Starting phenix.real_space_refine on Thu Feb 15 18:32:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gda_29944/02_2024/8gda_29944_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gda_29944/02_2024/8gda_29944.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gda_29944/02_2024/8gda_29944_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gda_29944/02_2024/8gda_29944_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gda_29944/02_2024/8gda_29944_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gda_29944/02_2024/8gda_29944.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gda_29944/02_2024/8gda_29944.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gda_29944/02_2024/8gda_29944_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gda_29944/02_2024/8gda_29944_neut_updated.pdb" } resolution = 3.3 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= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5445 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 48 5.16 5 C 4881 2.51 5 N 1349 2.21 5 O 1370 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 21": "OE1" <-> "OE2" Residue "A ARG 385": "NH1" <-> "NH2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "N GLU 46": "OE1" <-> "OE2" Residue "N ARG 67": "NH1" <-> "NH2" Residue "N ARG 98": "NH1" <-> "NH2" Residue "R ARG 46": "NH1" <-> "NH2" Residue "R GLU 116": "OE1" <-> "OE2" Residue "R PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 162": "NH1" <-> "NH2" Residue "R ARG 212": "NH1" <-> "NH2" Residue "R ARG 220": "NH1" <-> "NH2" Residue "R ARG 333": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7650 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1750 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 5, 'TRANS': 221} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 172 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 9, 'GLU:plan': 8, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 93 Chain: "B" Number of atoms: 2477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2477 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 5, 'TRANS': 334} Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 2, 'ASP:plan': 12, 'ASN%COO:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 108 Chain: "G" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 391 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "N" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 922 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "R" Number of atoms: 2080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2080 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 12, 'TRANS': 270} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 3, 'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 59 Chain: "R" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'YZV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.30, per 1000 atoms: 0.69 Number of scatterers: 7650 At special positions: 0 Unit cell: (95.2, 124.1, 100.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 F 2 9.00 O 1370 8.00 N 1349 7.00 C 4881 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 92 " - pdb=" SG CYS R 170 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.96 Conformation dependent library (CDL) restraints added in 1.5 seconds 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1946 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 10 sheets defined 35.4% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.80 Creating SS restraints... Processing helix chain 'A' and resid 11 through 31 Processing helix chain 'A' and resid 34 through 37 No H-bonds generated for 'chain 'A' and resid 34 through 37' Processing helix chain 'A' and resid 53 through 56 No H-bonds generated for 'chain 'A' and resid 53 through 56' Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 308 through 310 No H-bonds generated for 'chain 'A' and resid 308 through 310' Processing helix chain 'A' and resid 338 through 349 removed outlier: 4.134A pdb=" N ASP A 343 " --> pdb=" O TYR A 339 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 390 removed outlier: 3.563A pdb=" N ARG A 389 " --> pdb=" O ARG A 385 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLN A 390 " --> pdb=" O MET A 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 24 Processing helix chain 'B' and resid 30 through 35 removed outlier: 4.083A pdb=" N ASN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 22 Processing helix chain 'G' and resid 30 through 45 removed outlier: 3.628A pdb=" N ALA G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA G 45 " --> pdb=" O CYS G 41 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'R' and resid 23 through 43 removed outlier: 3.877A pdb=" N MET R 27 " --> pdb=" O ILE R 23 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N PHE R 28 " --> pdb=" O PRO R 24 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN R 35 " --> pdb=" O GLY R 31 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU R 36 " --> pdb=" O VAL R 32 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA R 38 " --> pdb=" O GLY R 34 " (cutoff:3.500A) Processing helix chain 'R' and resid 47 through 49 No H-bonds generated for 'chain 'R' and resid 47 through 49' Processing helix chain 'R' and resid 53 