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhn_36280/04_2024/8jhn_36280_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhn_36280/04_2024/8jhn_36280_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhn_36280/04_2024/8jhn_36280.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhn_36280/04_2024/8jhn_36280.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhn_36280/04_2024/8jhn_36280_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhn_36280/04_2024/8jhn_36280_updated.pdb" } resolution = 3.75 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= 0.035 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 45 5.16 5 C 4911 2.51 5 N 1368 2.21 5 O 1449 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 14": "OE1" <-> "OE2" Residue "A GLU 208": "OE1" <-> "OE2" Residue "A ASP 341": "OD1" <-> "OD2" Residue "B TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 195": "OD1" <-> "OD2" Residue "B PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 246": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 7773 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1489 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 4, 'TRANS': 201} Chain breaks: 2 Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 173 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 7, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 82 Chain: "B" Number of atoms: 2375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2375 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 226 Unresolved non-hydrogen angles: 282 Unresolved non-hydrogen dihedrals: 170 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 9, 'ARG:plan': 8, 'ASN:plan1': 3, 'ASP:plan': 12} Unresolved non-hydrogen planarities: 133 Chain: "D" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 1869 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 130} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 277} Chain breaks: 2 Unresolved non-hydrogen bonds: 526 Unresolved non-hydrogen angles: 669 Unresolved non-hydrogen dihedrals: 444 Unresolved non-hydrogen chiralities: 51 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 10, 'TYR:plan': 1, 'ASN:plan1': 6, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 20, 'GLU:plan': 5, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 289 Chain: "G" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 376 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "H" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1655 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ARG:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 56 Chain: "D" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'UR9': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.70, per 1000 atoms: 0.60 Number of scatterers: 7773 At special positions: 0 Unit cell: (86.922, 117.652, 132.578, 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 45 16.00 O 1449 8.00 N 1368 7.00 C 4911 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS D 18 " - pdb=" SG CYS D 183 " distance=2.04 Simple disulfide: pdb=" SG CYS D 19 " - pdb=" SG CYS D 266 " distance=2.04 Simple disulfide: pdb=" SG CYS D 100 " - pdb=" SG CYS D 177 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.87 Conformation dependent library (CDL) restraints added in 1.5 seconds 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2092 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 13 sheets defined 34.1% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'A' and resid 9 through 32 removed outlier: 3.993A pdb=" N LYS A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 52 Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 213 through 216 removed outlier: 3.503A pdb=" N PHE A 216 " --> pdb=" O ILE A 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 213 through 216' Processing helix chain 'A' and resid 246 through 255 Processing helix chain 'A' and resid 258 through 260 No H-bonds generated for 'chain 'A' and resid 258 through 260' Processing helix chain 'A' and resid 272 through 279 Processing helix chain 'A' and resid 297 through 311 removed outlier: 3.745A pdb=" N LYS A 311 " --> pdb=" O GLN A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 30 through 36 removed outlier: 