Starting phenix.real_space_refine on Sat Apr 6 11:51:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iy9_35817/04_2024/8iy9_35817_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iy9_35817/04_2024/8iy9_35817.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iy9_35817/04_2024/8iy9_35817.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iy9_35817/04_2024/8iy9_35817.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iy9_35817/04_2024/8iy9_35817_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iy9_35817/04_2024/8iy9_35817_updated.pdb" } resolution = 3.37 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= 0.045 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 47 5.16 5 C 5175 2.51 5 N 1412 2.21 5 O 1487 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 187": "OE1" <-> "OE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 252": "OD1" <-> "OD2" Residue "A ASP 273": "OD1" <-> "OD2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 277": "OE1" <-> "OE2" Residue "A TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 299": "OD1" <-> "OD2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 118": "OD1" <-> "OD2" Residue "B ASP 212": "OD1" <-> "OD2" Residue "B PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 303": "OD1" <-> "OD2" Residue "B ASP 323": "OD1" <-> "OD2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "H PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 246": "OE1" <-> "OE2" Residue "R PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 8121 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1551 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 4, 'TRANS': 203} Chain breaks: 2 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 6, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 57 Chain: "B" Number of atoms: 2399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2399 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 202 Unresolved non-hydrogen angles: 251 Unresolved non-hydrogen dihedrals: 153 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 7, 'ARG:plan': 8, 'ASN:plan1': 2, 'ASP:plan': 12} Unresolved non-hydrogen planarities: 118 Chain: "G" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 392 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "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: 144 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ARG:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 56 Chain: "R" Number of atoms: 2115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2115 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 285} Unresolved non-hydrogen bonds: 341 Unresolved non-hydrogen angles: 430 Unresolved non-hydrogen dihedrals: 298 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 3, 'ASP:plan': 7, 'PHE:plan': 9, 'GLU:plan': 4, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 185 Chain: "R" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'NIO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.73, per 1000 atoms: 0.58 Number of scatterers: 8121 At special positions: 0 Unit cell: (123.47, 95.0719, 128.409, 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 47 16.00 O 1487 8.00 N 1412 7.00 C 5175 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " distance=2.04 Simple disulfide: pdb=" SG CYS R 18 " - pdb=" SG CYS R 183 " distance=2.04 Simple disulfide: pdb=" SG CYS R 19 " - pdb=" SG CYS R 266 " distance=2.05 Simple disulfide: pdb=" SG CYS R 100 " - pdb=" SG CYS R 177 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.67 Conformation dependent library (CDL) restraints added in 1.5 seconds 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2112 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 14 sheets defined 34.0% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing helix chain 'A' and resid 11 through 32 removed outlier: 4.162A 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 209 through 211 No H-bonds generated for 'chain 'A' and resid 209 through 211' Processing helix chain 'A' and resid 213 through 218 removed outlier: 3.738A pdb=" N GLU A 217 " --> pdb=" O HIS A 214 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ASP A 218 " --> pdb=" O