Starting phenix.real_space_refine on Mon Mar 11 14:54:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wc5_37431/03_2024/8wc5_37431_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wc5_37431/03_2024/8wc5_37431.map 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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wc5_37431/03_2024/8wc5_37431.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wc5_37431/03_2024/8wc5_37431.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wc5_37431/03_2024/8wc5_37431_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wc5_37431/03_2024/8wc5_37431_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= 0.009 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 57 5.16 5 C 5419 2.51 5 N 1453 2.21 5 O 1582 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 14": "OE1" <-> "OE2" Residue "A GLU 20": "OE1" <-> "OE2" Residue "A ARG 356": "NH1" <-> "NH2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 92": "OE1" <-> "OE2" Residue "R ARG 309": "NH1" <-> "NH2" Residue "Y TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 42": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8511 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1839 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain breaks: 3 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 28 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: "B" Number of atoms: 2553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2553 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 33 Chain: "R" Number of atoms: 1949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1949 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 12, 'TRANS': 246} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 46 Chain: "S" Number of atoms: 1746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1746 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 9, 'TRANS': 222} Chain breaks: 2 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "Y" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 420 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "R" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'TMA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Time building chain proxies: 5.01, per 1000 atoms: 0.59 Number of scatterers: 8511 At special positions: 0 Unit cell: (112.2, 97.75, 131.75, 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 57 16.00 O 1582 8.00 N 1453 7.00 C 5419 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 95 " - pdb=" SG CYS R 181 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.44 Conformation dependent library (CDL) restraints added in 1.7 seconds 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2076 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 31 helices and 13 sheets defined 30.9% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.78 Creating SS restraints... Processing helix chain 'A' and resid 7 through 31 removed outlier: 3.664A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 49 No H-bonds generated for 'chain 'A' and resid 46 through 49' Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 233 through 244 Processing helix chain 'A' and resid 261 through 268 removed outlier: 3.599A pdb=" N ALA A 265 " --> pdb=" O GLN A 261 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU A 266 " --> pdb=" O ASP A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 284 removed outlier: 4.177A pdb=" N ALA A 283 " --> pdb=" O PRO A 280 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG A 284 " --> pdb=" O GLU A 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 284' Processing helix chain 'A' and resid 299 through 318 removed outlier: 4.564A pdb=" N ILE A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N SER A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR A 317 " --> pdb=" O LEU A 313 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA A 318 " --> pdb=" O ARG A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 355 removed outlier: 3.678A pdb=" N LEU A 355 " --> pdb=" O GLN A 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 25 removed outlier: 4.317A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 36 removed outlier: 5.463A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 33 through 48 removed outlier: 3.996A pdb=" N VAL R 38 " --> pdb=" O LEU R 34 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER R 48 " --> pdb=" O ILE R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 56 through 58 No H-bonds generated for 'chain 'R' and resid 56 through 58' Processing helix chain 'R' and resid 60 through 73 removed outlier: 3.586A pdb=" N LEU R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 84 removed outlier: 3.547A pdb=" N MET R 80 " --> pdb=" O MET R 76 " (cutoff:3.500A) Processing helix chain 'R' and resid 92 through 111 removed outlier: 3.765A pdb=" N LYS R 96 " --> pdb=" O GLU R 92 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL R 97 " --> pdb=" O ILE R 93 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER R 100 " --> pdb=" O LYS R 96 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N SER R 109 " --> pdb=" O LEU R 105 " (cutoff:3.500A) Processing helix chain 'R' and resid 113 through 125 removed outlier: 3.547A pdb=" N SER R 117 " --> pdb=" O LEU R 113 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE R 118 " --> pdb=" O ALA R 114 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 129 No H-bonds generated for 'chain 'R' and resid 127 through 129' Processing helix chain 'R' and resid 136 through 153 removed outlier: 3.852A pdb=" N VAL R 141 " --> pdb=" O SER R 137 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET R 142 " --> pdb=" O THR R 138 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER R 146 " --> pdb=" O MET R 142 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU R 149 " --> pdb=" O VAL R 145 " (cutoff:3.500A) Proline residue: R 150 - end of helix Processing helix chain 'R' and resid 155 through 158 No H-bonds generated for 'chain 'R' and resid 155 through 158' Processing helix chain 'R' and resid 168 through 174 removed outlier: 4.387A pdb=" N ARG R 172 " --> pdb=" O GLU R 168 " (cutoff:3.500A) Processing helix chain 'R' and resid 176 through 178 No H-bonds generated for 'chain 'R' and resid 176 through 178' Processing helix chain 'R' and resid 188 through 191 No H-bonds generated for 'chain 'R' and resid 188 through 191' Processing helix chain 'R' and resid 203 through 222 removed outlier: 3.633A pdb=" N TYR R 209 " --> pdb=" O MET R 205 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG R 211 " --> pdb=" O PHE R 207 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TYR R 213 " --> pdb=" O TYR R 209 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE R 214 " --> pdb=" O TYR R 210 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE R 215 " --> pdb=" O ARG R 211 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA R 216 " --> pdb=" O ILE R 212 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA R 220 " --> pdb=" O ALA R 216 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 252 removed outlier: 3.638A pdb=" N ILE R 252 " --> pdb=" O LYS R 248 " (cutoff:3.500A) Processing helix chain 'R' and resid 255 through 274 Proline residue: R 263 - end of helix removed outlier: 5.000A pdb=" N VAL R 269 " --> pdb=" O PHE R 265 " (cutoff:3.500A) Proline residue: R 272 - end of helix Processing helix chain 'R' and resid 280 through 285 removed outlier: 3.617A pdb=" N ASP R 284 " --> pdb=" O PRO R 280 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ALA R 285 " --> pdb=" O SER R 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 280 through 285' Processing helix chain 'R' and resid 287 through 301 removed outlier: 4.208A pdb=" N TYR R 291 " --> pdb=" O TYR R 287 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N LEU R 292 " --> pdb=" O TRP R 288 " (cutoff:3.500A) Proline residue: R 298 - end of helix Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 221 through 223 No H-bonds generated for 'chain 'S' and resid 221 through 223' Processing helix chain 'Y' and resid 11 through 22 removed outlier: 3.834A pdb=" N LEU Y 15 " --> pdb=" O GLN Y 11 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL Y 16 " --> pdb=" O ALA Y 12 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N MET Y 21 " --> pdb=" O GLU Y 17 " (cutoff:3.500A) Processing helix chain 'Y' and resid 30 through 47 removed outlier: 4.423A pdb=" N ALA Y 35 " --> pdb=" O SER Y 31 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASP Y 36 " --> pdb=" O LYS Y 32 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU Y 37 " --> pdb=" O ALA Y 33 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N MET Y 38 " --> pdb=" O ALA Y 34 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N TYR Y 40 " --> pdb=" O ASP Y 36 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N CYS Y 41 " --> pdb=" O LEU Y 37 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N LYS Y 46 " --> pdb=" O GLU Y 42 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N GLU Y 47 " --> pdb=" O ALA Y 43 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 253 through 259 removed outlier: 4.187A pdb=" N ALA A 220 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ASN A 195 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N LEU A 36 " --> pdb=" O ASN A 195 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N HIS A 197 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N LEU A 38 " --> pdb=" O HIS A 197 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N PHE A 199 