5.444A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 51 Proline residue: D 31 - end of helix removed outlier: 4.063A pdb=" N LEU D 47 " --> pdb=" O LEU D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 88 Proline residue: D 81 - end of helix Processing helix chain 'D' and resid 97 through 129 Processing helix chain 'D' and resid 141 through 164 removed outlier: 5.074A pdb=" N HIS D 161 " --> pdb=" O GLY D 157 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N LEU D 162 " --> pdb=" O LEU D 158 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LEU D 163 " --> pdb=" O THR D 159 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS D 164 " --> pdb=" O VAL D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 217 removed outlier: 3.838A pdb=" N PHE D 197 " --> pdb=" O PHE D 193 " (cutoff:3.500A) Proline residue: D 200 - end of helix Processing helix chain 'D' and resid 220 through 222 No H-bonds generated for 'chain 'D' and resid 220 through 222' Processing helix chain 'D' and resid 224 through 261 removed outlier: 4.178A pdb=" N ALA D 237 " --> pdb=" O ILE D 233 " (cutoff:3.500A) Proline residue: D 246 - end of helix Processing helix chain 'D' and resid 267 through 288 removed outlier: 3.941A pdb=" N ARG D 270 " --> pdb=" O GLU D 267 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER D 271 " --> pdb=" O VAL D 268 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER D 281 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR D 283 " --> pdb=" O LEU D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 294 Processing helix chain 'D' and resid 299 through 304 Processing helix chain 'G' and resid 8 through 24 removed outlier: 3.737A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 47 removed outlier: 3.510A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA G 45 " --> pdb=" O CYS G 41 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N LYS G 46 " --> pdb=" O GLU G 42 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N GLU G 47 " --> pdb=" O ALA G 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'H' and resid 53 through 55 No H-bonds generated for 'chain 'H' and resid 53 through 55' Processing helix chain 'H' and resid 221 through 223 No H-bonds generated for 'chain 'H' and resid 221 through 223' Processing sheet with id= A, first strand: chain 'A' and resid 265 through 270 removed outlier: 6.064A pdb=" N ILE A 222 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N PHE A 268 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N PHE A 224 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ASN A 270 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL A 226 " --> pdb=" O ASN A 270 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA A 221 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N HIS A 196 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N LEU A 36 " --> pdb=" O HIS A 196 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ARG A 198 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU A 38 " --> pdb=" O ARG A 198 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N PHE A 200 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.058A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.748A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 178 through 181 removed outlier: 4.634A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 198 through 202 removed outlier: 3.780A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.652A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.619A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.679A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'H' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.612A pdb=" N THR H 118 " --> pdb=" O GLY H 10 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'H' and resid 93 through 97 removed outlier: 3.709A pdb=" N VAL H 97 " --> pdb=" O HIS H 35 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'H' and resid 140 through 142 removed outlier: 3.578A pdb=" N VAL H 155 " --> pdb=" O ILE H 216 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE H 157 " --> pdb=" O LEU H 214 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N CYS H 159 " --> pdb=" O PHE H 212 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE H 212 " --> pdb=" O CYS H 159 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA H 211 " --> pdb=" O SER H 208 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR H 213 " --> pdb=" O SER H 206 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'H' and resid 243 through 245 removed outlier: 3.556A pdb=" N GLY H 225 " --> pdb=" O LEU H 245 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N LEU H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N LEU H 187 " --> pdb=" O LEU H 178 " (cutoff:3.500A) 366 hydrogen bonds defined for protein. 