Starting phenix.real_space_refine (version: dev) on Mon Feb 20 09:38:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cmo_7517/02_2023/6cmo_7517.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cmo_7517/02_2023/6cmo_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cmo_7517/02_2023/6cmo_7517.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cmo_7517/02_2023/6cmo_7517.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cmo_7517/02_2023/6cmo_7517.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cmo_7517/02_2023/6cmo_7517.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Process input model Symmetric amino acids flipped Residue "R PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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 chiralities: 2 Time building chain proxies: 6.88, per 1000 atoms: 0.58 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG C 1 " - " ASN R 15 " Time building additional restraints: 4.48 Conformation dependent library (CDL) restraints added in 1.8 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: 0.70 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: 3.75 Time building geometry restraints manager: 4.80 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=" C PHE R 52 " pdb=" N PRO R 53 " ideal model delta sigma weight residual 1.336 1.356 -0.020 1.23e-02 6.61e+03 2.69e+00 ... (remaining 12094 not shown) Histogram of bond angle deviations from ideal: 98.19 - 105.51: 226 105.51 - 112.82: 6140 112.82 - 120.13: 4721 120.13 - 127.45: 5200 127.45 - 134.76: 125 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: 6747 14.99 - 29.97: 342 29.97 - 44.96: 90 44.96 - 59.95: 11 59.95 - 74.93: 7 Dihedral angle restraints: 7197 sinusoidal: 2780 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 7194 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 2.440 nonbonded pdb=" O ASP A 173 " pdb=" OG1 THR A 177 " model vdw 2.270 2.440 nonbonded pdb=" OH TYR B 264 " pdb=" O ALA B 299 " model vdw 2.277 2.440 nonbonded pdb=" O SER A 44 " pdb=" OG1 THR A 48 " model vdw 2.280 2.440 nonbonded pdb=" O LYS A 248 " pdb=" OG SER A 252 " model vdw 2.322 2.440 ... (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 ========== 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 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. 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.540 Check model and map are aligned: 0.180 Process input model: 32.280 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.100 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.400 ------------------------------------------------------------------------------- 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 12099 Z= 0.270 Angle : 0.994 14.662 16412 Z= 0.533 Chirality : 0.063 1.029 1844 Planarity : 0.007 0.064 2089 Dihedral : 10.427 74.935 4339 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 % 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 *********************** 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 fitting. rotamer outliers: 1 poor density : 330 time to evaluate : 1.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 330 average time/residue: 0.2812 time to fit residues: 125.3532 Evaluate side-chains 166 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 1.398 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8963 ------------------------------------------------------------------------------- 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: 6.9990 chunk 113 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 chunk 38 optimal weight: 0.8980 chunk 76 optimal weight: 7.9990 chunk 60 optimal weight: 0.0570 chunk 117 optimal weight: 8.9990 chunk 45 optimal weight: 9.9990 chunk 71 optimal weight: 6.9990 chunk 87 optimal weight: 7.9990 chunk 136 optimal weight: 0.9990 overall best weight: 2.3904 ------------------------------------------------------------------------------- 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** A 195 HIS B 88 ASN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 159 ASN L 199 HIS L 211 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 12099 Z= 0.296 Angle : 0.726 9.743 16412 Z= 0.389 Chirality : 0.047 0.287 1844 Planarity : 0.006 0.101 2089 Dihedral : 5.894 51.927 1655 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer Outliers : 0.39 % 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: -1.24 (0.19), residues: 1504 helix: -0.42 (0.21), residues: 523 sheet: -0.18 (0.28), residues: 270 loop : -1.33 (0.20), residues: 711 *********************** 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 217 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 212 time to evaluate : 1.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 216 average time/residue: 0.2296 time to fit residues: 72.0424 Evaluate side-chains 151 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 149 time to evaluate : 1.383 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1206 time to fit residues: 2.3834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 113 optimal weight: 0.0570 chunk 92 optimal weight: 0.2980 chunk 37 optimal weight: 7.9990 chunk 136 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 chunk 135 optimal weight: 0.0870 chunk 46 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 ASN B 340 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 91 GLN L 159 ASN L 199 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 12099 Z= 0.156 Angle : 0.619 9.948 16412 Z= 0.323 Chirality : 0.043 0.298 1844 Planarity : 0.005 0.075 2089 Dihedral : 5.267 46.319 1655 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer Outliers : 0.16 % 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: -0.85 (0.20), residues: 1504 helix: 0.03 (0.22), residues: 516 sheet: 0.17 (0.30), residues: 263 loop : -1.26 (0.20), residues: 725 *********************** 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 217 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 215 time to evaluate : 1.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 217 average time/residue: 0.2459 time to fit residues: 76.4274 Evaluate side-chains 153 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 152 time to evaluate : 1.472 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1417 time to fit residues: 2.3108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 0.8980 chunk 102 optimal weight: 0.6980 chunk 70 optimal weight: 0.0060 chunk 15 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 136 optimal weight: 0.8980 chunk 144 optimal weight: 20.0000 chunk 71 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 78 ASN R 278 HIS R 302 ASN ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN B 340 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 91 GLN L 159 ASN L 199 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 12099 Z= 0.152 Angle : 0.593 9.111 16412 Z= 0.312 Chirality : 0.043 0.255 1844 Planarity : 0.004 0.070 2089 Dihedral : 4.948 40.979 1655 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer Outliers : 0.16 % 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: -0.69 (0.20), residues: 1504 helix: 0.29 (0.22), residues: 512 sheet: 0.07 (0.30), residues: 275 loop : -1.19 (0.20), residues: 717 *********************** 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 206 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 204 time to evaluate : 1.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 206 average time/residue: 0.2258 time to fit residues: 68.3952 Evaluate side-chains 150 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 149 time to evaluate : 1.409 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1415 time to fit residues: 2.0770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 0.3980 chunk 82 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 107 optimal weight: 9.9990 chunk 59 optimal weight: 3.9990 chunk 123 optimal weight: 20.0000 chunk 100 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 74 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 78 ASN R 200 ASN ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 340 ASN ** G 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 91 GLN L 159 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 12099 Z= 0.225 Angle : 0.633 10.560 16412 Z= 0.336 Chirality : 0.044 0.246 1844 Planarity : 0.005 0.056 2089 Dihedral : 5.037 37.911 1655 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer Outliers : 0.08 % 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: -0.85 (0.20), residues: 1504 helix: 0.16 (0.22), residues: 510 sheet: -0.15 (0.30), residues: 278 loop : -1.22 (0.20), residues: 716 *********************** 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 207 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 206 time to evaluate : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 207 average time/residue: 0.2215 time to fit residues: 68.3704 Evaluate side-chains 149 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 148 time to evaluate : 1.466 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2208 time to fit residues: 2.7300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 0.0870 chunk 130 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 145 optimal weight: 4.9990 chunk 120 optimal weight: 9.9990 chunk 67 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 76 optimal weight: 0.0980 chunk 139 optimal weight: 3.9990 overall best weight: 0.5560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: