Starting phenix.real_space_refine on Wed Jul 30 01:49:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6cmo_7517/07_2025/6cmo_7517.cif Found real_map, /net/cci-nas-00/data/ceres_data/6cmo_7517/07_2025/6cmo_7517.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6cmo_7517/07_2025/6cmo_7517.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6cmo_7517/07_2025/6cmo_7517.map" model { file = "/net/cci-nas-00/data/ceres_data/6cmo_7517/07_2025/6cmo_7517.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6cmo_7517/07_2025/6cmo_7517.cif" } resolution = 4.5 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= 0.005 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 83 5.16 5 C 7519 2.51 5 N 1979 2.21 5 O 2253 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11834 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2567 Classifications: {'peptide': 323} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 304} Chain: "A" Number of atoms: 2834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2834 Classifications: {'peptide': 354} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 349} Chain: "B" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2616 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "G" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "L" Number of atoms: 1602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1602 Classifications: {'peptide': 211} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 200} Chain: "H" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1743 Classifications: {'peptide': 230} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 216} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 7.38, per 1000 atoms: 0.62 Number of scatterers: 11834 At special positions: 0 Unit cell: (99.008, 152.32, 167.552, 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 83 16.00 O 2253 8.00 N 1979 7.00 C 7519 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS R 2 " - pdb=" SG CYS R 282 " distance=2.03 Simple disulfide: pdb=" SG CYS R 110 " - pdb=" SG CYS R 187 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.03 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS H 158 " - pdb=" SG CYS H 214 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG C 1 " - " ASN R 15 " Time building additional restraints: 2.86 Conformation dependent library (CDL) restraints added in 1.6 seconds 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2840 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 19 sheets defined 37.1% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'R' and resid 33 through 65 removed outlier: 3.663A pdb=" N PHE R 37 " --> pdb=" O GLU R 33 " (cutoff:3.500A) Proline residue: R 53 - end of helix Processing helix chain 'R' and resid 66 through 69 removed outlier: 3.650A pdb=" N ARG R 69 " --> pdb=" O LYS R 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 66 through 69' Processing helix chain 'R' and resid 70 through 101 removed outlier: 3.929A pdb=" N ILE R 75 " --> pdb=" O PRO R 71 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY R 101 " --> pdb=" O THR R 97 " (cutoff:3.500A) Processing helix chain 'R' and resid 106 through 141 removed outlier: 3.684A pdb=" N CYS R 110 " --> pdb=" O GLY R 106 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS R 141 " --> pdb=" O VAL R 137 " (cutoff:3.500A) Processing helix chain 'R' and resid 149 through 173 removed outlier: 4.130A pdb=" N ALA R 153 " --> pdb=" O GLY R 149 " (cutoff:3.500A) Proline residue: R 170 - end of helix Processing helix chain 'R' and resid 200 through 238 Proline residue: R 215 - end of helix Processing helix chain 'R' and resid 240 through 278 removed outlier: 3.904A pdb=" N GLN R 244 " --> pdb=" O SER R 240 " (cutoff:3.500A) Proline residue: R 267 - end of helix Processing helix chain 'R' and resid 289 through 308 removed outlier: 3.987A pdb=" N PHE R 293 " --> pdb=" O THR R 289 " (cutoff:3.500A) Proline residue: R 303 - end of helix Processing helix chain 'R' and resid 310 through 323 Processing helix chain 'A' and resid 2 through 32 Processing helix chain 'A' and resid 42 through 53 Processing helix chain 'A' and resid 62 through 90 Processing helix chain 'A' and resid 100 through 113 removed outlier: 3.599A pdb=" N ALA A 104 " --> pdb=" O ARG A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.560A pdb=" N ALA A 124 " --> pdb=" O THR A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 143 removed outlier: 3.938A pdb=" N GLN A 137 " --> pdb=" O ASP A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 146 No H-bonds generated for 'chain 'A' and resid 144 through 146' Processing helix chain 'A' and resid 151 through 163 Processing helix chain 'A' and resid 170 through 178 removed outlier: 4.185A pdb=" N VAL A 174 " --> pdb=" O THR A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 214 Processing helix chain 'A' and resid 226 through 231 removed outlier: 4.036A pdb=" N TYR A 230 " --> pdb=" O LEU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 removed outlier: 4.266A pdb=" N GLU A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.608A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 281 Processing helix chain 'A' and resid 289 through 293 removed outlier: 4.489A pdb=" N SER A 293 " --> pdb=" O TYR A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 310 removed outlier: 3.585A pdb=" N TYR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ILE A 303 " --> pdb=" O ALA A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 351 removed outlier: 3.907A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 25 Processing helix chain 'B' and resid 29 through 36 removed outlier: 4.221A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 24 removed outlier: 3.984A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 