1020 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: 2.20 Time building geometry restraints manager: 3.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1280 1.31 - 1.44: 2223 1.44 - 1.57: 4372 1.57 - 1.69: 0 1.69 - 1.82: 59 Bond restraints: 7934 Sorted by residual: bond pdb=" C ALA D 174 " pdb=" N ASN D 175 " ideal model delta sigma weight residual 1.329 1.269 0.060 1.38e-02 5.25e+03 1.89e+01 bond pdb=" C LEU D 280 " pdb=" O LEU D 280 " ideal model delta sigma weight residual 1.236 1.189 0.046 1.32e-02 5.74e+03 1.23e+01 bond pdb=" O UR9 D 401 " pdb=" C1 UR9 D 401 " ideal model delta sigma weight residual 1.408 1.340 0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" N SER D 261 " pdb=" CA SER D 261 " ideal model delta sigma weight residual 1.459 1.490 -0.031 9.10e-03 1.21e+04 1.13e+01 bond pdb=" N THR D 263 " pdb=" CA THR D 263 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.22e-02 6.72e+03 9.07e+00 ... (remaining 7929 not shown) Histogram of bond angle deviations from ideal: 99.68 - 106.60: 190 106.60 - 113.52: 4331 113.52 - 120.43: 2946 120.43 - 127.35: 3292 127.35 - 134.27: 88 Bond angle restraints: 10847 Sorted by residual: angle pdb=" C1 UR9 D 401 " pdb=" C2 UR9 D 401 " pdb=" C3 UR9 D 401 " ideal model delta sigma weight residual 152.65 119.29 33.36 3.00e+00 1.11e-01 1.24e+02 angle pdb=" C ILE D 169 " pdb=" N GLN D 170 " pdb=" CA GLN D 170 " ideal model delta sigma weight residual 122.84 114.69 8.15 1.30e+00 5.92e-01 3.93e+01 angle pdb=" O ILE D 169 " pdb=" C ILE D 169 " pdb=" N GLN D 170 " ideal model delta sigma weight residual 123.18 116.56 6.62 1.08e+00 8.57e-01 3.75e+01 angle pdb=" N ASN D 17 " pdb=" CA ASN D 17 " pdb=" C ASN D 17 " ideal model delta sigma weight residual 110.30 101.18 9.12 1.50e+00 4.44e-01 3.70e+01 angle pdb=" N PHE D 197 " pdb=" CA PHE D 197 " pdb=" C PHE D 197 " ideal model delta sigma weight residual 113.55 106.57 6.98 1.26e+00 6.30e-01 3.07e+01 ... (remaining 10842 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.70: 4211 16.70 - 33.40: 305 33.40 - 50.10: 70 50.10 - 66.80: 9 66.80 - 83.50: 6 Dihedral angle restraints: 4601 sinusoidal: 1367 harmonic: 3234 Sorted by residual: dihedral pdb=" CB CYS D 19 " pdb=" SG CYS D 19 " pdb=" SG CYS D 266 " pdb=" CB CYS D 266 " ideal model delta sinusoidal sigma weight residual 93.00 176.50 -83.50 1 1.00e+01 1.00e-02 8.51e+01 dihedral pdb=" CB CYS H 159 " pdb=" SG CYS H 159 " pdb=" SG CYS H 229 " pdb=" CB CYS H 229 " ideal model delta sinusoidal sigma weight residual 93.00 139.53 -46.53 1 1.00e+01 1.00e-02 3.00e+01 dihedral pdb=" CA ALA D 174 " pdb=" C ALA D 174 " pdb=" N ASN D 175 " pdb=" CA ASN D 175 " ideal model delta harmonic sigma weight residual 180.00 156.74 23.26 0 5.00e+00 4.00e-02 2.16e+01 ... (remaining 4598 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 862 0.037 - 0.074: 294 0.074 - 0.111: 89 0.111 - 0.148: 24 0.148 - 0.185: 6 Chirality restraints: 1275 Sorted by residual: chirality pdb=" CB VAL A 202 " pdb=" CA VAL A 202 " pdb=" CG1 VAL A 202 " pdb=" CG2 VAL A 202 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.56e-01 chirality pdb=" CA PHE D 25 " pdb=" N PHE D 25 " pdb=" C PHE D 25 " pdb=" CB PHE D 25 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.36e-01 chirality pdb=" CA LEU D 258 " pdb=" N LEU D 258 " pdb=" C LEU D 258 " pdb=" CB LEU D 258 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.93e-01 ... (remaining 1272 not shown) Planarity restraints: 1409 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 280 " -0.020 2.00e-02 2.50e+03 4.17e-02 1.74e+01 pdb=" C LEU D 280 " 0.072 2.00e-02 2.50e+03 pdb=" O LEU D 280 " -0.027 2.00e-02 2.50e+03 