through 82 removed outlier: 3.673A pdb=" N LEU R 57 " --> pdb=" O THR R 53 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP R 65 " --> pdb=" O LEU R 61 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU R 66 " --> pdb=" O ALA R 62 " (cutoff:3.500A) Proline residue: R 74 - end of helix Processing helix chain 'R' and resid 89 through 122 removed outlier: 3.663A pdb=" N ILE R 110 " --> pdb=" O GLY R 106 " (cutoff:3.500A) Processing helix chain 'R' and resid 124 through 130 Processing helix chain 'R' and resid 133 through 151 Processing helix chain 'R' and resid 154 through 156 No H-bonds generated for 'chain 'R' and resid 154 through 156' Processing helix chain 'R' and resid 179 through 205 removed outlier: 3.527A pdb=" N TYR R 184 " --> pdb=" O ALA R 180 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER R 185 " --> pdb=" O HIS R 181 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE R 194 " --> pdb=" O GLY R 190 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU R 195 " --> pdb=" O PHE R 191 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE R 196 " --> pdb=" O SER R 192 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N THR R 199 " --> pdb=" O LEU R 195 " (cutoff:3.500A) Processing helix chain 'R' and resid 212 through 220 Processing helix chain 'R' and resid 268 through 297 removed outlier: 3.713A pdb=" N LEU R 282 " --> pdb=" O SER R 278 " (cutoff:3.500A) Proline residue: R 287 - end of helix Processing helix chain 'R' and resid 306 through 308 No H-bonds generated for 'chain 'R' and resid 306 through 308' Processing helix chain 'R' and resid 312 through 329 removed outlier: 4.119A pdb=" N VAL R 320 " --> pdb=" O ARG R 316 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ASN R 321 " --> pdb=" O ILE R 317 " (cutoff:3.500A) Proline residue: R 322 - end of helix Proline residue: R 326 - end of helix Processing helix chain 'R' and resid 334 through 343 removed outlier: 3.603A pdb=" N LYS R 343 " --> pdb=" O LYS R 339 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 286 through 292 removed outlier: 4.001A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.978A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.850A 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: 6.630A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.601A 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: 6.863A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.828A 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: 6.946A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.262A 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: 6.917A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.164A 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: 6.648A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.446A 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: 6.662A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 4 through 7 removed outlier: 3.556A pdb=" N SER N 21 " --> pdb=" O SER N 7 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY N 16 " --> pdb=" O LEU N 86 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU N 86 " --> pdb=" O GLY N 16 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LEU N 18 " --> pdb=" O ASN N 84 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ASN N 84 " --> pdb=" O LEU N 18 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N LEU N 20 " --> pdb=" O GLN N 82 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N GLN N 82 " --> pdb=" O LEU N 20 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N CYS N 22 " --> pdb=" O TYR N 80 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N TYR N 80 " --> pdb=" O CYS N 22 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N ALA N 24 " --> pdb=" O THR N 78 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N THR N 78 " --> pdb=" O ALA N 24 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 122 through 124 removed outlier: 5.924A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) 327 hydrogen bonds defined for protein. 957 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: 3.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1220 1.31 - 1.44: 2167 1.44 - 1.56: 4348 1.56 - 1.68: 2 1.68 - 1.81: 65 Bond restraints: 7802 Sorted by residual: bond pdb=" C13 YZV R 501 " pdb=" C14 YZV R 501 " ideal model delta sigma weight residual 1.636 1.221 0.415 2.00e-02 2.50e+03 4.31e+02 bond pdb=" C11 YZV R 501 " pdb=" N01 YZV R 501 " ideal model delta sigma weight residual 1.591 1.211 0.380 2.00e-02 2.50e+03 3.60e+02 bond pdb=" C11 YZV R 501 " pdb=" C14 YZV R 501 " ideal model delta sigma weight residual 1.297 1.622 -0.325 2.00e-02 2.50e+03 2.64e+02 bond pdb=" C15 YZV R 501 " pdb=" N01 YZV R 501 " ideal model delta sigma weight residual 1.500 1.237 0.263 2.00e-02 2.50e+03 1.73e+02 bond pdb=" C12 YZV R 501 " pdb=" O02 YZV R 501 " ideal model delta sigma weight residual 1.443 1.300 0.143 2.00e-02 2.50e+03 5.14e+01 ... (remaining 7797 not shown) Histogram of bond angle deviations from ideal: 99.66 - 106.54: 173 106.54 - 113.41: 4305 113.41 - 120.29: 2879 120.29 - 127.17: 3194 127.17 - 134.05: 75 Bond angle restraints: 10626 Sorted by residual: angle pdb=" C20 YZV R 501 " pdb=" C21 YZV R 501 " pdb=" N05 YZV R 501 " ideal model delta sigma weight residual 116.04 126.61 -10.57 3.00e+00 1.11e-01 1.24e+01 angle pdb=" C ILE R 286 " pdb=" CA ILE R 286 " pdb=" CB ILE R 286 " ideal model delta sigma weight residual 114.35 110.80 3.55 1.06e+00 8.90e-01 1.12e+01 angle pdb=" C ILE B 58 " pdb=" N TYR B 59 " pdb=" CA TYR B 59 " ideal model delta sigma weight residual 122.11 116.67 5.44 1.64e+00 3.72e-01 1.10e+01 angle pdb=" N ILE R 23 " pdb=" CA ILE R 23 " pdb=" C ILE R 23 " ideal model delta sigma weight residual 108.88 115.97 -7.09 2.16e+00 2.14e-01 1.08e+01 angle pdb=" N ASP B 228 " pdb=" CA ASP B 228 " pdb=" C ASP B 228 " ideal model delta sigma weight residual 110.42 114.97 -4.55 1.46e+00 4.69e-01 9.71e+00 ... (remaining 10621 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.44: 4348 22.44 - 44.89: 198 44.89 - 67.33: 23 67.33 - 89.77: 9 89.77 - 112.21: 2 Dihedral angle restraints: 4580 sinusoidal: 1572 harmonic: 3008 Sorted by residual: dihedral pdb=" CA GLY A 353 " pdb=" C GLY A 353 " pdb=" N ASP A 354 " pdb=" CA ASP A 354 " ideal model delta harmonic sigma weight residual -180.00 -155.00 -25.00 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CB CYS R 92 " pdb=" SG CYS R 92 " pdb=" SG CYS R 170 " pdb=" CB CYS R 170 " ideal model delta sinusoidal sigma weight residual 93.00 132.74 -39.74 1 1.00e+01 1.00e-02 2.22e+01 dihedral pdb=" C05 YZV R 501 " pdb=" C07 YZV R 501 " pdb=" C08 YZV R 501 " pdb=" O01 YZV R 501 " ideal model delta sinusoidal sigma weight residual 56.87 169.08 -112.21 1 3.00e+01 1.11e-03 1.47e+01 ... (remaining 4577 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 960 0.052 - 0.104: 245 0.104 - 0.156: 42 0.156 - 0.207: 3 0.207 - 0.259: 2 Chirality restraints: 1252 Sorted by residual: chirality pdb=" CA SER R 319 " pdb=" N SER R 319 " pdb=" C SER R 319 " pdb=" CB SER R 319 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA ILE R 23 " pdb=" N ILE R 23 " pdb=" C ILE R 23 " pdb=" CB ILE R 23 " both_signs ideal model delta sigma weight residual False 2.43 2.21 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" C12 YZV R 501 " pdb=" C13 YZV R 501 " pdb=" N01 YZV R 501 " pdb=" O02 YZV R 501 " both_signs ideal model delta sigma weight residual False -2.34 -2.53 0.19 2.00e-01 2.50e+01 8.63e-01 ... (remaining 1249 not shown) Planarity restraints: 1347 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP R 174 " 0.020 2.00e-02 2.50e+03 1.85e-02 8.59e+00 pdb=" CG TRP R 174 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP R 174 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP R 174 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP R 174 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP R 174 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP R 174 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 174 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 174 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP R 174 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 102 " 0.009 2.00e-02 2.50e+03 1.78e-02 3.18e+00 pdb=" C PHE R 102 " -0.031 2.00e-02 2.50e+03 pdb=" O PHE R 102 " 0.011 2.00e-02 2.50e+03 pdb=" N SER R 103 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.026 5.00e-02 4.00e+02 3.95e-02 2.50e+00 pdb=" N PRO B 236 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.022 5.00e-02 4.00e+02 ... (remaining 1344 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 861 2.75 - 3.28: 7336 3.28 - 3.82: 12056 3.82 - 4.36: 14153 4.36 - 4.90: 25400 Nonbonded interactions: 59806 Sorted by model distance: nonbonded pdb=" OD1 ASP B 205 " pdb=" OG SER B 207 " model vdw 2.207 2.440 nonbonded pdb=" O GLY A 52 " pdb=" OG1 THR A 55 " model vdw 2.232 2.440 nonbonded pdb=" OH TYR A 318 " pdb=" O TYR A 339 " model vdw 2.244 2.440 nonbonded pdb=" O CYS B 204 " pdb=" OH TYR N 117 " model vdw 2.275 2.440 nonbonded pdb=" O PHE N 29 " pdb=" NH2 ARG N 72 " model vdw 2.289 2.520 ... (remaining 59801 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 1.910 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 25.910 Find NCS groups from input model: 0.420 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 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 : 0.010 0.415 7802 Z= 0.737 Angle : 0.679 10.574 10626 Z= 0.387 Chirality : 0.046 0.259 1252 Planarity : 0.004 0.040 1347 Dihedral : 13.704 112.213 2625 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.41 % Allowed : 1.09 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.27), residues: 1016 helix: 0.40 (0.27), residues: 406 sheet: -0.17 (0.35), residues: 220 loop : -1.34 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP R 174 HIS 0.004 0.001 HIS B 91 PHE 0.017 0.002 PHE A 376 TYR 0.014 0.002 TYR R 130 ARG 0.012 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 181 time to evaluate : 0.925 Fit side-chains revert: symmetry clash REVERT: A 16 GLU cc_start: 0.6557 (mm-30) cc_final: 0.6084 (mm-30) REVERT: A 24 LYS cc_start: 0.7881 (ttmm) cc_final: 0.7499 (ttmm) REVERT: A 31 GLN cc_start: 0.7654 (tp40) cc_final: 0.7199 (tp40) REVERT: A 33 ASP cc_start: 0.7117 (t0) cc_final: 0.6695 (t0) REVERT: A 36 VAL cc_start: 0.8318 (t) cc_final: 0.7857 (p) REVERT: A 211 LYS cc_start: 0.8501 (mttm) cc_final: 0.8258 (mttm) REVERT: A 274 ASP cc_start: 0.7488 (t70) cc_final: 0.7237 (t70) REVERT: A 343 ASP cc_start: 0.7752 (m-30) cc_final: 0.7477 (m-30) REVERT: B 13 GLN cc_start: 0.6733 (pp30) cc_final: 0.6448 (pp30) REVERT: B 14 LEU cc_start: 0.7508 (mt) cc_final: 0.7171 (mm) REVERT: B 19 ARG cc_start: 0.7619 (ttm-80) cc_final: 0.7294 (ttp80) REVERT: B 46 ARG cc_start: 0.6553 (mtp-110) cc_final: 0.6211 (mtp-110) REVERT: B 66 ASP cc_start: 0.7345 (p0) cc_final: 0.6961 (p0) REVERT: B 78 LYS cc_start: 0.8491 (tppt) cc_final: 0.8084 (mmtt) REVERT: B 155 ASN cc_start: 0.8550 (t0) cc_final: 0.8124 (t0) REVERT: B 189 SER cc_start: 0.8598 (p) cc_final: 0.7968 (m) REVERT: B 233 CYS cc_start: 0.7866 (t) cc_final: 0.7075 (t) REVERT: B 239 ASN cc_start: 0.7797 (m110) cc_final: 0.7532 (m-40) REVERT: B 243 THR cc_start: 0.8307 (m) cc_final: 0.8058 (t) REVERT: B 303 ASP cc_start: 0.7418 (m-30) cc_final: 0.7126 (m-30) REVERT: B 308 LEU cc_start: 0.8107 (mt) cc_final: 0.7722 (mp) REVERT: R 27 MET cc_start: 0.7413 (mtm) cc_final: 0.7175 (mtp) REVERT: R 30 PHE cc_start: 0.8307 (m-10) cc_final: 0.7729 (m-80) REVERT: R 72 VAL cc_start: 0.7528 (OUTLIER) cc_final: 0.7311 (p) REVERT: R 94 TYR cc_start: 0.7316 (t80) cc_final: 0.6968 (t80) REVERT: R 113 MET cc_start: 0.8073 (mtp) cc_final: 0.7837 (mtp) REVERT: R 184 TYR cc_start: 0.7886 (t80) cc_final: 0.6596 (t80) REVERT: R 327 TRP cc_start: 0.8880 (m100) cc_final: 0.8324 (m100) REVERT: R 331 LEU cc_start: 0.8210 (mt) cc_final: 0.7823 (mp) outliers start: 3 outliers final: 1 residues processed: 183 average time/residue: 0.2797 time to fit residues: 63.5144 Evaluate side-chains 160 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 158 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain R residue 72 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 79 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN B 119 ASN B 155 ASN B 176 GLN B 183 HIS N 31 ASN R 321 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7802 Z= 0.266 Angle : 0.554 7.352 10626 Z= 0.299 Chirality : 0.043 0.157 1252 Planarity : 0.004 0.038 1347 Dihedral : 7.720 119.273 1133 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.09 % Allowed : 10.12 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.39 (0.27), residues: 1016 helix: 0.66 (0.27), residues: 409 sheet: -0.26 (0.34), residues: 226 loop : -1.18 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 174 HIS 0.004 0.001 HIS A 220 PHE 0.020 0.002 PHE A 376 TYR 0.012 0.002 TYR R 118 ARG 0.003 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 158 time to evaluate : 0.919 Fit side-chains revert: symmetry clash REVERT: A 16 GLU cc_start: 0.6612 (mm-30) cc_final: 0.6385 (mm-30) REVERT: A 24 LYS cc_start: 0.7891 (ttmm) cc_final: 0.7674 (ttmm) REVERT: A 31 GLN cc_start: 0.7623 (tp40) cc_final: 0.7279 (tp40) REVERT: A 33 ASP cc_start: 0.7151 (t0) cc_final: 0.6868 (t0) REVERT: A 46 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8292 (mp) REVERT: A 211 LYS cc_start: 0.8724 (mttm) cc_final: 0.8425 (mttm) REVERT: A 274 ASP cc_start: 0.7344 (t70) cc_final: 0.7022 (t0) REVERT: A 286 SER cc_start: 0.8971 (m) cc_final: 0.8676 (t) REVERT: A 317 ARG cc_start: 0.7380 (OUTLIER) cc_final: 0.7125 (mpp-170) REVERT: A 390 GLN cc_start: 0.8630 (pt0) cc_final: 0.8292 (pt0) REVERT: B 13 GLN cc_start: 0.6669 (pp30) cc_final: 0.6404 (pp30) REVERT: B 14 LEU cc_start: 0.7592 (mt) cc_final: 0.6839 (mm) REVERT: B 19 ARG cc_start: 0.7592 (ttm-80) cc_final: 0.7280 (ttp80) REVERT: B 66 ASP cc_start: 0.7284 (p0) cc_final: 0.6930 (p0) REVERT: B 78 LYS cc_start: 0.8484 (tppt) cc_final: 0.8185 (mmtt) REVERT: B 189 SER cc_start: 0.8540 (p) cc_final: 0.7994 (m) REVERT: B 239 ASN cc_start: 0.7707 (m110) cc_final: 0.7452 (m-40) REVERT: B 243 THR cc_start: 0.8319 (m) cc_final: 0.8101 (t) REVERT: B 307 VAL cc_start: 0.8785 (t) cc_final: 0.8092 (p) REVERT: B 308 LEU cc_start: 0.8026 (mt) cc_final: 0.7671 (mp) REVERT: G 27 ARG cc_start: 0.8822 (mtt90) cc_final: 0.8550 (mtm180) REVERT: R 30 PHE cc_start: 0.8319 (m-10) cc_final: 0.7757 (m-80) REVERT: R 54 PHE cc_start: 0.7814 (t80) cc_final: 0.7576 (t80) REVERT: R 55 TYR cc_start: 0.6781 (t80) cc_final: 0.6330 (t80) REVERT: R 72 VAL cc_start: 0.7586 (OUTLIER) cc_final: 0.7313 (p) REVERT: R 94 TYR cc_start: 0.7355 (t80) cc_final: 0.6906 (t80) REVERT: R 113 MET cc_start: 0.8195 (mtp) cc_final: 0.7968 (mtp) REVERT: R 184 TYR cc_start: 0.7846 (t80) cc_final: 0.6644 (t80) REVERT: R 331 LEU cc_start: 0.8225 (mt) cc_final: 0.7797 (mp) outliers start: 8 outliers final: 5 residues processed: 160 average time/residue: 0.2619 time to fit residues: 53.5606 Evaluate side-chains 164 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 156 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 72 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 chunk 99 optimal weight: 0.4980 chunk 81 optimal weight: 0.8980 chunk 31 optimal weight: 0.0040 chunk 73 optimal weight: 2.9990 chunk 90 optimal weight: 0.0980 overall best weight: 0.