47 Processing helix chain 'L' and resid 122 through 129 removed outlier: 3.604A pdb=" N LEU L 126 " --> pdb=" O SER L 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 189 Processing helix chain 'H' and resid 90 through 94 removed outlier: 4.092A pdb=" N THR H 94 " --> pdb=" O ALA H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 172 through 176 removed outlier: 3.663A pdb=" N GLY H 175 " --> pdb=" O TRP H 172 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA H 176 " --> pdb=" O ASN H 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 172 through 176' Processing helix chain 'H' and resid 203 through 208 removed outlier: 3.852A pdb=" N LEU H 207 " --> pdb=" O SER H 204 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLY H 208 " --> pdb=" O SER H 205 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 179 through 181 removed outlier: 3.969A pdb=" N ILE R 179 " --> pdb=" O GLY R 188 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N SER R 186 " --> pdb=" O GLU R 181 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 191 removed outlier: 3.559A pdb=" N THR A 187 " --> pdb=" O MET A 198 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU A 194 " --> pdb=" O PHE A 191 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE A 199 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N CYS A 224 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE A 221 " --> pdb=" O SER A 263 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.022A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.757A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER B 72 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.588A pdb=" N THR B 102 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA B 113 " --> pdb=" O ALA B 104 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE B 123 " --> pdb=" O ARG B 137 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 151 removed outlier: 3.675A pdb=" N VAL B 158 " --> pdb=" O ARG B 150 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.259A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY B 202 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 232 through 234 removed outlier: 3.590A pdb=" N CYS B 233 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 252 " --> pdb=" O MET B 262 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 276 through 278 removed outlier: 3.675A pdb=" N ALA B 287 " --> pdb=" O ASN B 295 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN B 295 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 20 through 25 removed outlier: 3.552A pdb=" N VAL L 20 " --> pdb=" O ILE L 76 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE L 76 " --> pdb=" O VAL L 20 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR L 73 " --> pdb=" O SER L 66 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR L 75 " --> pdb=" O SER L 64 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.812A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 115 through 118 removed outlier: 4.856A pdb=" N CYS L 135 " --> pdb=" O SER L 178 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N SER L 178 " --> pdb=" O CYS L 135 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N LEU L 137 " --> pdb=" O LEU L 176 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N LEU L 176 " --> pdb=" O LEU L 137 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 130 through 131 removed outlier: 4.053A pdb=" N ALA L 131 " --> pdb=" O LEU L 182 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU L 182 " --> pdb=" O ALA L 131 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'L' and resid 149 through 151 removed outlier: 4.056A pdb=" N LYS L 150 " --> pdb=" O ALA L 194 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ALA L 194 " --> pdb=" O LYS L 150 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'H' and resid 6 through 10 removed outlier: 4.125A pdb=" N GLN H 6 " --> pdb=" O SER H 28 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER H 28 " --> pdb=" O GLN H 6 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL H 8 " --> pdb=" O ALA H 26 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU H 21 " --> pdb=" O MET H 86 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR H 81 " --> pdb=" O ASP H 76 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER H 74 " --> pdb=" O TYR H 83 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR H 72 " --> pdb=" O GLN H 85 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 13 through 15 removed outlier: 4.119A pdb=" N GLY H 13 " --> pdb=" O LEU H 126 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR H 128 " --> pdb=" O GLY H 13 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR H 125 " --> pdb=" O TYR H 97 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR H 98 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL H 40 " --> pdb=" O TYR H 98 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 13 through 15 removed outlier: 4.119A pdb=" N GLY H 13 " --> pdb=" O LEU H 126 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR H 128 " --> pdb=" O GLY H 13 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR H 125 " --> pdb=" O TYR H 97 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N TYR H 120 " --> pdb=" O ARG H 101 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 138 through 141 removed outlier: 4.267A pdb=" N CYS H 158 " --> pdb=" O SER H 198 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N SER H 198 " --> pdb=" O CYS H 158 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N TYR H 194 " --> pdb=" O ASP H 162 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N SER H 195 " --> pdb=" O ALA H 186 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ALA H 186 " --> pdb=" O SER H 195 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N SER H 197 " --> pdb=" O PHE H 184 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 214 through 218 removed outlier: 4.512A pdb=" N CYS H 214 " --> pdb=" O LYS H 227 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LYS H 227 " --> pdb=" O CYS H 214 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL H 216 " --> pdb=" O VAL H 225 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL H 225 " --> pdb=" O VAL H 216 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N HIS H 218 " --> pdb=" O THR H 223 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR H 223 " --> pdb=" O HIS H 218 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 519 hydrogen bonds defined for protein. 