CYS A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 254 Processing helix chain 'A' and resid 272 through 279 Processing helix chain 'A' and resid 284 through 286 No H-bonds generated for 'chain 'A' and resid 284 through 286' Processing helix chain 'A' and resid 297 through 311 removed outlier: 4.296A pdb=" N ALA A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) removed outlier: 4.412A 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: 5.316A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 23 Processing helix chain 'G' and resid 30 through 43 removed outlier: 4.144A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' 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 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing helix chain 'H' and resid 221 through 223 No H-bonds generated for 'chain 'H' and resid 221 through 223' Processing helix chain 'R' and resid 25 through 54 Proline residue: R 31 - end of helix removed outlier: 4.096A pdb=" N LEU R 47 " --> pdb=" O LEU R 43 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 88 removed outlier: 3.608A pdb=" N LEU R 80 " --> pdb=" O LEU R 76 " (cutoff:3.500A) Proline residue: R 81 - end of helix Processing helix chain 'R' and resid 96 through 129 Processing helix chain 'R' and resid 135 through 138 Processing helix chain 'R' and resid 141 through 157 Processing helix chain 'R' and resid 160 through 164 Processing helix chain 'R' and resid 188 through 217 removed outlier: 3.931A pdb=" N PHE R 197 " --> pdb=" O PHE R 193 " (cutoff:3.500A) Proline residue: R 200 - end of helix Processing helix chain 'R' and resid 224 through 261 removed outlier: 3.678A pdb=" N ALA R 237 " --> pdb=" O ILE R 233 " (cutoff:3.500A) Proline residue: R 246 - end of helix removed outlier: 3.529A pdb=" N VAL R 250 " --> pdb=" O PRO R 246 " (cutoff:3.500A) Processing helix chain 'R' and resid 266 through 293 removed outlier: 3.770A pdb=" N ARG R 270 " --> pdb=" O GLU R 267 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N SER R 271 " --> pdb=" O VAL R 268 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN R 286 " --> pdb=" O THR R 283 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU R 289 " --> pdb=" O ASN R 286 " (cutoff:3.500A) Proline residue: R 291 - end of helix Processing helix chain 'R' and resid 300 through 303 No H-bonds generated for 'chain 'R' and resid 300 through 303' Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 7.049A pdb=" N ILE A 265 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N HIS A 322 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU A 267 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE A 222 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N PHE A 268 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N PHE A 224 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ASN A 270 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL A 226 " --> pdb=" O ASN A 270 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA A 221 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N HIS A 196 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N LEU A 36 " --> pdb=" O HIS A 196 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ARG A 198 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LEU A 38 " --> pdb=" O ARG A 198 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N PHE A 200 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N GLY A 40 " --> pdb=" O PHE A 200 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.905A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.817A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.729A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.723A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.239A 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: 6.793A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.975A 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: 6.376A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.590A 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: 6.648A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.626A 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: 5.977A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'H' and resid 140 through 142 removed outlier: 3.694A pdb=" N ALA H 211 " --> pdb=" O SER H 208 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'H' and resid 146 through 149 removed outlier: 6.517A pdb=" N LYS H 244 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N VAL H 149 " --> pdb=" O LYS H 244 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N GLU H 246 " --> pdb=" O VAL H 149 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N LEU H 187 " --> pdb=" O LEU H 178 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'R' and resid 11 through 13 Processing sheet with id= N, first strand: chain 'R' and resid 169 through 171 395 hydrogen bonds defined for protein. 1068 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: 2.29 Time building geometry restraints manager: 3.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1320 1.32 - 1.45: 2364 1.45 - 1.58: 4551 1.58 - 1.71: 0 1.71 - 1.84: 62 Bond restraints: 8297 Sorted by residual: bond pdb=" C GLY B 330 " pdb=" O GLY B 330 " ideal model delta sigma weight residual 1.235 1.187 0.048 1.35e-02 5.49e+03 1.27e+01 bond pdb=" CA ILE R 98 " pdb=" CB ILE R 98 " ideal model delta sigma weight residual 1.539 1.521 0.018 5.40e-03 3.43e+04 1.10e+01 bond pdb=" CA ALA A 7 " pdb=" CB ALA A 7 " ideal model delta sigma weight residual 1.530 1.475 0.056 1.69e-02 3.50e+03 1.08e+01 bond pdb=" C SER B 331 " pdb=" O SER B 331 " ideal model delta sigma weight residual 1.235 1.199 0.036 1.14e-02 7.69e+03 9.96e+00 bond pdb=" C6 NIO R 401 " pdb=" O2 NIO R 401 " ideal model delta sigma weight residual 1.245 1.307 -0.062 2.00e-02 2.50e+03 9.56e+00 ... (remaining 8292 not shown) Histogram of bond angle deviations from ideal: 98.42 - 105.57: 140 105.57 - 112.73: 4316 112.73 - 119.88: 2938 119.88 - 127.03: 3819 127.03 - 134.18: 105 Bond angle restraints: 11318 Sorted by residual: angle pdb=" N GLU A 8 " pdb=" CA GLU A 8 " pdb=" C GLU A 8 " ideal model delta sigma weight residual 112.97 104.97 8.00 1.06e+00 8.90e-01 5.69e+01 angle pdb=" C GLU A 8 " pdb=" CA GLU A 8 " pdb=" CB GLU A 8 " ideal model delta sigma weight residual 111.17 100.51 10.66 1.53e+00 4.27e-01 4.85e+01 angle pdb=" N GLU A 9 " pdb=" CA GLU A 9 " pdb=" C GLU A 9 " ideal model delta sigma weight residual 112.88 103.91 8.97 1.29e+00 6.01e-01 4.84e+01 angle pdb=" N ARG A 10 " pdb=" CA ARG A 10 " pdb=" C ARG A 10 " ideal model delta sigma weight residual 113.12 106.55 6.57 1.25e+00 6.40e-01 2.76e+01 angle pdb=" N CYS R 183 " pdb=" CA CYS R 183 " pdb=" C CYS R 183 " ideal model delta sigma weight residual 107.73 114.19 -6.46 1.61e+00 3.86e-01 1.61e+01 ... (remaining 11313 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.19: 4466 17.19 - 34.38: 290 34.38 - 51.57: 54 51.57 - 68.76: 5 68.76 - 85.95: 9 Dihedral angle restraints: 4824 sinusoidal: 1558 harmonic: 3266 Sorted by residual: dihedral pdb=" C GLU A 8 " pdb=" N GLU A 8 " pdb=" CA GLU A 8 " pdb=" CB GLU A 8 " ideal model delta harmonic sigma weight residual -122.60 -109.49 -13.11 0 2.50e+00 1.60e-01 2.75e+01 dihedral pdb=" CA CYS R 79 " pdb=" C CYS R 79 " pdb=" N LEU R 80 " pdb=" CA LEU R 80 " ideal model delta harmonic sigma weight residual -180.00 -156.80 -23.20 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA TRP R 91 " pdb=" C TRP R 91 " pdb=" N ASP R 92 " pdb=" CA ASP R 92 " ideal model delta harmonic sigma weight residual 180.00 157.28 22.72 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 4821 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1089 0.066 - 0.132: 208 0.132 - 0.198: 21 0.198 - 0.264: 2 0.264 - 0.330: 1 Chirality restraints: 1321 Sorted by residual: chirality pdb=" CA GLU A 8 " pdb=" N GLU A 8 " pdb=" C GLU A 8 " pdb=" CB GLU A 8 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CB THR R 279 " pdb=" CA THR R 279 " pdb=" OG1 THR R 279 " pdb=" CG2 THR R 279 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CB ILE A 344 " pdb=" CA ILE A 344 " pdb=" CG1 ILE A 344 " pdb=" CG2 ILE A 344 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 1318 not shown) Planarity restraints: 1455 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 7 " -0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C