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN N 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7802 Z= 0.177 Angle : 0.485 6.913 10626 Z= 0.262 Chirality : 0.041 0.149 1252 Planarity : 0.003 0.036 1347 Dihedral : 7.274 125.303 1131 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.78 % Allowed : 13.27 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.02 (0.27), residues: 1016 helix: 1.13 (0.27), residues: 403 sheet: -0.24 (0.34), residues: 230 loop : -1.02 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 174 HIS 0.003 0.001 HIS A 220 PHE 0.015 0.001 PHE A 376 TYR 0.009 0.001 TYR R 130 ARG 0.005 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 168 time to evaluate : 0.804 Fit side-chains revert: symmetry clash REVERT: A 16 GLU cc_start: 0.6597 (mm-30) cc_final: 0.6368 (mm-30) REVERT: A 17 LYS cc_start: 0.7103 (OUTLIER) cc_final: 0.6830 (tmmt) REVERT: A 24 LYS cc_start: 0.7895 (ttmm) cc_final: 0.7680 (ttmm) REVERT: A 25 LYS cc_start: 0.7403 (ttmm) cc_final: 0.7170 (tttt) REVERT: A 31 GLN cc_start: 0.7501 (tp40) cc_final: 0.7113 (tp40) REVERT: A 46 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8299 (mp) REVERT: A 211 LYS cc_start: 0.8659 (mttm) cc_final: 0.8424 (mttm) REVERT: A 267 GLN cc_start: 0.8824 (tp-100) cc_final: 0.8603 (tp40) REVERT: A 274 ASP cc_start: 0.7310 (t70) cc_final: 0.7002 (t0) REVERT: A 286 SER cc_start: 0.8955 (m) cc_final: 0.8685 (t) REVERT: A 390 GLN cc_start: 0.8598 (pt0) cc_final: 0.8247 (pt0) REVERT: B 13 GLN cc_start: 0.6666 (pp30) cc_final: 0.6406 (pp30) REVERT: B 14 LEU cc_start: 0.7591 (mt) cc_final: 0.6753 (mm) REVERT: B 19 ARG cc_start: 0.7592 (ttm-80) cc_final: 0.7211 (ttp80) REVERT: B 66 ASP cc_start: 0.7245 (p0) cc_final: 0.6899 (p0) REVERT: B 78 LYS cc_start: 0.8512 (tppt) cc_final: 0.8167 (mmtt) REVERT: B 189 SER cc_start: 0.8600 (p) cc_final: 0.8033 (m) REVERT: B 243 THR cc_start: 0.8306 (m) cc_final: 0.8022 (t) REVERT: B 253 PHE cc_start: 0.8152 (m-80) cc_final: 0.7363 (m-80) REVERT: B 307 VAL cc_start: 0.8738 (t) cc_final: 0.8069 (p) REVERT: B 308 LEU cc_start: 0.8032 (mt) cc_final: 0.7673 (mp) REVERT: G 27 ARG cc_start: 0.8828 (mtt90) cc_final: 0.8518 (mtm180) REVERT: R 30 PHE cc_start: 0.8187 (m-10) cc_final: 0.7618 (m-80) REVERT: R 55 TYR cc_start: 0.6793 (t80) cc_final: 0.6381 (t80) REVERT: R 72 VAL cc_start: 0.7292 (p) cc_final: 0.7092 (p) REVERT: R 94 TYR cc_start: 0.7318 (t80) cc_final: 0.6857 (t80) REVERT: R 113 MET cc_start: 0.8182 (mtp) cc_final: 0.7843 (mtp) REVERT: R 184 TYR cc_start: 0.7766 (t80) cc_final: 0.6624 (t80) outliers start: 13 outliers final: 11 residues processed: 172 average time/residue: 0.2619 time to fit residues: 56.5036 Evaluate side-chains 175 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 162 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 0.0570 chunk 47 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 97 optimal weight: 0.0670 chunk 48 optimal weight: 0.7980 chunk 87 optimal weight: 0.0470 chunk 26 optimal weight: 0.5980 chunk 81 optimal weight: 0.9990 overall best weight: 0.2934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN A 294 GLN N 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7802 Z= 0.142 Angle : 0.455 6.260 10626 Z= 0.246 Chirality : 0.040 0.146 1252 Planarity : 0.003 0.035 1347 Dihedral : 7.010 128.074 1130 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.64 % Allowed : 15.87 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.26 (0.27), residues: 1016 helix: 1.39 (0.28), residues: 404 sheet: -0.11 (0.34), residues: 228 loop : -0.89 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.002 0.001 HIS A 220 PHE 0.017 0.001 PHE R 191 TYR 0.009 0.001 TYR R 130 ARG 0.004 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 168 time to evaluate : 0.853 Fit side-chains REVERT: A 16 GLU cc_start: 0.6569 (mm-30) cc_final: 0.6344 (mm-30) REVERT: A 24 LYS cc_start: 0.7891 (ttmm) cc_final: 0.7684 (ttmm) REVERT: A 29 GLN cc_start: 0.8375 (tp-100) cc_final: 0.8053 (tp-100) REVERT: A 31 GLN cc_start: 0.7474 (tp40) cc_final: 0.7130 (tp40) REVERT: A 46 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8294 (mp) REVERT: A 211 LYS cc_start: 0.8675 (mttm) cc_final: 0.7697 (mttm) REVERT: A 274 ASP cc_start: 0.7275 (t70) cc_final: 0.7009 (t0) REVERT: A 286 SER cc_start: 0.8917 (m) cc_final: 0.8681 (t) REVERT: A 343 ASP cc_start: 0.7587 (m-30) cc_final: 0.7318 (m-30) REVERT: A 390 GLN cc_start: 0.8549 (pt0) cc_final: 0.8223 (pt0) REVERT: B 13 GLN cc_start: 0.6724 (pp30) cc_final: 0.6398 (pp30) REVERT: B 14 LEU cc_start: 0.7618 (mt) cc_final: 0.6759 (mm) REVERT: B 19 ARG cc_start: 0.7581 (ttm-80) cc_final: 0.7226 (ttp80) REVERT: B 66 ASP cc_start: 0.7201 (p0) cc_final: 0.6872 (p0) REVERT: B 78 LYS cc_start: 0.8531 (tppt) cc_final: 0.8128 (mmtt) REVERT: B 189 SER cc_start: 0.8620 (p) cc_final: 0.8047 (m) REVERT: B 243 THR cc_start: 0.8280 (m) cc_final: 0.7999 (t) REVERT: B 253 PHE cc_start: 0.8053 (m-80) cc_final: 0.7543 (m-80) REVERT: B 307 VAL cc_start: 0.8688 (t) cc_final: 0.8051 (p) REVERT: R 30 PHE cc_start: 0.8190 (m-10) cc_final: 0.7592 (m-80) REVERT: R 94 TYR cc_start: 0.7169 (t80) cc_final: 0.6688 (t80) REVERT: R 113 MET cc_start: 0.8227 (mtp) cc_final: 0.7946 (mtp) REVERT: R 184 TYR cc_start: 0.7716 (t80) cc_final: 0.6609 (t80) REVERT: R 296 GLN cc_start: 0.8055 (tp40) cc_final: 0.7821 (tp40) outliers start: 12 outliers final: 8 residues processed: 172 average time/residue: 0.2594 time to fit residues: 56.3748 Evaluate side-chains 176 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 