1488 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: 3.70 Time building geometry restraints manager: 3.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3759 1.34 - 1.46: 2865 1.46 - 1.58: 5356 1.58 - 1.70: 0 1.70 - 1.82: 119 Bond restraints: 12099 Sorted by residual: bond pdb=" C ASN R 302 " pdb=" N PRO R 303 " ideal model delta sigma weight residual 1.335 1.363 -0.027 1.36e-02 5.41e+03 4.08e+00 bond pdb=" CB PHE R 91 " pdb=" CG PHE R 91 " ideal model delta sigma weight residual 1.502 1.547 -0.045 2.30e-02 1.89e+03 3.78e+00 bond pdb=" C ILE R 214 " pdb=" N PRO R 215 " ideal model delta sigma weight residual 1.336 1.359 -0.023 1.23e-02 6.61e+03 3.53e+00 bond pdb=" C VAL R 266 " pdb=" N PRO R 267 " ideal model delta sigma weight residual 1.335 1.359 -0.024 1.28e-02 6.10e+03 3.50e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.14e+00 ... (remaining 12094 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.93: 16077 2.93 - 5.87: 275 5.87 - 8.80: 46 8.80 - 11.73: 12 11.73 - 14.66: 2 Bond angle restraints: 16412 Sorted by residual: angle pdb=" N GLU A 297 " pdb=" CA GLU A 297 " pdb=" C GLU A 297 " ideal model delta sigma weight residual 111.11 118.12 -7.01 1.20e+00 6.94e-01 3.42e+01 angle pdb=" CA TYR R 43 " pdb=" CB TYR R 43 " pdb=" CG TYR R 43 " ideal model delta sigma weight residual 113.90 123.74 -9.84 1.80e+00 3.09e-01 2.99e+01 angle pdb=" C THR A 327 " pdb=" N ASP A 328 " pdb=" CA ASP A 328 " ideal model delta sigma weight residual 120.38 127.74 -7.36 1.46e+00 4.69e-01 2.54e+01 angle pdb=" N ILE R 290 " pdb=" CA ILE R 290 " pdb=" C ILE R 290 " ideal model delta sigma weight residual 108.88 118.21 -9.33 2.16e+00 2.14e-01 1.87e+01 angle pdb=" C ALA A 203 " pdb=" N GLN A 204 " pdb=" CA GLN A 204 " ideal model delta sigma weight residual 120.63 127.57 -6.94 1.61e+00 3.86e-01 1.86e+01 ... (remaining 16407 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.99: 6774 14.99 - 29.97: 343 29.97 - 44.96: 92 44.96 - 59.95: 11 59.95 - 74.93: 7 Dihedral angle restraints: 7227 sinusoidal: 2810 harmonic: 4417 Sorted by residual: dihedral pdb=" CA CYS R 110 " pdb=" C CYS R 110 " pdb=" N ASN R 111 " pdb=" CA ASN R 111 " ideal model delta harmonic sigma weight residual 180.00 156.69 23.31 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA SER A 151 " pdb=" C SER A 151 " pdb=" N ALA A 152 " pdb=" CA ALA A 152 " ideal model delta harmonic sigma weight residual -180.00 -158.08 -21.92 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA ASN A 149 " pdb=" C ASN A 149 " pdb=" N ASP A 150 " pdb=" CA ASP A 150 " ideal model delta harmonic sigma weight residual -180.00 -159.21 -20.79 0 5.00e+00 4.00e-02 1.73e+01 ... (remaining 7224 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.206: 1834 0.206 - 0.411: 9 0.411 - 0.617: 0 0.617 - 0.823: 0 0.823 - 1.029: 1 Chirality restraints: 1844 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN R 15 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.37 -1.03 2.00e-01 2.50e+01 2.65e+01 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.34 -0.06 2.00e-02 2.50e+03 1.01e+01 chirality pdb=" CB ILE R 123 " pdb=" CA ILE R 123 " pdb=" CG1 ILE R 123 " pdb=" CG2 ILE R 123 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.21e+00 ... (remaining 1841 not shown) Planarity restraints: 2090 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN R 15 " 0.195 2.00e-02 2.50e+03 2.09e-01 5.46e+02 pdb=" CG ASN R 15 " -0.092 2.00e-02 2.50e+03 pdb=" OD1 ASN R 15 " -0.051 2.00e-02 2.50e+03 pdb=" ND2 ASN R 15 " -0.316 2.00e-02 2.50e+03 pdb=" C1 NAG C 1 " 0.264 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 35 " 0.022 2.00e-02 2.50e+03 1.74e-02 7.56e+00 pdb=" CG TRP R 35 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP R 35 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP R 35 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP R 35 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP R 35 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP R 35 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 35 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 35 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP R 35 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " 0.042 5.00e-02 4.00e+02 6.38e-02 6.50e+00 pdb=" N PRO G 49 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " 0.035 5.00e-02 4.00e+02 ... (remaining 2087 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 453 2.72 - 3.27: 11087 3.27 - 3.81: 17965 3.81 - 4.36: 20784 4.36 - 4.90: 35731 Nonbonded interactions: 86020 Sorted by model distance: nonbonded pdb=" O LEU R 88 " pdb=" OG1 THR R 92 " model vdw 2.181 3.040 nonbonded pdb=" O ASP A 173 " pdb=" OG1 THR A 177 " model vdw 2.270 3.040 nonbonded pdb=" OH TYR B 264 " pdb=" O ALA B 299 " model vdw 2.277 3.040 nonbonded pdb=" O SER A 44 " pdb=" OG1 THR A 48 " model vdw 2.280 3.040 nonbonded pdb=" O LYS A 248 " pdb=" OG SER A 252 " model vdw 2.322 3.040 ... (remaining 86015 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 30.170 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.060 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6842 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 : 0.004 0.069 12107 Z= 0.223 Angle : 1.011 18.756 16430 Z= 0.537 Chirality : 0.063 1.029 1844 Planarity : 0.007 0.064 2089 Dihedral : 10.429 74.935 4369 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.08 % Allowed : 4.34 % Favored : 95.