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 49 through 51 removed outlier: 3.531A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.998A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.829A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 178 through 181 removed outlier: 4.733A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.877A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 252 through 254 Processing sheet with id= H, first strand: chain 'B' and resid 294 through 298 removed outlier: 3.565A pdb=" N LEU B 286 " --> pdb=" O SER B 277 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'S' and resid 5 through 7 removed outlier: 3.513A pdb=" N SER S 21 " --> pdb=" O SER S 7 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'S' and resid 93 through 97 removed outlier: 3.917A pdb=" N TRP S 36 " --> pdb=" O ALA S 49 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 155 through 160 Processing sheet with id= L, first strand: chain 'S' and resid 174 through 176 Processing sheet with id= M, first strand: chain 'S' and resid 225 through 227 removed outlier: 3.804A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) 269 hydrogen bonds defined for protein. 774 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: 2.40 Time building geometry restraints manager: 3.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1370 1.29 - 1.42: 2382 1.42 - 1.56: 4855 1.56 - 1.69: 9 1.69 - 1.82: 82 Bond restraints: 8698 Sorted by residual: bond pdb=" CA LEU R 71 " pdb=" C LEU R 71 " ideal model delta sigma weight residual 1.524 1.447 0.077 1.27e-02 6.20e+03 3.65e+01 bond pdb=" C PRO R 56 " pdb=" O PRO R 56 " ideal model delta sigma weight residual 1.238 1.163 0.075 1.33e-02 5.65e+03 3.19e+01 bond pdb=" C PHE R 303 " pdb=" O PHE R 303 " ideal model delta sigma weight residual 1.234 1.290 -0.056 1.00e-02 1.00e+04 3.15e+01 bond pdb=" N ASP R 177 " pdb=" CA ASP R 177 " ideal model delta sigma weight residual 1.457 1.386 0.071 1.35e-02 5.49e+03 2.80e+01 bond pdb=" CA ASP R 68 " pdb=" C ASP R 68 " ideal model delta sigma weight residual 1.524 1.593 -0.069 1.32e-02 5.74e+03 2.73e+01 ... (remaining 8693 not shown) Histogram of bond angle deviations from ideal: 99.52 - 106.50: 235 106.50 - 113.47: 4598 113.47 - 120.45: 3486 120.45 - 127.43: 3400 127.43 - 134.41: 89 Bond angle restraints: 11808 Sorted by residual: angle pdb=" N GLU A 337 " pdb=" CA GLU A 337 " pdb=" C GLU A 337 " ideal model delta sigma weight residual 113.89 100.51 13.38 1.58e+00 4.01e-01 7.17e+01 angle pdb=" N THR R 99 " pdb=" CA THR R 99 " pdb=" C THR R 99 " ideal model delta sigma weight residual 111.28 119.42 -8.14 1.09e+00 8.42e-01 5.57e+01 angle pdb=" N ASN R 283 " pdb=" CA ASN R 283 " pdb=" C ASN R 283 " ideal model delta sigma weight residual 112.38 121.39 -9.01 1.22e+00 6.72e-01 5.46e+01 angle pdb=" N ALA R 35 " pdb=" CA ALA R 35 " pdb=" C ALA R 35 " ideal model delta sigma weight residual 113.55 104.51 9.04 1.26e+00 6.30e-01 5.15e+01 angle pdb=" C PRO R 77 " pdb=" N CYS R 78 " pdb=" CA CYS R 78 " ideal model delta sigma weight residual 120.38 130.05 -9.67 1.37e+00 5.33e-01 4.98e+01 ... (remaining 11803 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 4594 17.99 - 35.97: 407 35.97 - 53.96: 81 53.96 - 71.95: 23 71.95 - 89.93: 7 Dihedral angle restraints: 5112 sinusoidal: 1892 harmonic: 3220 Sorted by residual: dihedral pdb=" N TYR S 235 " pdb=" C TYR S 235 " pdb=" CA TYR S 235 " pdb=" CB TYR S 235 " ideal model delta harmonic sigma weight residual 122.80 148.93 -26.13 0 2.50e+00 1.60e-01 1.09e+02 dihedral pdb=" C TYR S 235 " pdb=" N TYR S 235 " pdb=" CA TYR S 235 " pdb=" CB TYR S 235 " ideal model delta harmonic sigma weight residual -122.60 -148.71 26.11 0 2.50e+00 1.60e-01 1.09e+02 dihedral pdb=" N ASN R 283 " pdb=" C ASN R 283 " pdb=" CA ASN R 283 " pdb=" CB ASN R 283 " ideal model delta harmonic sigma weight residual 122.80 136.26 -13.46 0 2.50e+00 1.60e-01 2.90e+01 ... (remaining 5109 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.237: 1322 0.237 - 0.473: 13 0.473 - 0.710: 1 0.710 - 0.946: 0 0.946 - 1.183: 1 Chirality restraints: 1337 Sorted by residual: chirality pdb=" CA TYR S 235 " pdb=" N TYR S 235 " pdb=" C TYR S 235 " pdb=" CB TYR S 235 " both_signs ideal model delta sigma weight residual False 2.51 1.33 1.18 2.00e-01 2.50e+01 3.50e+01 chirality pdb=" CA ASN R 283 " pdb=" N ASN R 283 " pdb=" C ASN R 283 " pdb=" CB ASN R 283 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.67e+00 chirality pdb=" CA MET A 353 " pdb=" N MET A 353 " pdb=" C MET A 353 " pdb=" CB MET A 353 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 2.98e+00 ... (remaining 1334 not shown) Planarity restraints: 1499 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET R 76 " 0.087 5.00e-02 4.00e+02 1.33e-01 2.83e+01 pdb=" N PRO R 77 " -0.230 5.00e-02 4.00e+02 pdb=" CA PRO R 77 " 0.067 5.00e-02 4.00e+02 pdb=" CD PRO R 77 " 0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY R 72 " 0.023 2.00e-02 2.50e+03 4.54e-02 2.06e+01 pdb=" C GLY R 72 " -0.078 2.00e-02 2.50e+03 pdb=" O GLY R 72 " 0.030 2.00e-02 2.50e+03 pdb=" N CYS R 73 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 355 " -0.016 2.00e-02 2.50e+03 3.23e-02 1.05e+01 pdb=" C LEU A 355 " 0.056 2.00e-02 2.50e+03 pdb=" O LEU A 355 " -0.021 2.00e-02 2.50e+03 pdb=" N ARG A 356 " -0.019 2.00e-02 2.50e+03 ... (remaining 1496 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 844 2.75 - 3.28: 8108 3.28 - 3.82: 13246 3.82 - 4.36: 16132 4.36 - 4.90: 27930 Nonbonded interactions: 66260 Sorted by model distance: nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.206 2.440 nonbonded pdb=" OG1 THR B 128 " pdb=" O GLU B 130 " model vdw 2.262 2.440 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.266 2.440 nonbonded pdb=" O HIS S 232 " pdb=" ND1 HIS S 232 " model vdw 2.278 2.520 nonbonded pdb=" O PHE R 289 " pdb=" N LEU R 292 " model vdw 2.289 2.520 ... (remaining 66255 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: 0.290 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: 0.000 Extract box with map and model: 1.790 Check model and map are aligned: 0.160 Set scattering table: 0.090 Process input model: 27.520 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6623 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 : 0.006 0.077 8698 Z= 0.409 Angle : 1.093 14.199 11808 Z= 0.726 Chirality : 0.076 1.183 1337 Planarity : 0.007 0.133 1499 Dihedral : 14.804 89.932 3027 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 1.80 % Allowed : 4.94 % Favored : 93.27 % Cbeta Deviations : 0.29 % 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: -2.33 (0.24), residues: 1089 helix: -1.70 (0.27), residues: 338 sheet: -0.74 (0.33), residues: 257 loop : -1.78 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP R 147 HIS 0.010 0.002 HIS R 112 PHE 0.023 0.002 PHE B 253 TYR 0.036 0.002 TYR S 235 ARG 0.004 0.001 ARG S 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 113 time to evaluate : 0.887 Fit side-chains REVERT: R 186 SER cc_start: 0.6207 (p) cc_final: 0.5896 (m) outliers start: 16 outliers final: 7 residues processed: 127 average time/residue: 0.2065 time to fit residues: 35.8817 Evaluate side-chains 99 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 92 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 75 ILE Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 244 THR Chi-restraints excluded: chain R residue 248 LYS Chi-restraints excluded: chain R residue 270 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 5.9990 chunk 81 optimal weight: 0.0980 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 55 optimal weight: 20.0000 chunk 43 optimal weight: 10.0000 chunk 84 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 51 optimal weight: 0.0870 chunk 63 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 overall best weight: 1.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN B 259 GLN R 62 HIS R 98 HIS R 174 GLN R 293 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6598 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 : 0.003 0.045 8698 Z= 0.165 Angle : 0.585 8.250 11808 Z= 0.312 Chirality : 0.044 0.301 1337 Planarity : 0.005 0.065 1499 Dihedral : 5.647 58.483 1212 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.23 % Allowed : 9.65 % Favored : 89.11 % 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: -1.69 (0.25), residues: 1089 helix: -0.83 (0.28), residues: 336 sheet: -0.31 (0.33), residues: 270 loop : -1.75 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP S 36 HIS 0.006 0.001 HIS S 35 PHE 0.014 0.001 PHE B 199 TYR 0.033 0.002 TYR S 235 ARG 0.003 0.000 ARG A 341 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 101 time to evaluate : 0.981 Fit side-chains REVERT: R 186 SER cc_start: 0.6018 (p) cc_final: 0.5778 (m) REVERT: S 235 TYR cc_start: 0.6123 (OUTLIER) cc_final: 0.5614 (t80) outliers start: 11 outliers final: 9 residues processed: 107 average time/residue: 0.1925 time to fit residues: 29.2350 Evaluate side-chains 103 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 93 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain R residue 57 THR Chi-restraints excluded: chain R residue 75 ILE Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 66 optimal weight: 9.9990 chunk 27 optimal weight: 7.9990 chunk 98 optimal weight: 9.9990 chunk 106 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 98 HIS ** S 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6743 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8698 Z= 0.292 Angle : 0.680 9.692 11808 Z= 0.362 Chirality : 0.047 0.348 1337 