167 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 83 optimal weight: 0.3980 chunk 67 optimal weight: 0.0980 chunk 0 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN N 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7802 Z= 0.212 Angle : 0.485 6.799 10626 Z= 0.262 Chirality : 0.041 0.150 1252 Planarity : 0.003 0.035 1347 Dihedral : 7.043 128.351 1130 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.46 % Allowed : 15.73 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.31 (0.27), residues: 1016 helix: 1.47 (0.28), residues: 400 sheet: -0.11 (0.34), residues: 228 loop : -0.88 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 174 HIS 0.003 0.001 HIS R 129 PHE 0.020 0.002 PHE A 376 TYR 0.009 0.001 TYR R 130 ARG 0.003 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 165 time to evaluate : 0.869 Fit side-chains REVERT: A 16 GLU cc_start: 0.6628 (mm-30) cc_final: 0.6408 (mm-30) REVERT: A 31 GLN cc_start: 0.7465 (tp40) cc_final: 0.7080 (tp40) REVERT: A 46 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8301 (mp) REVERT: A 211 LYS cc_start: 0.8551 (mttm) cc_final: 0.8280 (mttm) REVERT: A 220 HIS cc_start: 0.7832 (m170) cc_final: 0.7144 (m-70) REVERT: A 274 ASP cc_start: 0.7247 (t70) cc_final: 0.6962 (t0) REVERT: A 286 SER cc_start: 0.8909 (m) cc_final: 0.8695 (t) REVERT: A 317 ARG cc_start: 0.7416 (OUTLIER) cc_final: 0.7000 (mpp-170) REVERT: A 390 GLN cc_start: 0.8567 (pt0) cc_final: 0.8233 (pt0) REVERT: B 13 GLN cc_start: 0.6759 (pp30) cc_final: 0.6396 (pp30) REVERT: B 14 LEU cc_start: 0.7613 (mt) cc_final: 0.6703 (mm) REVERT: B 19 ARG cc_start: 0.7569 (ttm-80) cc_final: 0.7229 (ttp80) REVERT: B 66 ASP cc_start: 0.7207 (p0) cc_final: 0.6888 (p0) REVERT: B 78 LYS cc_start: 0.8517 (tppt) cc_final: 0.8150 (mmtt) REVERT: B 187 VAL cc_start: 0.6401 (t) cc_final: 0.6083 (t) REVERT: B 189 SER cc_start: 0.8546 (p) cc_final: 0.7932 (m) REVERT: B 243 THR cc_start: 0.8302 (m) cc_final: 0.7984 (t) REVERT: B 253 PHE cc_start: 0.8061 (m-80) cc_final: 0.7583 (m-80) REVERT: B 307 VAL cc_start: 0.8732 (t) cc_final: 0.8100 (p) REVERT: N 38 ARG cc_start: 0.8172 (ptt90) cc_final: 0.7943 (ptt180) REVERT: R 30 PHE cc_start: 0.7752 (m-10) cc_final: 0.7172 (m-80) REVERT: R 94 TYR cc_start: 0.7221 (t80) cc_final: 0.6691 (t80) REVERT: R 113 MET cc_start: 0.8222 (mtp) cc_final: 0.7985 (mtp) REVERT: R 184 TYR cc_start: 0.7773 (t80) cc_final: 0.6741 (t80) outliers start: 18 outliers final: 14 residues processed: 172 average time/residue: 0.2586 time to fit residues: 56.3647 Evaluate side-chains 179 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 163 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 170 CYS Chi-restraints excluded: chain R residue 174 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 81 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 8 optimal weight: 0.2980 chunk 32 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 94 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7802 Z= 0.240 Angle : 0.502 7.186 10626 Z= 0.271 Chirality : 0.042 0.149 1252 Planarity : 0.003 0.036 1347 Dihedral : 7.126 128.347 1130 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.33 % Allowed : 17.37 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.27 (0.27), residues: 1016 helix: 1.45 (0.27), residues: 399 sheet: -0.12 (0.34), residues: 228 loop : -0.91 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 174 HIS 0.003 0.001 HIS R 129 PHE 0.021 0.002 PHE A 376 TYR 0.010 0.001 TYR R 118 ARG 0.002 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 160 time to evaluate : 0.875 Fit side-chains REVERT: A 16 GLU cc_start: 0.6648 (mm-30) cc_final: 0.6447 (mm-30) REVERT: A 31 GLN cc_start: 0.7468 (tp40) cc_final: 0.7098 (tp40) REVERT: A 46 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8253 (mp) REVERT: A 211 LYS cc_start: 0.8633 (mttm) cc_final: 0.8293 (mttm) REVERT: A 274 ASP cc_start: 0.7268 (t70) cc_final: 0.6964 (t0) REVERT: A 286 SER cc_start: 0.8916 (m) cc_final: 0.8690 (t) REVERT: A 317 ARG cc_start: 0.7418 (OUTLIER) cc_final: 0.7046 (mpp-170) REVERT: A 390 GLN cc_start: 0.8562 (pt0) cc_final: 0.8249 (pt0) REVERT: B 13 GLN cc_start: 0.6755 (pp30) cc_final: 0.6426 (pp30) REVERT: B 19 ARG cc_start: 0.7569 (ttm-80) cc_final: 0.7233 (ttp80) REVERT: B 66 ASP cc_start: 0.7207 (p0) cc_final: 0.6892 (p0) REVERT: B 78 LYS cc_start: 0.8535 (tppt) cc_final: 0.8085 (mmtt) REVERT: B 187 VAL cc_start: 0.6362 (t) cc_final: 0.6033 (t) REVERT: B 189 SER cc_start: 0.8546 (p) cc_final: 0.7927 (m) REVERT: B 243 THR cc_start: 0.8290 (m) cc_final: 0.7944 (t) REVERT: B 307 VAL cc_start: 0.8770 (t) cc_final: 0.8162 (p) REVERT: R 30 PHE cc_start: 0.7748 (m-10) cc_final: 0.7167 (m-80) REVERT: R 94 TYR cc_start: 0.7371 (t80) cc_final: 0.6811 (t80) outliers start: 17 outliers final: 14 residues processed: 166 average time/residue: 0.2653 time to fit residues: 55.4539 Evaluate side-chains 176 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 160 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 170 CYS Chi-restraints excluded: chain R residue 174 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 0.0970 chunk 55 optimal weight: 2.9990 chunk 71 optimal weight: 0.0170 chunk 82 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 