pdb=" N SER D 281 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 169 " 0.016 2.00e-02 2.50e+03 2.97e-02 8.80e+00 pdb=" C ILE D 169 " -0.051 2.00e-02 2.50e+03 pdb=" O ILE D 169 " 0.018 2.00e-02 2.50e+03 pdb=" N GLN D 170 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 260 " -0.013 2.00e-02 2.50e+03 2.71e-02 7.33e+00 pdb=" C THR D 260 " 0.047 2.00e-02 2.50e+03 pdb=" O THR D 260 " -0.018 2.00e-02 2.50e+03 pdb=" N SER D 261 " -0.016 2.00e-02 2.50e+03 ... (remaining 1406 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 589 2.74 - 3.28: 7811 3.28 - 3.82: 12557 3.82 - 4.36: 13374 4.36 - 4.90: 24691 Nonbonded interactions: 59022 Sorted by model distance: nonbonded pdb=" NE2 GLN A 333 " pdb=" OD2 ASP A 337 " model vdw 2.198 2.520 nonbonded pdb=" O LEU D 66 " pdb=" OH TYR D 294 " model vdw 2.236 2.440 nonbonded pdb=" OG1 THR B 86 " pdb=" OD1 ASN B 88 " model vdw 2.240 2.440 nonbonded pdb=" O TYR D 284 " pdb=" OG SER D 287 " model vdw 2.262 2.440 nonbonded pdb=" OG1 THR H 91 " pdb=" O LEU H 117 " model vdw 2.269 2.440 ... (remaining 59017 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 group one per residue 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: 3.160 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: 9.930 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 24.550 Find NCS groups from input model: 0.240 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 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 : 0.003 0.068 7934 Z= 0.244 Angle : 0.725 33.364 10847 Z= 0.421 Chirality : 0.044 0.185 1275 Planarity : 0.004 0.045 1409 Dihedral : 12.822 75.311 2494 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.60 % Allowed : 0.75 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.27), residues: 1098 helix: 2.06 (0.29), residues: 360 sheet: -0.46 (0.32), residues: 276 loop : -0.29 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 297 HIS 0.005 0.001 HIS A 322 PHE 0.010 0.001 PHE B 151 TYR 0.010 0.001 TYR H 190 ARG 0.007 0.000 ARG H 160 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 133 time to evaluate : 0.804 Fit side-chains REVERT: A 53 MET cc_start: 0.5565 (mpp) cc_final: 0.3331 (mtm) REVERT: A 211 LYS cc_start: 0.7759 (mmtt) cc_final: 0.7374 (mmtp) REVERT: A 333 GLN cc_start: 0.7929 (tm-30) cc_final: 0.7670 (tm-30) REVERT: H 246 GLU cc_start: 0.8276 (mp0) cc_final: 0.7519 (pm20) outliers start: 4 outliers final: 0 residues processed: 137 average time/residue: 0.1962 time to fit residues: 36.5068 Evaluate side-chains 107 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 0.905 ------------------------------------------------------------------------------- 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: 1.9990 chunk 28 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 98 optimal weight: 0.6980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN B 17 GLN B 293 ASN D 68 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7934 Z= 0.292 Angle : 0.554 8.802 10847 Z= 0.297 Chirality : 0.044 0.158 1275 Planarity : 0.004 0.050 1409 Dihedral : 4.394 48.503 1180 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.64 % Allowed : 9.84 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.26), residues: 1098 helix: 2.37 (0.28), residues: 365 sheet: -0.49 (0.31), residues: 283 loop : -0.31 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 169 HIS 0.003 0.001 HIS A 322 PHE 0.016 0.001 PHE B 151 TYR 0.016 0.002 TYR H 190 ARG 0.010 0.001 ARG D 128 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 110 time to evaluate : 0.908 Fit side-chains REVERT: A 211 LYS cc_start: 0.7846 (mmtt) cc_final: 0.7343 (mmtp) REVERT: A 295 ASN cc_start: 0.8141 (t0) cc_final: 0.7734 (t0) REVERT: A 319 ILE cc_start: 0.9084 (mt) cc_final: 0.8817 (mt) REVERT: A 333 GLN cc_start: 0.8011 (tm-30) cc_final: 0.7274 (tm-30) REVERT: A 337 ASP cc_start: 0.8041 (m-30) cc_final: 0.7587 (m-30) REVERT: D 125 ARG cc_start: 0.8719 (ttm-80) cc_final: 0.8514 (ttp-110) REVERT: D 219 GLN cc_start: 0.8865 (tp40) cc_final: 0.8650 (tp-100) outliers start: 11 outliers final: 9 residues processed: 116 average time/residue: 0.1919 time to fit residues: 30.7433 Evaluate side-chains 108 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 