Planarity : 0.006 0.050 1499 Dihedral : 5.738 59.263 1204 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 2.58 % Allowed : 11.90 % Favored : 85.52 % 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: -1.68 (0.25), residues: 1089 helix: -0.75 (0.28), residues: 336 sheet: -0.33 (0.32), residues: 274 loop : -1.80 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP S 36 HIS 0.006 0.001 HIS B 54 PHE 0.018 0.002 PHE A 189 TYR 0.041 0.002 TYR S 235 ARG 0.005 0.001 ARG S 67 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 100 time to evaluate : 1.035 Fit side-chains REVERT: R 140 LEU cc_start: 0.7240 (OUTLIER) cc_final: 0.6919 (mt) REVERT: R 186 SER cc_start: 0.6193 (p) cc_final: 0.5939 (m) REVERT: R 304 PHE cc_start: 0.7141 (t80) cc_final: 0.6654 (t80) REVERT: S 93 MET cc_start: 0.4832 (mmt) cc_final: 0.4372 (mmm) REVERT: S 235 TYR cc_start: 0.6640 (OUTLIER) cc_final: 0.5938 (t80) outliers start: 23 outliers final: 12 residues processed: 114 average time/residue: 0.2099 time to fit residues: 33.1766 Evaluate side-chains 109 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 95 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain R residue 57 THR Chi-restraints excluded: chain R residue 75 ILE Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 140 LEU Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 223 ASP Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 chunk 50 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 46 optimal weight: 8.9990 chunk 65 optimal weight: 0.3980 chunk 98 optimal weight: 20.0000 chunk 104 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 93 optimal weight: 20.0000 chunk 28 optimal weight: 6.9990 overall best weight: 3.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS R 54 HIS R 58 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8698 Z= 0.284 Angle : 0.665 8.997 11808 Z= 0.353 Chirality : 0.047 0.331 1337 Planarity : 0.005 0.043 1499 Dihedral : 5.863 59.588 1204 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 2.92 % Allowed : 13.47 % Favored : 83.61 % 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: -1.71 (0.25), residues: 1089 helix: -0.74 (0.28), residues: 340 sheet: -0.31 (0.32), residues: 268 loop : -1.85 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 63 HIS 0.007 0.002 HIS B 225 PHE 0.019 0.002 PHE B 151 TYR 0.041 0.002 TYR S 235 ARG 0.004 0.001 ARG S 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 103 time to evaluate : 0.999 Fit side-chains REVERT: A 281 GLU cc_start: 0.6753 (OUTLIER) cc_final: 0.6534 (mp0) REVERT: S 81 LEU cc_start: 0.4954 (OUTLIER) cc_final: 0.4690 (tp) outliers start: 26 outliers final: 18 residues processed: 120 average time/residue: 0.2069 time to fit residues: 34.5281 Evaluate side-chains 114 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 94 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain R residue 75 ILE Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 196 THR Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 223 ASP Chi-restraints excluded: chain S residue 226 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 1 optimal weight: 0.7980 chunk 77 optimal weight: 0.0000 chunk 43 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 0 optimal weight: 0.8980 chunk 53 optimal weight: 8.9990 chunk 93 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6636 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8698 Z= 0.129 Angle : 0.508 6.760 11808 Z= 0.270 Chirality : 0.043 0.220 1337 Planarity : 0.004 0.041 1499 Dihedral : 5.138 58.907 1204 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.68 % Allowed : 15.71 % Favored : 82.60 % 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: -1.20 (0.25), residues: 1089 helix: -0.16 (0.29), residues: 336 sheet: -0.12 (0.33), residues: 254 loop : -1.58 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 307 HIS 0.003 0.001 HIS S 35 PHE 0.033 0.001 PHE R 304 TYR 0.027 0.001 TYR S 235 ARG 0.002 0.000 ARG S 191 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 99 time to evaluate : 1.057 Fit side-chains REVERT: A 28 GLN cc_start: 0.7256 (tp-100) cc_final: 0.6614 (mm-40) REVERT: S 93 MET cc_start: 0.4542 (mmt) cc_final: 0.4206 (mmm) outliers start: 15 outliers final: 12 residues processed: 110 average time/residue: 0.2100 time to fit residues: 32.5585 Evaluate side-chains 105 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 93 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain R residue 75 ILE Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 196 THR Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 223 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 9.9990 chunk 94 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 25 optimal weight: 0.0170 chunk 104 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 