60 optimal weight: 0.0030 chunk 59 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.3626 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7802 Z= 0.157 Angle : 0.455 6.486 10626 Z= 0.245 Chirality : 0.040 0.166 1252 Planarity : 0.003 0.036 1347 Dihedral : 6.892 129.629 1130 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.92 % Allowed : 18.47 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.50 (0.28), residues: 1016 helix: 1.73 (0.28), residues: 396 sheet: -0.15 (0.34), residues: 227 loop : -0.79 (0.32), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.003 0.001 HIS R 129 PHE 0.013 0.001 PHE R 194 TYR 0.008 0.001 TYR R 130 ARG 0.002 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 164 time to evaluate : 0.880 Fit side-chains revert: symmetry clash REVERT: A 16 GLU cc_start: 0.6599 (mm-30) cc_final: 0.6397 (mm-30) REVERT: A 31 GLN cc_start: 0.7438 (tp40) cc_final: 0.7081 (tp40) REVERT: A 46 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8268 (mp) REVERT: A 211 LYS cc_start: 0.8453 (mttm) cc_final: 0.8209 (mttm) REVERT: A 274 ASP cc_start: 0.7260 (t70) cc_final: 0.6972 (t0) REVERT: A 390 GLN cc_start: 0.8518 (pt0) cc_final: 0.8206 (pt0) REVERT: B 13 GLN cc_start: 0.6751 (pp30) cc_final: 0.6409 (pp30) REVERT: B 19 ARG cc_start: 0.7564 (ttm-80) cc_final: 0.7230 (ttp80) REVERT: B 66 ASP cc_start: 0.7142 (p0) cc_final: 0.6879 (p0) REVERT: B 78 LYS cc_start: 0.8499 (tppt) cc_final: 0.8157 (mmtt) REVERT: B 134 ARG cc_start: 0.6676 (mtp-110) cc_final: 0.6472 (mtp-110) REVERT: B 187 VAL cc_start: 0.6333 (t) cc_final: 0.6032 (t) REVERT: B 189 SER cc_start: 0.8607 (p) cc_final: 0.7968 (m) REVERT: B 243 THR cc_start: 0.8249 (m) cc_final: 0.7936 (t) REVERT: B 307 VAL cc_start: 0.8683 (t) cc_final: 0.8108 (p) REVERT: R 30 PHE cc_start: 0.7748 (m-10) cc_final: 0.7169 (m-80) REVERT: R 94 TYR cc_start: 0.7482 (t80) cc_final: 0.6919 (t80) REVERT: R 184 TYR cc_start: 0.7725 (t80) cc_final: 0.7501 (t80) outliers start: 14 outliers final: 11 residues processed: 170 average time/residue: 0.2636 time to fit residues: 56.5563 Evaluate side-chains 173 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 161 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 45 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 0.3980 chunk 19 optimal weight: 1.9990 chunk 18 optimal weight: 0.0770 chunk 61 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 88 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7802 Z= 0.216 Angle : 0.489 6.893 10626 Z= 0.262 Chirality : 0.041 0.148 1252 Planarity : 0.003 0.037 1347 Dihedral : 6.959 128.599 1130 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.60 % Allowed : 17.65 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.27), residues: 1016 helix: 1.67 (0.28), residues: 398 sheet: -0.14 (0.34), residues: 222 loop : -0.79 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 174 HIS 0.004 0.001 HIS R 129 PHE 0.019 0.002 PHE A 376 TYR 0.009 0.001 TYR R 130 ARG 0.006 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 158 time to evaluate : 0.785 Fit side-chains REVERT: A 16 GLU cc_start: 0.6634 (mm-30) cc_final: 0.6429 (mm-30) REVERT: A 31 GLN cc_start: 0.7464 (tp40) cc_final: 0.7103 (tp40) REVERT: A 46 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8258 (mp) REVERT: A 211 LYS cc_start: 0.8505 (mttm) cc_final: 0.8132 (mtmm) REVERT: A 274 ASP cc_start: 0.7245 (t70) cc_final: 0.6941 (t0) REVERT: A 390 GLN cc_start: 0.8559 (pt0) cc_final: 0.8264 (pt0) REVERT: B 13 GLN cc_start: 0.6760 (pp30) cc_final: 0.6414 (pp30) REVERT: B 19 ARG cc_start: 0.7563 (ttm-80) cc_final: 0.7227 (ttp80) REVERT: B 66 ASP cc_start: 0.7175 (p0) cc_final: 0.6876 (p0) REVERT: B 78 LYS cc_start: 0.8529 (tppt) cc_final: 0.8084 (mmtt) REVERT: B 187 VAL cc_start: 0.6347 (t) cc_final: 0.6027 (t) REVERT: B 189 SER cc_start: 0.8565 (p) cc_final: 0.7938 (m) REVERT: B 243 THR cc_start: 0.8238 (m) cc_final: 0.7905 (t) REVERT: B 307 VAL cc_start: 0.8756 (t) cc_final: 0.8158 (p) REVERT: R 30 PHE cc_start: 0.7735 (m-10) cc_final: 0.7150 (m-80) REVERT: R 94 TYR cc_start: 0.7508 (t80) cc_final: 0.6917 (t80) REVERT: R 184 TYR cc_start: 0.7766 (t80) cc_final: 0.7447 (t80) outliers start: 19 outliers final: 17 residues processed: 167 average time/residue: 0.2526 time to fit residues: 53.1702 Evaluate side-chains 176 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 158 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 45 SER Chi-restraints excluded: chain R residue 170 CYS Chi-restraints excluded: chain R residue 174 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 0.0770 chunk 93 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 39 optimal weight: 0.2980 chunk 71 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 85 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7802 Z= 0.194 Angle : 0.477 6.779 10626 Z= 0.256 Chirality : 0.041 0.156 1252 Planarity : 0.003 0.036 1347 Dihedral : 6.913 129.005 1130 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.19 % Allowed : 18.33 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.28), residues: 1016 helix: 1.77 (0.28), residues: 398 sheet: -0.15 (0.34), residues: 222 loop : -0.74 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP R 174 HIS 0.003 0.001 HIS R 129 PHE 0.015 0.001 PHE A 376 TYR 0.009 0.001 TYR R 130 ARG 0.003 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 155 time to evaluate : 0.887 Fit side-chains REVERT: A 16 GLU cc_start: 0.6620 (mm-30) cc_final: 0.6417 (mm-30) REVERT: A 31 GLN cc_start: 0.7451 (tp40) cc_final: 0.7100 (tp40) REVERT: A 46 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8250 (mp) REVERT: A 211 LYS cc_start: 0.8500 (mttm) cc_final: 0.8137 (mtmm) REVERT: A 274 ASP cc_start: 0.7242 (t70) cc_final: 0.6950 (t0) REVERT: A 390 GLN cc_start: 0.8546 (pt0) cc_final: 0.8244 (pt0) REVERT: B 13 GLN cc_start: 0.6713 (pp30) cc_final: 0.6423 (pp30) REVERT: B 19 ARG cc_start: 0.7560 (ttm-80) cc_final: 0.7227 (ttp80) REVERT: B 66 ASP cc_start: 0.7165 (p0) cc_final: 0.6871 (p0) REVERT: B 78 LYS cc_start: 0.8514 (tppt) cc_final: 0.8191 (mmtt) REVERT: B 187 VAL cc_start: 0.6328 (t) cc_final: 0.6001 (t) REVERT: B 189 SER cc_start: 0.8572 (p) cc_final: 0.7951 (m) REVERT: B 243 THR cc_start: 0.8224 (m) cc_final: 0.7896 (t) REVERT: B 307 VAL cc_start: 0.8737 (t) cc_final: 0.8138 (p) REVERT: R 30 PHE cc_start: 0.7734 (m-10) cc_final: 0.7123 (m-80) REVERT: R 94 TYR cc_start: 0.7506 (t80) cc_final: 0.6901 (t80) REVERT: R 184 TYR cc_start: 0.7740 (t80) cc_final: 0.7438 (t80) outliers start: 16 outliers final: 14 residues processed: 162 average time/residue: 0.2707 time to fit residues: 55.5947 Evaluate side-chains 171 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 156 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 45 SER Chi-restraints excluded: chain R residue 170 CYS Chi-restraints excluded: chain R residue 174 TRP Chi-restraints excluded: chain R residue 283 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 80 optimal weight: 0.0070 chunk 8 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 63 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 24 optimal weight: 0.3980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7802 Z= 0.191 Angle : 0.477 6.709 10626 Z= 0.256 Chirality : 0.041 0.153 1252 Planarity : 0.003 0.036 1347 Dihedral : 6.895 129.296 1130 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.33 % Allowed : 18.60 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.28), residues: 1016 helix: 1.82 (0.28), residues: 398 sheet: -0.13 (0.34), residues: 222 loop : -0.72 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 174 HIS 0.003 0.001 HIS R 129 PHE 0.023 0.002 PHE R 191 TYR 0.009 0.001 TYR R 130 ARG 0.003 0.000 ARG A 317 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 153 time to evaluate : 0.934 Fit side-chains REVERT: A 16 GLU cc_start: 0.6621 (mm-30) cc_final: 0.6420 (mm-30) REVERT: A 31 GLN cc_start: 0.7435 (tp40) cc_final: 0.7016 (tp40) REVERT: A 46 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8248 (mp) REVERT: A 211 LYS cc_start: 0.8508 (mttm) cc_final: 0.8135 (mtmm) REVERT: A 274 ASP cc_start: 0.7242 (t70) cc_final: 0.6952 (t0) REVERT: A 390 GLN cc_start: 0.8548 (pt0) cc_final: 0.8235 (pt0) REVERT: B 13 GLN cc_start: 0.6728 (pp30) cc_final: 0.6425 (pp30) REVERT: B 19 ARG cc_start: 0.7562 (ttm-80) cc_final: 0.7229 (ttp80) REVERT: B 66 ASP cc_start: 0.7165 (p0) cc_final: 0.6868 (p0) REVERT: B 78 LYS cc_start: 0.8531 (tppt) cc_final: 0.8075 (mmtt) REVERT: B 187 VAL cc_start: 0.6325 (t) cc_final: 0.6000 (t) REVERT: B 189 SER cc_start: 0.8571 (p) cc_final: 0.7954 (m) REVERT: B 243 THR cc_start: 0.8217 (m) cc_final: 0.7879 (t) REVERT: B 307 VAL cc_start: 0.8739 (t) cc_final: 0.8143 (p) REVERT: R 94 TYR cc_start: 0.7502 (t80) cc_final: 0.6897 (t80) REVERT: R 184 TYR cc_start: 0.7736 (t80) cc_final: 0.7474 (t80) outliers start: 17 outliers final: 15 residues processed: 161 average time/residue: 0.2616 time to fit residues: 53.2634 Evaluate side-chains 168 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 152 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 45 SER Chi-restraints excluded: chain R residue 170 CYS Chi-restraints excluded: chain R residue 174 TRP Chi-restraints excluded: chain R residue 283 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 0.6980 chunk 11 optimal weight: 0.0670 chunk 22 optimal weight: 4.9990 chunk 80 optimal weight: 0.3980 chunk 33 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 70 optimal weight: 0.6980 chunk 4 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.119076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.105971 restraints weight = 10930.992| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.39 r_work: 0.3173 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7802 Z= 0.194 Angle : 0.478 6.712 10626 Z= 0.256 Chirality : 0.041 0.149 1252 Planarity : 0.003 0.036 1347 Dihedral : 6.873 129.172 1130 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.19 % Allowed : 18.60 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.68 (0.28), residues: 1016 helix: 1.95 (0.28), residues: 387 sheet: -0.09 (0.34), residues: 222 loop : -0.66 (0.32), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 174 HIS 0.003 0.001 HIS R 129 PHE 0.016 0.001 PHE A 376 TYR 0.009 0.001 TYR R 130 ARG 0.003 0.000 ARG A 317 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2108.90 seconds wall clock time: 38 minutes 44.57 seconds (2324.57 seconds total)