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.97 (0.18), residues: 1504 helix: -1.67 (0.19), residues: 507 sheet: 0.09 (0.28), residues: 255 loop : -1.49 (0.18), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP R 35 HIS 0.009 0.002 HIS R 100 PHE 0.033 0.003 PHE R 37 TYR 0.022 0.002 TYR A 296 ARG 0.006 0.000 ARG R 69 Details of bonding type rmsd link_NAG-ASN : bond 0.03150 ( 1) link_NAG-ASN : angle 12.68548 ( 3) link_BETA1-4 : bond 0.00611 ( 1) link_BETA1-4 : angle 1.95576 ( 3) hydrogen bonds : bond 0.18521 ( 515) hydrogen bonds : angle 9.45612 ( 1488) SS BOND : bond 0.00235 ( 6) SS BOND : angle 2.13738 ( 12) covalent geometry : bond 0.00422 (12099) covalent geometry : angle 0.99534 (16412) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 330 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 143 MET cc_start: 0.6283 (mtm) cc_final: 0.5672 (mtt) REVERT: R 175 TRP cc_start: 0.3848 (t-100) cc_final: 0.3164 (t-100) REVERT: R 225 GLN cc_start: 0.7327 (tp40) cc_final: 0.7034 (tp40) REVERT: R 278 HIS cc_start: 0.5773 (m90) cc_final: 0.5420 (m90) REVERT: A 107 LEU cc_start: 0.7557 (tt) cc_final: 0.6630 (mm) REVERT: A 154 TYR cc_start: 0.7520 (t80) cc_final: 0.7299 (t80) REVERT: A 195 HIS cc_start: 0.6407 (m-70) cc_final: 0.6159 (m90) REVERT: A 234 LEU cc_start: 0.5271 (tp) cc_final: 0.4831 (tp) REVERT: A 269 ASN cc_start: 0.7909 (m-40) cc_final: 0.7558 (p0) REVERT: A 290 TYR cc_start: 0.4900 (t80) cc_final: 0.4208 (t80) REVERT: A 347 ASN cc_start: 0.7609 (m110) cc_final: 0.7360 (m-40) REVERT: B 9 GLN cc_start: 0.7029 (mp10) cc_final: 0.6698 (mp10) REVERT: B 75 GLN cc_start: 0.7007 (mt0) cc_final: 0.6021 (tm-30) REVERT: B 76 ASP cc_start: 0.6995 (p0) cc_final: 0.6290 (p0) REVERT: B 120 ILE cc_start: 0.8531 (mt) cc_final: 0.8141 (mm) REVERT: B 201 SER cc_start: 0.8353 (t) cc_final: 0.7962 (p) REVERT: B 254 ASP cc_start: 0.7160 (t0) cc_final: 0.6896 (t70) REVERT: B 264 TYR cc_start: 0.7183 (m-10) cc_final: 0.6897 (m-10) REVERT: B 340 ASN cc_start: 0.6160 (t160) cc_final: 0.5916 (t0) REVERT: G 38 MET cc_start: 0.7865 (ppp) cc_final: 0.6654 (tpt) REVERT: L 64 SER cc_start: 0.7485 (m) cc_final: 0.7148 (p) REVERT: L 166 GLU cc_start: 0.6768 (mt-10) cc_final: 0.6561 (mt-10) REVERT: H 105 TYR cc_start: 0.5377 (p90) cc_final: 0.4515 (p90) outliers start: 1 outliers final: 0 residues processed: 330 average time/residue: 0.2795 time to fit residues: 124.9765 Evaluate side-chains 179 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 7.9990 chunk 113 optimal weight: 3.9990 chunk 63 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 60 optimal weight: 0.0980 chunk 117 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 136 optimal weight: 1.9990 overall best weight: 3.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 111 ASN ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 ASN B 259 GLN B 293 ASN B 311 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 11 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 138 ASN L 159 ASN ** L 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 211 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.123649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.101065 restraints weight = 32326.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.099650 restraints weight = 33705.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.100739 restraints weight = 27994.623| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12107 Z= 0.244 Angle : 0.793 10.815 16430 Z= 0.423 Chirality : 0.049 0.183 1844 Planarity : 0.006 0.090 2089 Dihedral : 6.378 49.478 1685 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.54 % Allowed : 5.04 % Favored : 94.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.19), residues: 1504 helix: -0.50 (0.21), residues: 528 sheet: -0.24 (0.29), residues: 267 loop : -1.48 (0.19), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP R 35 HIS 0.009 0.002 HIS H 38 PHE 0.031 0.003 PHE B 241 TYR 0.045 0.003 TYR A 290 ARG 0.016 0.001 ARG R 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00353 ( 1) link_NAG-ASN : angle 3.71955 ( 3) link_BETA1-4 : bond 0.00124 ( 1) link_BETA1-4 : angle 1.71657 ( 3) hydrogen bonds : bond 0.05950 ( 515) hydrogen bonds : angle 6.10227 ( 1488) SS BOND : bond 0.00744 ( 6) SS BOND : angle 1.24197 ( 12) covalent geometry : bond 0.00542 (12099) covalent geometry : angle 0.79125 (16412) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 207 time to evaluate : 1.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 175 TRP cc_start: 0.4746 (t-100) cc_final: 0.4025 (t-100) REVERT: A 139 CYS cc_start: 0.7634 (m) cc_final: 0.7402 (m) REVERT: A 302 TYR cc_start: 0.4293 (t80) cc_final: 0.3217 (t80) REVERT: A 346 ASN cc_start: 0.6898 (t0) cc_final: 0.6657 (t0) REVERT: B 57 LYS cc_start: 0.8260 (mmmm) cc_final: 0.7027 (mttt) REVERT: B 75 GLN cc_start: 0.7047 (mt0) cc_final: 0.6386 (tm-30) REVERT: B 254 ASP cc_start: 0.7244 (t0) cc_final: 0.6982 (t0) REVERT: B 331 SER cc_start: 0.9025 (t) cc_final: 0.8469 (m) REVERT: G 28 ILE cc_start: 0.8477 (mm) cc_final: 0.8169 (tt) REVERT: G 38 MET cc_start: 0.6633 (ppp) cc_final: 0.6263 (tpt) outliers start: 7 outliers final: 5 residues processed: 213 average time/residue: 0.3067 time to fit residues: 93.9694 Evaluate side-chains 151 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 146 time to evaluate : 2.