99 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 chunk 99 optimal weight: 7.9990 chunk 107 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 GLN D 86 ASN H 179 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7934 Z= 0.299 Angle : 0.529 6.561 10847 Z= 0.286 Chirality : 0.043 0.163 1275 Planarity : 0.004 0.033 1409 Dihedral : 4.384 50.640 1180 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.94 % Allowed : 14.01 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.74 (0.27), residues: 1098 helix: 2.50 (0.28), residues: 363 sheet: -0.68 (0.31), residues: 287 loop : -0.30 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 211 HIS 0.005 0.001 HIS A 322 PHE 0.018 0.001 PHE B 151 TYR 0.016 0.002 TYR H 190 ARG 0.006 0.001 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 111 time to evaluate : 0.907 Fit side-chains REVERT: A 211 LYS cc_start: 0.7882 (mmtt) cc_final: 0.7363 (mmtp) REVERT: A 319 ILE cc_start: 0.9027 (mt) cc_final: 0.8748 (mt) REVERT: A 333 GLN cc_start: 0.7931 (tm-30) cc_final: 0.7204 (tm-30) REVERT: A 337 ASP cc_start: 0.8014 (m-30) cc_final: 0.7028 (m-30) REVERT: H 86 LEU cc_start: 0.8708 (mp) cc_final: 0.8503 (mt) REVERT: H 246 GLU cc_start: 0.8360 (mp0) cc_final: 0.7457 (pm20) outliers start: 13 outliers final: 9 residues processed: 117 average time/residue: 0.1857 time to fit residues: 30.2535 Evaluate side-chains 112 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 103 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 66 optimal weight: 9.9990 chunk 99 optimal weight: 8.9990 chunk 105 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7934 Z= 0.252 Angle : 0.522 8.150 10847 Z= 0.279 Chirality : 0.043 0.166 1275 Planarity : 0.003 0.035 1409 Dihedral : 4.289 51.336 1180 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.83 % Allowed : 15.50 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.27), residues: 1098 helix: 2.56 (0.28), residues: 363 sheet: -0.78 (0.31), residues: 287 loop : -0.27 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.005 0.001 HIS A 322 PHE 0.013 0.001 PHE B 151 TYR 0.013 0.001 TYR H 190 ARG 0.005 0.001 ARG H 160 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 110 time to evaluate : 0.885 Fit side-chains REVERT: A 319 ILE cc_start: 0.9053 (mt) cc_final: 0.8749 (mt) REVERT: A 333 GLN cc_start: 0.7956 (tm-30) cc_final: 0.7243 (tm-30) REVERT: A 337 ASP cc_start: 0.7999 (m-30) cc_final: 0.7477 (m-30) outliers start: 19 outliers final: 15 residues processed: 121 average time/residue: 0.1907 time to fit residues: 32.9109 Evaluate side-chains 121 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 106 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 183 CYS Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 78 optimal weight: 0.0980 chunk 43 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 307 GLN B 17 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7934 Z= 0.178 Angle : 0.487 8.653 10847 Z= 0.259 Chirality : 0.042 0.160 1275 Planarity : 0.003 0.037 1409 Dihedral : 4.116 50.905 1180 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.53 % Allowed : 16.10 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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 (0.27), residues: 1098 helix: 2.66 (0.28), residues: 362 sheet: -0.81 (0.30), residues: 292 loop : -0.24 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.004 0.001 HIS A 322 PHE 0.010 0.001 PHE H 68 TYR 0.010 0.001 TYR H 190 ARG 0.006 0.000 ARG H 160 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 114 time to evaluate : 0.901 Fit side-chains REVERT: A 309 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7479 (mm-30) REVERT: A 319 ILE cc_start: 0.9087 (mt) cc_final: 0.8781 (mt) REVERT: A 333 GLN cc_start: 0.7922 (tm-30) cc_final: 0.7188 (tm-30) REVERT: A 337 ASP cc_start: 0.7972 (m-30) cc_final: 0.7442 (m-30) outliers start: 17 outliers final: 14 residues processed: 121 average time/residue: 0.1784 time to fit residues: 30.5536 Evaluate side-chains 119 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 105 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain D residue 183 CYS Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 51 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 