ALA A 7 " 0.056 2.00e-02 2.50e+03 pdb=" O ALA A 7 " -0.020 2.00e-02 2.50e+03 pdb=" N GLU A 8 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 282 " -0.054 5.00e-02 4.00e+02 8.00e-02 1.02e+01 pdb=" N PRO A 283 " 0.138 5.00e-02 4.00e+02 pdb=" CA PRO A 283 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 283 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 40 " -0.012 2.00e-02 2.50e+03 2.38e-02 5.64e+00 pdb=" C GLY A 40 " 0.041 2.00e-02 2.50e+03 pdb=" O GLY A 40 " -0.016 2.00e-02 2.50e+03 pdb=" N ALA A 41 " -0.014 2.00e-02 2.50e+03 ... (remaining 1452 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 138 2.68 - 3.23: 8196 3.23 - 3.79: 12055 3.79 - 4.34: 16404 4.34 - 4.90: 28057 Nonbonded interactions: 64850 Sorted by model distance: nonbonded pdb=" O ASN R 175 " pdb=" OD1 ASN R 175 " model vdw 2.123 3.040 nonbonded pdb=" OG1 THR A 183 " pdb=" OD1 ASN B 119 " model vdw 2.260 2.440 nonbonded pdb=" O SER B 67 " pdb=" OG SER B 67 " model vdw 2.272 2.440 nonbonded pdb=" OD1 ASP R 23 " pdb=" N ASP R 24 " model vdw 2.281 2.520 nonbonded pdb=" OD1 ASP B 27 " pdb=" N ALA B 28 " model vdw 2.337 2.520 ... (remaining 64845 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.340 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: 4.050 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 25.530 Find NCS groups from input model: 0.230 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 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 0.077 8297 Z= 0.355 Angle : 0.904 10.659 11318 Z= 0.531 Chirality : 0.052 0.330 1321 Planarity : 0.007 0.080 1455 Dihedral : 12.938 85.946 2697 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.07 % Allowed : 7.99 % Favored : 90.95 % Cbeta Deviations : 0.09 % 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: -0.48 (0.24), residues: 1112 helix: -0.14 (0.25), residues: 361 sheet: -0.07 (0.30), residues: 274 loop : -0.44 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP B 63 HIS 0.016 0.003 HIS R 189 PHE 0.034 0.003 PHE B 235 TYR 0.029 0.003 TYR R 294 ARG 0.007 0.001 ARG R 218 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 124 time to evaluate : 0.907 Fit side-chains REVERT: A 53 MET cc_start: 0.8338 (mpp) cc_final: 0.7905 (mpp) REVERT: A 303 TYR cc_start: 0.8632 (t80) cc_final: 0.8411 (t80) REVERT: G 20 LYS cc_start: 0.7202 (mtpt) cc_final: 0.6304 (mmmt) REVERT: R 90 ARG cc_start: 0.6276 (mmm-85) cc_final: 0.6065 (tmt-80) REVERT: R 294 TYR cc_start: 0.7218 (OUTLIER) cc_final: 0.5188 (m-80) outliers start: 8 outliers final: 4 residues processed: 132 average time/residue: 0.1861 time to fit residues: 34.2121 Evaluate side-chains 113 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 108 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain R residue 292 VAL Chi-restraints excluded: chain R residue 294 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN B 17 GLN B 119 ASN B 155 ASN R 141 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8297 Z= 0.279 Angle : 0.620 11.265 11318 Z= 0.333 Chirality : 0.045 0.149 1321 Planarity : 0.005 0.045 1455 Dihedral : 5.516 54.825 1207 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.66 % Allowed : 8.92 % Favored : 88.42 % 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: 0.14 (0.24), residues: 1112 helix: 1.01 (0.26), residues: 359 sheet: -0.27 (0.28), residues: 285 loop : -0.25 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 82 HIS 0.006 0.001 HIS B 91 PHE 0.018 0.002 PHE B 235 TYR 0.019 0.002 TYR A 354 ARG 0.003 0.001 ARG R 216 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 119 time to evaluate : 0.816 Fit side-chains REVERT: A 10 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.8221 (mtp180) REVERT: A 303 TYR cc_start: 0.8703 (t80) cc_final: 0.8445 (t80) REVERT: A 312 ASN cc_start: 0.8324 (p0) cc_final: 0.8022 (p0) REVERT: B 137 ARG cc_start: 0.7778 (tpp-160) cc_final: 0.7506 (tpp-160) REVERT: G 20 LYS cc_start: 0.7421 (mtpt) cc_final: 0.6248 (mmmt) REVERT: G 51 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8330 (pp) REVERT: H 109 ASP cc_start: 0.7662 (p0) cc_final: 0.7267 (t0) REVERT: R 210 ARG cc_start: 0.7443 (mmm-85) cc_final: 