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 140 optimal weight: 7.9990 chunk 103 optimal weight: 0.8980 chunk 128 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 126 optimal weight: 40.0000 chunk 116 optimal weight: 0.0980 chunk 115 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 80 optimal weight: 0.0050 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 111 ASN ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 138 ASN L 159 ASN L 199 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.127901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.104711 restraints weight = 32132.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.104032 restraints weight = 27846.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.105065 restraints weight = 23609.677| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12107 Z= 0.125 Angle : 0.637 9.538 16430 Z= 0.332 Chirality : 0.044 0.212 1844 Planarity : 0.005 0.077 2089 Dihedral : 5.716 52.688 1685 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.08 % Allowed : 3.49 % Favored : 96.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.90 (0.20), residues: 1504 helix: 0.08 (0.22), residues: 518 sheet: 0.13 (0.30), residues: 267 loop : -1.37 (0.20), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 35 HIS 0.008 0.001 HIS L 199 PHE 0.021 0.002 PHE R 115 TYR 0.024 0.002 TYR L 141 ARG 0.005 0.000 ARG B 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00226 ( 1) link_NAG-ASN : angle 3.48522 ( 3) link_BETA1-4 : bond 0.00040 ( 1) link_BETA1-4 : angle 1.33840 ( 3) hydrogen bonds : bond 0.04897 ( 515) hydrogen bonds : angle 5.45654 ( 1488) SS BOND : bond 0.01325 ( 6) SS BOND : angle 0.86819 ( 12) covalent geometry : bond 0.00256 (12099) covalent geometry : angle 0.63459 (16412) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 219 time to evaluate : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 83 ASP cc_start: 0.7394 (t0) cc_final: 0.7169 (t0) REVERT: R 175 TRP cc_start: 0.4884 (t-100) cc_final: 0.3829 (t60) REVERT: R 255 ILE cc_start: 0.7624 (pt) cc_final: 0.7364 (mm) REVERT: R 257 TYR cc_start: 0.7286 (m-10) cc_final: 0.5458 (m-80) REVERT: A 24 ARG cc_start: 0.6908 (mmp-170) cc_final: 0.6580 (mmp-170) REVERT: A 178 ARG cc_start: 0.6434 (tpt170) cc_final: 0.6174 (ptp-110) REVERT: A 296 TYR cc_start: 0.5996 (p90) cc_final: 0.5755 (p90) REVERT: B 75 GLN cc_start: 0.6785 (mt0) cc_final: 0.6062 (tm-30) REVERT: B 201 SER cc_start: 0.8537 (t) cc_final: 0.8090 (p) REVERT: B 254 ASP cc_start: 0.7069 (t0) cc_final: 0.6789 (t70) REVERT: B 331 SER cc_start: 0.8951 (t) cc_final: 0.8461 (m) REVERT: G 28 ILE cc_start: 0.8416 (mm) cc_final: 0.8015 (tt) outliers start: 1 outliers final: 0 residues processed: 220 average time/residue: 0.3535 time to fit residues: 112.7128 Evaluate side-chains 156 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 5.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 141 optimal weight: 30.0000 chunk 25 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 27 optimal weight: 9.9990 chunk 134 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 GLN B 259 GLN B 340 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 91 GLN L 139 ASN L 159 ASN L 167 GLN L 199 HIS L 200 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.122842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.102619 restraints weight = 31920.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.102119 restraints weight = 37342.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.102844 restraints weight = 35320.286| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12107 Z= 0.198 Angle : 0.708 12.328 16430 Z= 0.376 Chirality : 0.046 0.200 1844 Planarity : 0.005 0.070 2089 Dihedral : 5.941 55.241 1685 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.16 % Allowed : 5.12 % Favored : 94.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.20), residues: 1504 helix: -0.09 (0.22), residues: 518 sheet: -0.30 (0.30), residues: 283 loop : -1.50 (0.20), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP R 35 HIS 0.008 0.002 HIS L 199 PHE 0.026 0.003 PHE R 91 TYR 0.034 0.002 TYR A 302 ARG 0.019 0.001 ARG B 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00098 ( 1) link_NAG-ASN : angle 1.77988 ( 3) link_BETA1-4 : bond 0.00177 ( 1) link_BETA1-4 : angle 1.69275 ( 3) hydrogen bonds : bond 0.05283 ( 515) hydrogen bonds : angle 5.48714 ( 1488) SS BOND : bond 0.00596 ( 6) SS BOND : angle 1.18670 ( 12) covalent geometry : bond 0.00438 (12099) covalent geometry : angle 0.70699 (16412) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 203 time to evaluate : 1.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 83 ASP cc_start: 0.7422 (t0) cc_final: 0.7163 (t70) REVERT: R 175 TRP cc_start: 0.4719 (t-100) cc_final: 0.3982 (t-100) REVERT: R 253 MET cc_start: 0.7713 (tpp) cc_final: 0.7376 (tpp) REVERT: R 257 TYR cc_start: 0.7143 (m-10) cc_final: 0.6794 (m-80) REVERT: A 24 ARG cc_start: 0.6981 (mmp-170) cc_final: 0.6738 (mmp-170) REVERT: A 74 TYR cc_start: 0.7469 (m-80) cc_final: 0.7058 (m-80) REVERT: A 103 ASP cc_start: 0.5560 (m-30) cc_final: 0.5336 (m-30) REVERT: A 164 GLN cc_start: 0.5514 (OUTLIER) cc_final: 0.4437 (tp40) REVERT: B 75 GLN cc_start: 0.7033 (mt0) cc_final: 0.6553 (tm-30) REVERT: B 254 ASP cc_start: 0.7266 (t0) cc_final: 0.7007 (t0) REVERT: B 331 SER cc_start: 0.9046 (t) cc_final: 0.8497 (m) REVERT: G 28 ILE cc_start: 0.8554 (mm) cc_final: 0.8150 (tt) REVERT: L 174 TYR cc_start: 0.4624 (m-80) cc_final: 0.4418 (m-80) REVERT: H 112 TYR cc_start: 0.6064 (m-10) cc_final: 0.5462 (m-80) outliers start: 2 outliers final: 1 residues processed: 205 average time/residue: 0.3169 time to fit residues: 94.9171 Evaluate side-chains 150 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 148 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 2 optimal weight: 0.1980 chunk 17 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 134 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 53 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** G 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 159 ASN L 167 GLN L 199 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.126198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.105473 restraints weight = 31791.