61 optimal weight: 0.0070 chunk 26 optimal weight: 0.0970 chunk 105 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 48 optimal weight: 0.1980 chunk 8 optimal weight: 0.2980 chunk 34 optimal weight: 0.4980 chunk 55 optimal weight: 0.0470 chunk 101 optimal weight: 0.9980 overall best weight: 0.1294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 7934 Z= 0.123 Angle : 0.468 7.297 10847 Z= 0.247 Chirality : 0.041 0.156 1275 Planarity : 0.003 0.038 1409 Dihedral : 3.859 50.202 1180 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.24 % Allowed : 17.29 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.95 (0.27), residues: 1098 helix: 2.67 (0.28), residues: 363 sheet: -0.66 (0.30), residues: 289 loop : -0.09 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 211 HIS 0.004 0.000 HIS A 322 PHE 0.017 0.001 PHE H 68 TYR 0.006 0.001 TYR B 264 ARG 0.008 0.000 ARG H 160 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 116 time to evaluate : 0.856 Fit side-chains REVERT: A 309 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7390 (mm-30) REVERT: A 333 GLN cc_start: 0.7921 (tm-30) cc_final: 0.7223 (tm-30) REVERT: A 337 ASP cc_start: 0.8030 (m-30) cc_final: 0.7422 (m-30) outliers start: 15 outliers final: 9 residues processed: 125 average time/residue: 0.1640 time to fit residues: 29.7189 Evaluate side-chains 114 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 105 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 183 CYS Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain H residue 2 VAL 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: 4.9990 chunk 77 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 GLN D 219 GLN ** H 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.073 7934 Z= 0.526 Angle : 0.676 12.852 10847 Z= 0.360 Chirality : 0.047 0.205 1275 Planarity : 0.004 0.036 1409 Dihedral : 4.800 52.332 1180 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.73 % Allowed : 17.73 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.51 (0.27), residues: 1098 helix: 2.39 (0.27), residues: 362 sheet: -0.98 (0.30), residues: 302 loop : -0.35 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 211 HIS 0.006 0.001 HIS A 322 PHE 0.025 0.002 PHE B 151 TYR 0.025 0.002 TYR H 50 ARG 0.006 0.001 ARG H 160 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 96 time to evaluate : 0.846 Fit side-chains REVERT: A 295 ASN cc_start: 0.8190 (t0) cc_final: 0.7726 (t0) REVERT: A 309 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7446 (mm-30) REVERT: A 333 GLN cc_start: 0.8049 (tm-30) cc_final: 0.7189 (tm-30) REVERT: A 337 ASP cc_start: 0.8039 (m-30) cc_final: 0.6990 (m-30) outliers start: 25 outliers final: 20 residues processed: 114 average time/residue: 0.1475 time to fit residues: 25.1679 Evaluate side-chains 113 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 93 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 183 CYS Chi-restraints excluded: chain D residue 220 MET Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 139 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 95 optimal weight: 0.6980 chunk 100 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7934 Z= 0.214 Angle : 0.519 9.134 10847 Z= 0.275 Chirality : 0.042 0.162 1275 Planarity : 0.003 0.037 1409 Dihedral : 4.326 50.216 1180 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.24 % Allowed : 19.97 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.64 (0.27), residues: 1098 helix: 2.54 (0.28), residues: 362 sheet: -0.85 (0.30), residues: 294 loop : -0.37 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 211 HIS 0.003 0.001 HIS A 322 PHE 0.016 0.001 PHE B 292 TYR 0.011 0.001 TYR H 190 ARG 0.007 0.000 ARG H 160 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 102 time to evaluate : 0.755 Fit side-chains REVERT: A 311 LYS cc_start: 0.8450 (mtpp) cc_final: 0.8234 (mtpp) REVERT: A 333 GLN cc_start: 0.7995 (tm-30) cc_final: 0.7184 (tm-30) REVERT: A 337 ASP cc_start: 0.7982 (m-30) cc_final: 0.7457 (m-30) REVERT: H 237 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.8039 (mt) outliers start: 15 outliers final: 13 residues processed: 114 average time/residue: 0.1395 time to fit residues: 24.0936 Evaluate