0.7123 (mmm160) REVERT: R 294 TYR cc_start: 0.7121 (OUTLIER) cc_final: 0.4703 (m-80) outliers start: 20 outliers final: 11 residues processed: 137 average time/residue: 0.1963 time to fit residues: 37.2202 Evaluate side-chains 121 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 107 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ARG Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 197 SER Chi-restraints excluded: chain R residue 143 THR Chi-restraints excluded: chain R residue 234 MET Chi-restraints excluded: chain R residue 294 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 0.4980 chunk 31 optimal weight: 0.6980 chunk 83 optimal weight: 6.9990 chunk 68 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 108 optimal weight: 0.9980 chunk 89 optimal weight: 0.0870 chunk 99 optimal weight: 5.9990 chunk 34 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN H 113 GLN R 112 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8297 Z= 0.186 Angle : 0.541 8.286 11318 Z= 0.286 Chirality : 0.043 0.159 1321 Planarity : 0.004 0.040 1455 Dihedral : 4.784 57.962 1199 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.53 % Allowed : 10.92 % Favored : 86.55 % 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: 0.45 (0.25), residues: 1112 helix: 1.52 (0.27), residues: 363 sheet: -0.39 (0.28), residues: 288 loop : -0.08 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 82 HIS 0.003 0.001 HIS B 183 PHE 0.018 0.001 PHE R 38 TYR 0.015 0.001 TYR H 190 ARG 0.004 0.000 ARG R 90 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 112 time to evaluate : 0.876 Fit side-chains REVERT: A 10 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.7967 (mtp180) REVERT: A 295 ASN cc_start: 0.7471 (t0) cc_final: 0.7158 (t0) REVERT: A 312 ASN cc_start: 0.8011 (p0) cc_final: 0.7670 (p0) REVERT: B 96 ARG cc_start: 0.7184 (ttm170) cc_final: 0.6757 (ttm170) REVERT: G 20 LYS cc_start: 0.7474 (mtpt) cc_final: 0.6221 (mmmt) REVERT: H 109 ASP cc_start: 0.7588 (p0) cc_final: 0.7238 (t0) REVERT: R 251 ARG cc_start: 0.7437 (mmm160) cc_final: 0.7223 (tpt170) outliers start: 19 outliers final: 8 residues processed: 128 average time/residue: 0.2018 time to fit residues: 35.6592 Evaluate side-chains 113 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 104 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ARG Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 197 SER Chi-restraints excluded: chain R residue 143 THR Chi-restraints excluded: chain R residue 294 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 47 optimal weight: 0.3980 chunk 67 optimal weight: 0.6980 chunk 100 optimal weight: 0.5980 chunk 106 optimal weight: 9.9990 chunk 52 optimal weight: 0.5980 chunk 95 optimal weight: 9.9990 chunk 28 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8297 Z= 0.199 Angle : 0.522 8.466 11318 Z= 0.277 Chirality : 0.042 0.149 1321 Planarity : 0.004 0.039 1455 Dihedral : 4.589 59.674 1199 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.66 % Allowed : 11.45 % Favored : 85.89 % 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: 0.56 (0.25), residues: 1112 helix: 1.76 (0.28), residues: 363 sheet: -0.50 (0.28), residues: 288 loop : -0.02 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.003 0.001 HIS B 183 PHE 0.035 0.002 PHE R 117 TYR 0.015 0.001 TYR H 190 ARG 0.003 0.000 ARG R 216 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 107 time to evaluate : 0.948 Fit side-chains REVERT: A 312 ASN cc_start: 0.8097 (p0) cc_final: 0.7755 (p0) REVERT: B 198 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7829 (pp) REVERT: G 20 LYS cc_start: 0.7577 (mtpt) cc_final: 0.6303 (mmmt) REVERT: H 109 ASP cc_start: 0.7552 (p0) cc_final: 0.7230 (t0) outliers start: 20 outliers final: 15 residues processed: 123 average time/residue: 0.1889 time to fit residues: 32.7622 Evaluate side-chains 117 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 101 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 197 SER Chi-restraints excluded: chain R residue 143 THR Chi-restraints excluded: chain R residue 204 ILE Chi-restraints excluded: chain R residue 272 VAL Chi-restraints excluded: chain R residue 294 TYR 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: 1.9990 chunk 1 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 73 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 54 optimal weight: 0.0870 chunk 95 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN H 171 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 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 : 0.003 0.029 8297 Z= 0.210 Angle : 0.516 8.376 11318 Z= 0.275 Chirality : 0.042 0.152 1321 Planarity : 0.004 0.039 1455 Dihedral : 4.454 58.017 1199 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.73 % Allowed : 12.38 % Favored : 83.89 % 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: 0.55 (0.25), residues: 1112 helix: 1.80 (0.28), residues: 368 sheet: -0.62 (0.28), residues: 289 loop : -0.00 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.003 0.001 HIS A 214 PHE 0.025 0.001 PHE R 117 TYR 0.015 0.001 TYR H 190 ARG 0.004 0.000 ARG R 90 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 102 time to evaluate : 1.000 Fit side-chains REVERT: A 10 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.8133 (mtp180) REVERT: A 312 ASN cc_start: 0.8130 (p0) cc_final: 0.7791 (p0) REVERT: B 96 ARG cc_start: 0.7218 (ttm170) cc_final: 0.6735 (ttm170) REVERT: B 198 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7835 (pp) REVERT: G 20 LYS cc_start: 0.7528 (mtpt) cc_final: 0.6479 (mmmt) REVERT: H 109 ASP cc_start: 0.7541 (p0) cc_final: 0.7241 (t0) outliers start: 28 outliers final: 24 residues processed: 126 average time/residue: 0.1814 time to fit residues: 32.3627 Evaluate side-chains 125 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 99 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ARG Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 133 VAL 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 B residue 213 VAL Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 197 SER Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 230 MET Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 143 THR Chi-restraints excluded: chain R residue 204 ILE Chi-restraints excluded: chain R residue 272 VAL Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain R residue 294 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.6980 chunk 95 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 106 optimal weight: 20.0000 chunk 88 optimal weight: 0.3980 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 55 optimal weight: 0.2980 chunk 102 optimal weight: 4.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 113 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8297 Z= 0.205 Angle : 0.508 8.960 11318 Z= 0.270 Chirality : 0.042 0.157 1321 Planarity : 0.004 0.040 1455 Dihedral : 4.319 55.048 1199 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 4.66 % Allowed : 12.12 % Favored : 83.22 % 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: 0.57 (0.25), residues: 1112 helix: 1.81 (0.28), residues: 369 sheet: -0.69 (0.28), residues: 295 loop : 0.08 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS A 214 PHE 0.021 0.001 PHE R 117 TYR 0.015 0.001 TYR H 190 ARG 0.005 0.000 ARG R 90 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 100 time to evaluate : 0.917 Fit side-chains REVERT: A 312 ASN cc_start: 0.8058 (p0) cc_final: 0.7756 (p0) REVERT: B 198 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7826 (pp) REVERT: G 20 LYS cc_start: 0.7534 (mtpt) cc_final: 0.6431 (mmmt) REVERT: H 109 ASP cc_start: 0.7510 (p0) cc_final: 0.7226 (t0) outliers start: 35 outliers final: 26 residues processed: 129 average time/residue: 0.1788 time to fit residues: 32.6775 Evaluate side-chains 123 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 96 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 197 SER Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 230 MET Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 143 THR Chi-restraints excluded: chain R residue 204 ILE Chi-restraints excluded: chain R residue 272 VAL Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain R residue 294 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 89 optimal weight: 8.9990 chunk 59 optimal weight: 5.9990 chunk 106 optimal weight: 7.9990 chunk 66 optimal weight: 0.2980 chunk 64 optimal weight: 0.6980 chunk 48 optimal weight: 0.0060 chunk 65 optimal weight: 0.5980 chunk 42 optimal weight: 0.0670 overall best weight: 0.3334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8297 Z= 0.142 Angle : 0.480 8.839 11318 Z= 0.251 Chirality : 0.041 0.154 1321 Planarity : 0.003 0.038 1455 Dihedral : 4.062 52.939 1199 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.06 % Allowed : 13.98 % Favored : 82.96 % 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: 0.67 (0.25), residues: 1112 helix: 1.92 (0.28), residues: 369 sheet: -0.64 (0.28), residues: 289 loop : 0.09 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.002 0.001 HIS B 142 PHE 0.017 0.001 PHE R 117 TYR 0.014 0.001 TYR H 190 ARG 0.006 0.000 ARG R 90 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 104 time to evaluate : 0.894 Fit side-chains REVERT: A 10 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.7726 (mtm180) REVERT: A 53 MET cc_start: 0.8372 (mpp) cc_final: 0.8069 (mpp) REVERT: B 170 ASP cc_start: 0.7774 (t70) cc_final: 0.7497 (t0) REVERT: B 198 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7781 (pp) REVERT: G 20 LYS cc_start: 0.7537 (mtpt) cc_final: 0.6433 (mmmt) outliers start: 23 outliers final: 17 residues processed: 122 average time/residue: 0.1924 time to fit residues: 32.6944 Evaluate side-chains 117 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 98 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ARG Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 230 MET Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 204 ILE Chi-restraints excluded: chain R residue 272 VAL Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain R residue 294 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.0770 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 9 optimal weight: 0.0170 chunk 83 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 92 optimal weight: 0.6980 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 113 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8297 Z= 0.171 Angle : 0.490 9.151 11318 Z= 0.259 Chirality : 0.041 0.163 1321 Planarity : 0.003 0.039 1455 Dihedral : 4.018 51.242 1199 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.06 % Allowed : 14.38 % Favored : 82.56 % 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 (0.25), residues: 1112 helix: 1.90 (0.28), residues: 369 sheet: -0.51 (0.28), residues: 294 loop : 0.10 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS A 214 PHE 0.012 0.001 PHE B 241 TYR 0.014 0.001 TYR H 190 ARG 0.003 0.000 ARG R 90 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 98 time to evaluate : 1.203 Fit side-chains REVERT: A 53 MET cc_start: 0.8395 (mpp) cc_final: 0.8075 (mpp) REVERT: B 170 ASP cc_start: 0.7727 (t70) cc_final: 0.7436 (t0) REVERT: B 198 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7794 (pp) REVERT: B 234 PHE cc_start: 0.8908 (OUTLIER) cc_final: 0.8522 (m-80) REVERT: G 20 LYS cc_start: 0.7554 (mtpt) cc_final: 0.6408 (mmmt) outliers start: 23 outliers final: 20 residues processed: 116 average time/residue: 0.2089 time to fit residues: 34.4494 Evaluate side-chains 119 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 97 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 230 MET Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 204 ILE Chi-restraints excluded: chain R residue 272 VAL Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain R residue 294 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 6.9990 chunk 101 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 chunk 43 optimal weight: 0.4980 chunk 77 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 93 optimal weight: 0.1980 chunk 64 optimal weight: 0.2980 chunk 104 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8297 Z= 0.171 Angle : 0.486 9.248 11318 Z= 0.258 Chirality : 0.041 0.158 1321 Planarity : 0.003 0.038 1455 Dihedral : 3.973 49.238 1199 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.99 % Allowed : 13.18 % Favored : 82.82 % 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: 0.70 (0.25), residues: 1112 helix: 