48 optimal weight: 6.9990 chunk 8 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 7.9990 overall best weight: 0.7222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN A 204 GLN ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6616 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8698 Z= 0.123 Angle : 0.506 8.370 11808 Z= 0.267 Chirality : 0.042 0.206 1337 Planarity : 0.004 0.045 1499 Dihedral : 4.848 56.359 1204 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.36 % Allowed : 15.71 % Favored : 81.93 % 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: -0.94 (0.26), residues: 1089 helix: 0.27 (0.30), residues: 335 sheet: -0.01 (0.33), residues: 255 loop : -1.57 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 261 HIS 0.003 0.001 HIS S 35 PHE 0.025 0.001 PHE R 304 TYR 0.026 0.001 TYR S 235 ARG 0.002 0.000 ARG S 191 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 96 time to evaluate : 0.985 Fit side-chains REVERT: A 28 GLN cc_start: 0.7225 (tp-100) cc_final: 0.6578 (mm-40) REVERT: R 307 TRP cc_start: 0.6176 (p-90) cc_final: 0.5948 (p-90) REVERT: S 93 MET cc_start: 0.4502 (mmt) cc_final: 0.4214 (mmm) outliers start: 21 outliers final: 14 residues processed: 113 average time/residue: 0.1896 time to fit residues: 30.6960 Evaluate side-chains 105 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 91 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain R residue 75 ILE Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 196 THR Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 216 ILE Chi-restraints excluded: chain S residue 223 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 20.0000 chunk 11 optimal weight: 0.9980 chunk 59 optimal weight: 10.0000 chunk 76 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 48 optimal weight: 9.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6624 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8698 Z= 0.128 Angle : 0.494 6.333 11808 Z= 0.262 Chirality : 0.043 0.220 1337 Planarity : 0.004 0.044 1499 Dihedral : 4.692 55.535 1204 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.13 % Allowed : 15.49 % Favored : 82.38 % 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: -0.81 (0.26), residues: 1089 helix: 0.53 (0.30), residues: 328 sheet: 0.19 (0.33), residues: 249 loop : -1.64 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.022 0.001 PHE R 304 TYR 0.026 0.001 TYR S 235 ARG 0.002 0.000 ARG S 67 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 91 time to evaluate : 0.999 Fit side-chains REVERT: A 28 GLN cc_start: 0.7233 (tp-100) cc_final: 0.6579 (mm-40) REVERT: B 297 TRP cc_start: 0.6494 (OUTLIER) cc_final: 0.5946 (m100) REVERT: R 307 TRP cc_start: 0.6152 (p-90) cc_final: 0.5913 (p-90) REVERT: S 93 MET cc_start: 0.4555 (mmt) cc_final: 0.4234 (mmm) outliers start: 19 outliers final: 16 residues processed: 106 average time/residue: 0.2159 time to fit residues: 32.6520 Evaluate side-chains 106 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 89 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 297 TRP Chi-restraints excluded: chain R residue 75 ILE Chi-restraints excluded: chain R residue 186 SER Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 196 THR Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 216 ILE Chi-restraints excluded: chain S residue 226 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 81 optimal weight: 0.9980 chunk 94 optimal weight: 9.9990 chunk 99 optimal weight: 3.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6761 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8698 Z= 0.296 Angle : 0.669 12.035 11808 Z= 0.352 Chirality : 0.048 0.291 1337 Planarity : 0.005 0.049 1499 Dihedral : 5.383 58.369 1203 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 2.58 % Allowed : 16.16 % Favored : 81.26 % 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: -1.28 (0.25), residues: 1089 helix: -0.02 (0.29), residues: 338 sheet: -0.41 (0.32), residues: 278 loop : -1.68 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 261 HIS 0.005 0.001 HIS B 225 PHE 0.021 0.002 PHE R 304 TYR 0.037 0.002 TYR S 235 ARG 0.004 0.001 ARG A 35 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 93 time to evaluate : 0.950 Fit side-chains outliers start: 23 outliers final: 21 residues processed: 111 average time/residue: 0.2105 time to fit residues: 32.5915 Evaluate side-chains 112 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 91 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain R residue 75 ILE Chi-restraints excluded: chain R residue 186 SER Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 196 THR Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 216 ILE Chi-restraints excluded: chain S residue 223 ASP Chi-restraints excluded: chain S residue 226 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 0.0020 chunk 97 optimal weight: 0.8980 chunk 99 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 76 optimal weight: 0.0070 chunk 29 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.5006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6616 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8698 Z= 0.122 Angle : 0.505 9.168 11808 Z= 0.265 Chirality : 0.043 0.222 1337 Planarity : 0.004 0.041 1499 Dihedral : 4.723 55.798 1203 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.02 % Allowed : 16.95 % Favored : 81.03 % 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: -0.86 (0.26), residues: 1089 helix: 0.56 (0.30), residues: 329 sheet: 0.06 (0.33), residues: 249 loop : -1.68 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 261 HIS 0.002 0.001 HIS S 35 PHE 0.029 0.001 PHE R 304 TYR 0.024 0.001 TYR S 235 ARG 0.003 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 98 time to evaluate : 0.956 Fit side-chains REVERT: A 28 GLN cc_start: 0.7214 (tp-100) cc_final: 0.6589 (mm-40) REVERT: S 93 MET cc_start: 0.4547 (mmt) cc_final: 0.4253 (mmm) outliers start: 18 outliers final: 15 residues processed: 113 average time/residue: 0.2104 time to fit residues: 32.9422 Evaluate side-chains 108 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 93 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain R residue 75 ILE Chi-restraints excluded: chain R residue 186 SER Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 196 THR Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 216 ILE Chi-restraints excluded: chain S residue 223 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 0.0670 chunk 71 optimal weight: 6.9990 chunk 107 optimal weight: 0.0070 chunk 99 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 chunk 66 optimal weight: 0.7980 chunk 52 optimal weight: 8.9990 chunk 68 optimal weight: 20.0000 overall best weight: 1.3740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6655 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8698 Z= 0.150 Angle : 0.528 8.880 11808 Z= 0.278 Chirality : 0.043 0.244 1337 Planarity : 0.004 0.048 1499 Dihedral : 4.768 56.394 1203 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.02 % Allowed : 17.06 % Favored : 80.92 % 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: -0.88 (0.26), residues: 1089 helix: 0.53 (0.30), residues: 334 sheet: -0.09 (0.33), residues: 256 loop : -1.63 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP R 261 HIS 0.003 0.001 HIS S 35 PHE 0.025 0.001 PHE R 304 TYR 0.028 0.001 TYR S 235 ARG 0.002 0.000 ARG S 67 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 93 time to evaluate : 0.987 Fit side-chains REVERT: A 28 GLN cc_start: 0.7349 (tp-100) cc_final: 0.6668 (mm-40) REVERT: B 273 ILE cc_start: 0.7215 (mp) cc_final: 0.7012 (mp) REVERT: S 93 MET cc_start: 0.4659 (mmt) cc_final: 0.4324 (mmm) outliers start: 18 outliers final: 18 residues processed: 108 average time/residue: 0.2092 time to fit residues: 31.4546 Evaluate side-chains 111 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 93 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain R residue 75 ILE Chi-restraints excluded: chain R residue 186 SER Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 196 THR Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 216 ILE Chi-restraints excluded: chain S residue 223 ASP Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain Y residue 52 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 79 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 chunk 23 optimal weight: 8.9990 chunk 85 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 88 optimal weight: 9.9990 chunk 10 optimal weight: 0.3980 chunk 15 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.194590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.183662 restraints weight = 9039.259| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 0.74 r_work: 0.3862 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3809 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8698 Z= 0.225 Angle : 0.598 8.736 11808 Z= 0.315 Chirality : 0.046 0.260 1337 Planarity : 0.004 0.046 1499 Dihedral : 5.128 58.972 1203 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 2.36 % Allowed : 17.28 % Favored : 80.36 % 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: -1.02 (0.26), residues: 1089 helix: 0.47 (0.30), residues: 325 sheet: -0.31 (0.32), residues: 265 loop : -1.65 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP R 261 HIS 0.006 0.001 HIS B 225 PHE 0.025 0.002 PHE R 304 TYR 0.031 0.002 TYR S 235 ARG 0.003 0.000 ARG S 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1832.46 seconds wall clock time: 34 minutes 4.27 seconds (2044.27 seconds total)