side-chains 113 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 99 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 183 CYS Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 237 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 88 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 GLN ** H 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7934 Z= 0.190 Angle : 0.504 8.249 10847 Z= 0.266 Chirality : 0.042 0.152 1275 Planarity : 0.003 0.038 1409 Dihedral : 4.138 50.042 1180 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.53 % Allowed : 19.67 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.71 (0.27), residues: 1098 helix: 2.54 (0.28), residues: 368 sheet: -0.84 (0.30), residues: 292 loop : -0.30 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.003 0.001 HIS B 225 PHE 0.009 0.001 PHE A 190 TYR 0.011 0.001 TYR H 190 ARG 0.005 0.000 ARG H 160 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 101 time to evaluate : 0.833 Fit side-chains REVERT: A 333 GLN cc_start: 0.8018 (tm-30) cc_final: 0.7217 (tm-30) REVERT: A 337 ASP cc_start: 0.8006 (m-30) cc_final: 0.7543 (m-30) REVERT: H 237 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7926 (mt) outliers start: 17 outliers final: 15 residues processed: 113 average time/residue: 0.1409 time to fit residues: 24.1801 Evaluate side-chains 114 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 98 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 183 CYS Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 237 LEU Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 108 optimal weight: 1.9990 chunk 99 optimal weight: 0.0070 chunk 86 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 66 optimal weight: 7.9990 chunk 53 optimal weight: 0.0570 chunk 68 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS ** H 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 7934 Z= 0.153 Angle : 0.485 6.894 10847 Z= 0.257 Chirality : 0.041 0.140 1275 Planarity : 0.003 0.038 1409 Dihedral : 3.995 49.648 1180 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.09 % Allowed : 20.57 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.80 (0.27), residues: 1098 helix: 2.56 (0.28), residues: 368 sheet: -0.83 (0.30), residues: 296 loop : -0.15 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 211 HIS 0.004 0.001 HIS B 266 PHE 0.008 0.001 PHE A 190 TYR 0.008 0.001 TYR H 190 ARG 0.004 0.000 ARG H 160 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 101 time to evaluate : 0.841 Fit side-chains REVERT: A 333 GLN cc_start: 0.7994 (tm-30) cc_final: 0.7219 (tm-30) REVERT: A 337 ASP cc_start: 0.7999 (m-30) cc_final: 0.7537 (m-30) REVERT: H 237 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7985 (mt) outliers start: 14 outliers final: 12 residues processed: 110 average time/residue: 0.1413 time to fit residues: 23.5313 Evaluate side-chains 110 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 97 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 237 LEU Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 36 optimal weight: 0.2980 chunk 88 optimal weight: 0.0170 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 GLN D 219 GLN ** H 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.121947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.100468 restraints weight = 15030.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.099412 restraints weight = 15055.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.099567 restraints weight = 16289.822| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7934 Z= 0.163 Angle : 0.487 7.037 10847 Z= 0.257 Chirality : 0.041 0.142 1275 Planarity : 0.003 0.038 1409 Dihedral : 3.885 49.473 1180 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.53 % Allowed : 20.42 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.89 (0.27), residues: 1098 helix: 2.57 (0.28), residues: 368 sheet: -0.71 (0.31), residues: 294 loop : -0.09 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 211 HIS 0.003 0.000 HIS A 322 PHE 0.009 0.001 PHE A 260 TYR 0.009 0.001 TYR H 190 ARG 0.004 0.000 ARG H 160 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1829.38 seconds wall clock time: 34 minutes 3.71 seconds (2043.71 seconds total)