1.87 (0.27), residues: 370 sheet: -0.54 (0.29), residues: 289 loop : 0.12 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS A 214 PHE 0.012 0.001 PHE B 241 TYR 0.014 0.001 TYR H 190 ARG 0.001 0.000 ARG R 101 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 99 time to evaluate : 0.896 Fit side-chains REVERT: A 53 MET cc_start: 0.8397 (mpp) cc_final: 0.8089 (mpp) REVERT: B 170 ASP cc_start: 0.7730 (t70) cc_final: 0.7446 (t0) REVERT: B 198 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7797 (pp) REVERT: B 234 PHE cc_start: 0.8910 (OUTLIER) cc_final: 0.8530 (m-80) REVERT: G 20 LYS cc_start: 0.7551 (mtpt) cc_final: 0.6420 (mmmt) outliers start: 30 outliers final: 26 residues processed: 125 average time/residue: 0.1723 time to fit residues: 30.5971 Evaluate side-chains 126 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 98 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 197 SER Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 230 MET Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 143 THR Chi-restraints excluded: chain R residue 204 ILE Chi-restraints excluded: chain R residue 272 VAL Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain R residue 294 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 100 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 69 optimal weight: 0.0980 chunk 92 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8297 Z= 0.199 Angle : 0.498 9.295 11318 Z= 0.264 Chirality : 0.042 0.150 1321 Planarity : 0.004 0.040 1455 Dihedral : 3.993 46.033 1199 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.73 % Allowed : 14.11 % Favored : 82.16 % 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: 0.69 (0.25), residues: 1112 helix: 1.89 (0.27), residues: 370 sheet: -0.53 (0.29), residues: 295 loop : 0.08 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS A 214 PHE 0.014 0.001 PHE B 241 TYR 0.015 0.001 TYR H 190 ARG 0.006 0.000 ARG R 90 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 102 time to evaluate : 0.857 Fit side-chains REVERT: A 53 MET cc_start: 0.8547 (mpp) cc_final: 0.8298 (mpp) REVERT: B 170 ASP cc_start: 0.7751 (t70) cc_final: 0.7488 (t0) REVERT: B 198 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7823 (pp) REVERT: B 234 PHE cc_start: 0.8932 (OUTLIER) cc_final: 0.8579 (m-80) REVERT: G 20 LYS cc_start: 0.7566 (mtpt) cc_final: 0.6426 (mmmt) REVERT: R 11 LEU cc_start: 0.6467 (tp) cc_final: 0.6227 (tp) outliers start: 28 outliers final: 25 residues processed: 126 average time/residue: 0.1779 time to fit residues: 32.0913 Evaluate side-chains 126 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 99 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 197 SER Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 226 VAL Chi-restraints excluded: chain H residue 230 MET Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 204 ILE Chi-restraints excluded: chain R residue 272 VAL Chi-restraints excluded: chain R residue 294 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.0170 chunk 87 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 11 optimal weight: 0.2980 chunk 16 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 4 optimal weight: 0.3980 chunk 63 optimal weight: 0.0470 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.191227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.151232 restraints weight = 9243.272| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 2.07 r_work: 0.3385 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8297 Z= 0.142 Angle : 0.469 8.949 11318 Z= 0.248 Chirality : 0.041 0.146 1321 Planarity : 0.003 0.036 1455 Dihedral : 3.803 41.794 1199 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.93 % Allowed : 15.18 % Favored : 81.89 % 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: 0.86 (0.25), residues: 1112 helix: 2.02 (0.27), residues: 370 sheet: -0.36 (0.29), residues: 289 loop : 0.12 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS B 142 PHE 0.010 0.001 PHE B 241 TYR 0.013 0.001 TYR H 190 ARG 0.003 0.000 ARG R 90 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1891.27 seconds wall clock time: 35 minutes 9.63 seconds (2109.63 seconds total)