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.103244 restraints weight = 39583.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.104558 restraints weight = 32609.383| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12107 Z= 0.127 Angle : 0.640 11.247 16430 Z= 0.333 Chirality : 0.043 0.192 1844 Planarity : 0.005 0.068 2089 Dihedral : 5.463 45.279 1685 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.91 (0.20), residues: 1504 helix: 0.21 (0.22), residues: 512 sheet: -0.19 (0.32), residues: 269 loop : -1.33 (0.20), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 35 HIS 0.009 0.001 HIS L 199 PHE 0.025 0.002 PHE R 91 TYR 0.024 0.001 TYR A 74 ARG 0.005 0.000 ARG A 176 Details of bonding type rmsd link_NAG-ASN : bond 0.00362 ( 1) link_NAG-ASN : angle 2.06933 ( 3) link_BETA1-4 : bond 0.00582 ( 1) link_BETA1-4 : angle 1.66996 ( 3) hydrogen bonds : bond 0.04752 ( 515) hydrogen bonds : angle 5.18295 ( 1488) SS BOND : bond 0.00319 ( 6) SS BOND : angle 1.33934 ( 12) covalent geometry : bond 0.00264 (12099) covalent geometry : angle 0.63839 (16412) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 175 TRP cc_start: 0.4520 (t-100) cc_final: 0.3703 (t-100) REVERT: R 257 TYR cc_start: 0.7113 (m-10) cc_final: 0.6825 (m-80) REVERT: A 74 TYR cc_start: 0.7286 (m-80) cc_final: 0.6954 (m-80) REVERT: A 171 GLN cc_start: 0.8133 (pt0) cc_final: 0.7925 (pt0) REVERT: A 296 TYR cc_start: 0.6142 (p90) cc_final: 0.5833 (p90) REVERT: B 254 ASP cc_start: 0.7324 (t0) cc_final: 0.6693 (t0) REVERT: B 331 SER cc_start: 0.8957 (t) cc_final: 0.8617 (m) REVERT: G 28 ILE cc_start: 0.8471 (mm) cc_final: 0.8103 (tt) REVERT: L 174 TYR cc_start: 0.4638 (m-80) cc_final: 0.4296 (m-80) REVERT: H 112 TYR cc_start: 0.5742 (m-10) cc_final: 0.5000 (m-80) REVERT: H 167 PRO cc_start: 0.4498 (Cg_endo) cc_final: 0.4275 (Cg_exo) outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.2264 time to fit residues: 68.6667 Evaluate side-chains 151 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 0 optimal weight: 7.9990 chunk 131 optimal weight: 9.9990 chunk 74 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 106 optimal weight: 10.0000 chunk 95 optimal weight: 5.9990 chunk 50 optimal weight: 0.0870 chunk 3 optimal weight: 0.5980 chunk 105 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 chunk 134 optimal weight: 5.9990 overall best weight: 1.5162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 302 ASN ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS B 340 ASN ** G 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 159 ASN L 199 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.124672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.104410 restraints weight = 31753.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.103218 restraints weight = 39164.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.104417 restraints weight = 31183.004| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6812 moved from start: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12107 Z= 0.150 Angle : 0.654 11.385 16430 Z= 0.343 Chirality : 0.044 0.181 1844 Planarity : 0.005 0.082 2089 Dihedral : 5.301 34.032 1685 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.08 % Allowed : 3.33 % Favored : 96.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.00 (0.20), residues: 1504 helix: 0.14 (0.22), residues: 513 sheet: -0.32 (0.31), residues: 280 loop : -1.37 (0.21), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 35 HIS 0.010 0.001 HIS L 199 PHE 0.030 0.002 PHE R 37 TYR 0.021 0.002 TYR A 74 ARG 0.006 0.001 ARG B 197 Details of bonding type rmsd link_NAG-ASN : bond 0.00319 ( 1) link_NAG-ASN : angle 1.45132 ( 3) link_BETA1-4 : bond 0.00057 ( 1) link_BETA1-4 : angle 1.66090 ( 3) hydrogen bonds : bond 0.04774 ( 515) hydrogen bonds : angle 5.17306 ( 1488) SS BOND : bond 0.00445 ( 6) SS BOND : angle 1.08467 ( 12) covalent geometry : bond 0.00330 (12099) covalent geometry : angle 0.65287 (16412) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 199 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 83 ASP cc_start: 0.7232 (t0) cc_final: 0.6985 (t70) REVERT: R 175 TRP cc_start: 0.4622 (t-100) cc_final: 0.3841 (t-100) REVERT: R 253 MET cc_start: 0.7934 (tpp) cc_final: 0.7432 (tpp) REVERT: R 257 TYR cc_start: 0.7151 (m-10) cc_final: 0.6724 (m-80) REVERT: A 74 TYR cc_start: 0.7259 (m-80) cc_final: 0.6939 (m-80) REVERT: A 295 THR cc_start: 0.7233 (m) cc_final: 0.6190 (p) REVERT: A 296 TYR cc_start: 0.6301 (p90) cc_final: 0.5931 (p90) REVERT: B 254 ASP cc_start: 0.7286 (t0) cc_final: 0.6807 (t0) REVERT: B 331 SER cc_start: 0.9080 (t) cc_final: 0.8580 (m) REVERT: G 28 ILE cc_start: 0.8537 (mm) cc_final: 0.8099 (tt) REVERT: L 174 TYR cc_start: 0.4590 (m-80) cc_final: 0.4309 (m-80) REVERT: H 112 TYR cc_start: 0.6036 (m-10) cc_final: 0.5254 (m-80) outliers start: 1 outliers final: 0 residues processed: 200 average time/residue: 0.2079 time to fit residues: 62.3516 Evaluate side-chains 149 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 112 optimal weight: 0.4980 chunk 131 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 19 optimal weight: 0.0570 chunk 107 optimal weight: 0.0980 chunk 51 optimal weight: 4.9990 chunk 114 optimal weight: 6.9990 chunk 98 optimal weight: 0.0470 chunk 88 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 78 ASN R 113 GLN ** R 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN B 225 HIS B 340 ASN ** G 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 159 ASN L 199 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.127642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.107039 restraints weight = 31704.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.106493 restraints weight = 34694.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.107749 restraints weight = 28420.459| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6722 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12107 Z= 0.118 Angle : 0.637 12.644 16430 Z= 0.324 Chirality : 0.043 0.183 1844 Planarity : 0.004 0.079 2089 Dihedral : 4.919 29.055 1685 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.21), residues: 1504 helix: 0.38 (0.22), residues: 512 sheet: -0.21 (0.31), residues: 281 loop : -1.30 (0.21), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 35 HIS 0.010 0.001 HIS L 199 PHE 0.028 0.002 PHE R 91 TYR 0.020 0.001 TYR B 59 ARG 0.007 0.000 ARG A 176 Details of bonding type rmsd link_NAG-ASN : bond 0.00425 ( 1) link_NAG-ASN : angle 1.82223 ( 3) link_BETA1-4 : bond 0.00076 ( 1) link_BETA1-4 : angle 1.77436 ( 3) hydrogen bonds : bond 0.04448 ( 515) hydrogen bonds : angle 4.93213 ( 1488) SS BOND : bond 0.00320 ( 6) SS BOND : angle 1.00204 ( 12) covalent geometry : bond 0.00246 (12099) covalent geometry : angle 0.63583 (16412) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 1.416 Fit side-chains revert: symmetry clash REVERT: R 37 PHE cc_start: 0.7867 (p90) cc_final: 0.7662 (p90) REVERT: R 175 TRP cc_start: 0.4629 (t-100) cc_final: 0.3625 (t60) REVERT: R 253 MET cc_start: 0.7553 (tpp) cc_final: 0.7251 (tpp) REVERT: A 24 ARG cc_start: 0.6937 (mmp-170) cc_final: 0.6685 (mmp-170) REVERT: A 74 TYR cc_start: 0.7145 (m-80) cc_final: 0.6915 (m-80) REVERT: A 88 MET cc_start: 0.8011 (ppp) cc_final: 0.7376 (ppp) REVERT: A 296 TYR cc_start: 0.6048 (p90) cc_final: 0.5716 (p90) REVERT: A 309 ASP cc_start: 0.7184 (p0) cc_final: 0.6863 (p0) REVERT: B 186 ASP cc_start: 0.8428 (t0) cc_final: 0.8127 (t0) REVERT: B 254 ASP cc_start: 0.7187 (t0) cc_final: 0.6567 (t0) REVERT: B 331 SER cc_start: 0.8918 (t) cc_final: 0.8486 (m) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.2214 time to fit residues: 69.4891 Evaluate side-chains 154 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 46 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 53 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 114 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 107 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN B 156 GLN B 225 HIS B 259 GLN B 340 ASN ** G 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 159 ASN L 199 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.126952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.107077 restraints weight = 31592.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.105831 restraints weight = 41047.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.106893 restraints weight = 34803.147| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6745 moved from start: 0.4362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12107 Z= 0.123 Angle : 0.642 12.133 16430 Z= 0.329 Chirality : 0.044 0.172 1844 Planarity : 0.004 0.081 2089 Dihedral : 4.813 26.692 1685 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.83 (0.21), residues: 1504 helix: 0.30 (0.22), residues: 514 sheet: -0.19 (0.31), residues: 280 loop : -1.30 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 35 HIS 0.011 0.001 HIS L 199 PHE 0.030 0.002 PHE R 91 TYR 0.022 0.001 TYR A 302 ARG 0.003 0.000 ARG B 49 Details of bonding type rmsd link_NAG-ASN : bond 0.00357 ( 1) link_NAG-ASN : angle 1.48007 ( 3) link_BETA1-4 : bond 0.00035 ( 1) link_BETA1-4 : angle 1.72651 ( 3) hydrogen bonds : bond 0.04458 ( 515) hydrogen bonds : angle 4.94634 ( 1488) SS BOND : bond 0.00355 ( 6) SS BOND : angle 1.00498 ( 12) covalent geometry : bond 0.00266 (12099) covalent geometry : angle 0.64123 (16412) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 1.220 Fit side-chains revert: symmetry clash REVERT: R 175 TRP cc_start: 0.4724 (t-100) cc_final: 0.3732 (t60) REVERT: R 184 GLN cc_start: 0.7348 (mm-40) cc_final: 0.6870 (mp10) REVERT: R 207 MET cc_start: 0.7030 (mtm) cc_final: 0.6730 (ptt) REVERT: R 309 MET cc_start: 0.6986 (mpp) cc_final: 0.6717 (mpp) REVERT: R 312 GLN cc_start: 0.8306 (mt0) cc_final: 0.7730 (mt0) REVERT: A 88 MET cc_start: 0.8021 (ppp) cc_final: 0.7340 (ppp) REVERT: A 296 TYR cc_start: 0.6132 (p90) cc_final: 0.5854 (p90) REVERT: B 254 ASP cc_start: 0.7085 (t0) cc_final: 0.6671 (t0) REVERT: B 331 SER cc_start: 0.8989 (t) cc_final: 0.8447 (m) REVERT: H 105 TYR cc_start: 0.5802 (p90) cc_final: 0.5135 (p90) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.2306 time to fit residues: 70.7635 Evaluate side-chains 152 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 147 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 121 optimal weight: 20.0000 chunk 148 optimal weight: 0.9990 chunk 99 optimal weight: 10.0000 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 200 ASN R 238 GLN ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 159 ASN L 167 GLN L 199 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.124576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.104770 restraints weight = 31895.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.102887 restraints weight = 43108.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.104182 restraints weight = 36512.046| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6819 moved from start: 0.4576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12107 Z= 0.162 Angle : 0.692 15.477 16430 Z= 0.360 Chirality : 0.045 0.202 1844 Planarity : 0.005 0.070 2089 Dihedral : 5.067 27.632 1685 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.92 (0.21), residues: 1504 helix: 0.24 (0.22), residues: 513 sheet: -0.36 (0.31), residues: 274 loop : -1.31 (0.21), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 175 HIS 0.012 0.001 HIS L 199 PHE 0.031 0.002 PHE R 91 TYR 0.028 0.002 TYR A 302 ARG 0.004 0.000 ARG R 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00360 ( 1) link_NAG-ASN : angle 1.01071 ( 3) link_BETA1-4 : bond 0.00098 ( 1) link_BETA1-4 : angle 1.80222 ( 3) hydrogen bonds : bond 0.04740 ( 515) hydrogen bonds : angle 5.04051 ( 1488) SS BOND : bond 0.00527 ( 6) SS BOND : angle 1.12584 ( 12) covalent geometry : bond 0.00360 (12099) covalent geometry : angle 0.69102 (16412) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 1.212 Fit side-chains revert: symmetry clash REVERT: R 37 PHE cc_start: 0.8043 (p90) cc_final: 0.7796 (p90) REVERT: R 83 ASP cc_start: 0.7498 (t70) cc_final: 0.7184 (t70) REVERT: R 184 GLN cc_start: 0.7490 (mm-40) cc_final: 0.6939 (mp10) REVERT: R 207 MET cc_start: 0.6786 (mtm) cc_final: 0.6584 (ptt) REVERT: R 253 MET cc_start: 0.7705 (tpp) cc_final: 0.7438 (tpp) REVERT: R 309 MET cc_start: 0.6968 (mpp) cc_final: 0.6715 (mpp) REVERT: R 312 GLN cc_start: 0.8335 (mt0) cc_final: 0.7835 (mt0) REVERT: A 88 MET cc_start: 0.8064 (ppp) cc_final: 0.7385 (ppp) REVERT: B 254 ASP cc_start: 0.7266 (t0) cc_final: 0.6684 (t0) REVERT: B 331 SER cc_start: 0.9109 (t) cc_final: 0.8603 (m) REVERT: H 105 TYR cc_start: 0.6003 (p90) cc_final: 0.5398 (p90) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.2265 time to fit residues: 66.9225 Evaluate side-chains 151 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 125 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 63 optimal weight: 7.9990 chunk 116 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 18 optimal weight: 7.9990 chunk 145 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 55 ASN ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 159 ASN L 199 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.123875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.102927 restraints weight = 32298.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.101170 restraints weight = 39715.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.102359 restraints weight = 33856.786| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.4704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12107 Z= 0.170 Angle : 0.706 12.935 16430 Z= 0.365 Chirality : 0.045 0.182 1844 Planarity : 0.005 0.073 2089 Dihedral : 5.213 28.707 1685 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.09 (0.20), residues: 1504 helix: 0.02 (0.22), residues: 512 sheet: -0.52 (0.32), residues: 272 loop : -1.30 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 126 HIS 0.013 0.001 HIS L 199 PHE 0.034 0.002 PHE R 91 TYR 0.020 0.002 TYR A 302 ARG 0.007 0.001 ARG A 176 Details of bonding type rmsd link_NAG-ASN : bond 0.00325 ( 1) link_NAG-ASN : angle 0.95300 ( 3) link_BETA1-4 : bond 0.00019 ( 1) link_BETA1-4 : angle 1.76110 ( 3) hydrogen bonds : bond 0.04859 ( 515) hydrogen bonds : angle 5.10030 ( 1488) SS BOND : bond 0.00437 ( 6) SS BOND : angle 1.07412 ( 12) covalent geometry : bond 0.00382 (12099) covalent geometry : angle 0.70577 (16412) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 1.358 Fit side-chains revert: symmetry clash REVERT: R 37 PHE cc_start: 0.8016 (p90) cc_final: 0.7790 (p90) REVERT: R 184 GLN cc_start: 0.7621 (mm-40) cc_final: 0.6992 (mp10) REVERT: R 207 MET cc_start: 0.7071 (mtm) cc_final: 0.6751 (ptt) REVERT: R 312 GLN cc_start: 0.8360 (mt0) cc_final: 0.7883 (mt0) REVERT: A 88 MET cc_start: 0.7961 (ppp) cc_final: 0.7258 (ppp) REVERT: B 254 ASP cc_start: 0.7140 (t0) cc_final: 0.6569 (t0) REVERT: B 331 SER cc_start: 0.9096 (t) cc_final: 0.8579 (m) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.2201 time to fit residues: 63.5266 Evaluate side-chains 145 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 34 optimal weight: 0.9980 chunk 102 optimal weight: 6.9990 chunk 109 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 142 optimal weight: 0.7980 chunk 44 optimal weight: 5.9990 chunk 141 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 159 ASN ** L 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.125844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.104472 restraints weight = 31953.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.103412 restraints weight = 33368.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.104678 restraints weight = 28383.836| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6802 moved from start: 0.4751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12107 Z= 0.124 Angle : 0.674 13.718 16430 Z= 0.341 Chirality : 0.044 0.165 1844 Planarity : 0.004 0.070 2089 Dihedral : 4.938 25.551 1685 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.92 (0.21), residues: 1504 helix: 0.21 (0.22), residues: 513 sheet: -0.40 (0.32), residues: 276 loop : -1.27 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP R 126 HIS 0.005 0.001 HIS G 44 PHE 0.027 0.002 PHE R 91 TYR 0.033 0.001 TYR R 257 ARG 0.003 0.000 ARG R 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00436 ( 1) link_NAG-ASN : angle 1.32657 ( 3) link_BETA1-4 : bond 0.00040 ( 1) link_BETA1-4 : angle 1.67850 ( 3) hydrogen bonds : bond 0.04496 ( 515) hydrogen bonds : angle 4.89585 ( 1488) SS BOND : bond 0.00325 ( 6) SS BOND : angle 0.86200 ( 12) covalent geometry : bond 0.00267 (12099) covalent geometry : angle 0.67323 (16412) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3833.00 seconds wall clock time: 71 minutes 44.19 seconds (4304.19 seconds total)