Starting phenix.real_space_refine on Thu Feb 15 09:33:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cmo_7517/02_2024/6cmo_7517.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cmo_7517/02_2024/6cmo_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_2024/6cmo_7517.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cmo_7517/02_2024/6cmo_7517.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cmo_7517/02_2024/6cmo_7517.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cmo_7517/02_2024/6cmo_7517.pdb" } 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 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 6.74, per 1000 atoms: 0.57 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: 4.68 Conformation dependent library (CDL) restraints added in 2.3 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: 1.05 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: 2.95 Time building geometry restraints manager: 5.04 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: 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: 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 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 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: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.050 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 33.070 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.480 ------------------------------------------------------------------------------- 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= 0.273 Angle : 0.995 14.662 16412 Z= 0.533 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 *********************** 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 : 1.446 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: 0.2813 time to fit residues: 125.2725 Evaluate side-chains 179 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 1.420 ------------------------------------------------------------------------------- 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: 3.9990 chunk 63 optimal weight: 7.9990 chunk 38 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 60 optimal weight: 0.0370 chunk 117 optimal weight: 8.9990 chunk 45 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 chunk 87 optimal weight: 0.0970 chunk 136 optimal weight: 0.9990 overall best weight: 1.2060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 78 ASN R 111 ASN B 88 ASN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN B 259 GLN B 293 ASN B 311 HIS B 340 ASN G 11 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 91 GLN L 139 ASN L 159 ASN L 199 HIS L 211 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12099 Z= 0.194 Angle : 0.661 10.028 16412 Z= 0.347 Chirality : 0.044 0.227 1844 Planarity : 0.006 0.115 2089 Dihedral : 5.757 54.738 1685 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.39 % Allowed : 3.64 % Favored : 95.97 % 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 (0.19), residues: 1504 helix: -0.28 (0.21), residues: 523 sheet: 0.19 (0.29), residues: 256 loop : -1.23 (0.19), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 35 HIS 0.008 0.001 HIS L 199 PHE 0.023 0.002 PHE R 115 TYR 0.037 0.002 TYR A 290 ARG 0.008 0.001 ARG L 109 *********************** 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 238 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 233 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 91 PHE cc_start: 0.6741 (t80) cc_final: 0.6507 (t80) REVERT: R 175 TRP cc_start: 0.4096 (t-100) cc_final: 0.3432 (t-100) REVERT: R 225 GLN cc_start: 0.7007 (tp40) cc_final: 0.6756 (tp40) REVERT: R 255 ILE cc_start: 0.7439 (pt) cc_final: 0.7181 (mm) REVERT: A 240 MET cc_start: 0.5393 (ttp) cc_final: 0.5192 (ttp) REVERT: A 269 ASN cc_start: 0.8238 (m-40) cc_final: 0.7748 (p0) REVERT: A 277 LYS cc_start: 0.8613 (mmtm) cc_final: 0.8301 (pttp) REVERT: A 302 TYR cc_start: 0.6394 (t80) cc_final: 0.5395 (t80) REVERT: A 341 ASP cc_start: 0.8324 (t70) cc_final: 0.7913 (p0) REVERT: A 347 ASN cc_start: 0.7602 (m110) cc_final: 0.7359 (m-40) REVERT: B 75 GLN cc_start: 0.7149 (mt0) cc_final: 0.6445 (tm-30) REVERT: B 76 ASP cc_start: 0.7148 (p0) cc_final: 0.6439 (p0) REVERT: B 201 SER cc_start: 0.8340 (t) cc_final: 0.7935 (p) REVERT: B 254 ASP cc_start: 0.7375 (t0) cc_final: 0.7014 (t70) REVERT: G 28 ILE cc_start: 0.7595 (mm) cc_final: 0.7323 (tt) REVERT: G 38 MET cc_start: 0.7593 (ppp) cc_final: 0.7116 (tpt) REVERT: L 64 SER cc_start: 0.7199 (m) cc_final: 0.6915 (p) outliers start: 5 outliers final: 2 residues processed: 237 average time/residue: 0.2214 time to fit residues: 75.8002 Evaluate side-chains 157 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 155 time to evaluate : 1.292 ------------------------------------------------------------------------------- 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: 2.9990 chunk 42 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 136 optimal weight: 5.9990 chunk 147 optimal weight: 9.9990 chunk 121 optimal weight: 20.0000 chunk 135 optimal weight: 10.0000 chunk 46 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 111 ASN R 211 HIS R 302 ASN ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 HIS ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 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 L 200 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 12099 Z= 0.437 Angle : 0.841 10.650 16412 Z= 0.452 Chirality : 0.050 0.216 1844 Planarity : 0.007 0.079 2089 Dihedral : 6.966 85.620 1685 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.23 % Allowed : 6.20 % Favored : 93.57 % 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: -1.69 (0.19), residues: 1504 helix: -0.67 (0.21), residues: 525 sheet: -0.46 (0.29), residues: 272 loop : -1.70 (0.20), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 99 HIS 0.011 0.002 HIS B 54 PHE 0.040 0.003 PHE L 99 TYR 0.028 0.003 TYR L 141 ARG 0.009 0.001 ARG B 197 *********************** 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 194 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 191 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 83 ASP cc_start: 0.7693 (t0) cc_final: 0.7387 (t70) REVERT: R 206 TYR cc_start: 0.5252 (OUTLIER) cc_final: 0.4657 (m-10) REVERT: R 232 GLU cc_start: 0.8445 (pp20) cc_final: 0.8213 (pp20) REVERT: R 253 MET cc_start: 0.7683 (tmm) cc_final: 0.7448 (tmm) REVERT: R 257 TYR cc_start: 0.7316 (m-80) cc_final: 0.7052 (m-80) REVERT: A 290 TYR cc_start: 0.3873 (t80) cc_final: 0.3537 (t80) REVERT: A 302 TYR cc_start: 0.6849 (t80) cc_final: 0.6296 (t80) REVERT: B 75 GLN cc_start: 0.7151 (mt0) cc_final: 0.6320 (tm-30) REVERT: B 254 ASP cc_start: 0.7566 (t0) cc_final: 0.7240 (t0) REVERT: G 38 MET cc_start: 0.7612 (ppp) cc_final: 0.6956 (tpt) REVERT: H 112 TYR cc_start: 0.6324 (m-80) cc_final: 0.5962 (m-80) outliers start: 3 outliers final: 2 residues processed: 194 average time/residue: 0.2235 time to fit residues: 63.1639 Evaluate side-chains 148 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 145 time to evaluate : 1.328 ------------------------------------------------------------------------------- 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: 0.4980 chunk 102 optimal weight: 5.9990 chunk 70 optimal weight: 9.9990 chunk 15 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 144 optimal weight: 20.0000 chunk 71 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 111 ASN R 211 HIS R 225 GLN ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** 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 199 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12099 Z= 0.176 Angle : 0.648 13.773 16412 Z= 0.335 Chirality : 0.044 0.185 1844 Planarity : 0.005 0.068 2089 Dihedral : 6.079 83.336 1685 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.08 % Allowed : 4.19 % Favored : 95.74 % 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: -1.20 (0.20), residues: 1504 helix: 0.02 (0.22), residues: 518 sheet: -0.35 (0.30), residues: 273 loop : -1.58 (0.20), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP R 35 HIS 0.009 0.001 HIS L 199 PHE 0.023 0.002 PHE R 221 TYR 0.017 0.002 TYR A 74 ARG 0.004 0.000 ARG G 62 *********************** 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 223 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 222 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 175 TRP cc_start: 0.4165 (t-100) cc_final: 0.3700 (t-100) REVERT: R 312 GLN cc_start: 0.7851 (mt0) cc_final: 0.7253 (mm-40) REVERT: A 15 ARG cc_start: 0.6075 (mtm-85) cc_final: 0.5480 (ptm160) REVERT: A 74 TYR cc_start: 0.7859 (m-80) cc_final: 0.7650 (m-80) REVERT: A 283 LEU cc_start: 0.8187 (pt) cc_final: 0.7933 (tt) REVERT: A 290 TYR cc_start: 0.4528 (t80) cc_final: 0.3923 (t80) REVERT: A 302 TYR cc_start: 0.7126 (t80) cc_final: 0.6573 (t80) REVERT: A 309 ASP cc_start: 0.7256 (p0) cc_final: 0.6966 (p0) REVERT: A 341 ASP cc_start: 0.8343 (t70) cc_final: 0.7622 (p0) REVERT: A 346 ASN cc_start: 0.7792 (t0) cc_final: 0.7447 (t0) REVERT: B 254 ASP cc_start: 0.7406 (t0) cc_final: 0.6829 (t0) REVERT: B 269 ILE cc_start: 0.6921 (mm) cc_final: 0.6695 (mm) REVERT: G 38 MET cc_start: 0.7574 (ppp) cc_final: 0.7046 (tpt) REVERT: L 64 SER cc_start: 0.7093 (m) cc_final: 0.6821 (p) REVERT: L 146 LYS cc_start: 0.6453 (tmtt) cc_final: 0.6246 (tptp) REVERT: H 112 TYR cc_start: 0.6577 (m-80) cc_final: 0.5979 (m-80) outliers start: 1 outliers final: 0 residues processed: 222 average time/residue: 0.2475 time to fit residues: 78.4325 Evaluate side-chains 154 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 1.463 ------------------------------------------------------------------------------- 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: 5.9990 chunk 82 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 107 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 74 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 55 ASN R 237 GLN ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.4324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 12099 Z= 0.300 Angle : 0.713 10.619 16412 Z= 0.379 Chirality : 0.046 0.173 1844 Planarity : 0.005 0.072 2089 Dihedral : 6.112 66.607 1685 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 0.16 % Allowed : 3.95 % Favored : 95.89 % 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: -1.46 (0.20), residues: 1504 helix: -0.20 (0.22), residues: 519 sheet: -0.52 (0.30), residues: 276 loop : -1.71 (0.20), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP R 35 HIS 0.009 0.002 HIS L 199 PHE 0.029 0.003 PHE B 241 TYR 0.030 0.002 TYR A 69 ARG 0.008 0.001 ARG A 176 *********************** 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 195 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 193 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 37 PHE cc_start: 0.8450 (p90) cc_final: 0.7879 (p90) REVERT: R 255 ILE cc_start: 0.8546 (mm) cc_final: 0.8339 (tt) REVERT: R 312 GLN cc_start: 0.7882 (mt0) cc_final: 0.7301 (mm-40) REVERT: A 240 MET cc_start: 0.6091 (ttp) cc_final: 0.5454 (tmm) REVERT: A 290 TYR cc_start: 0.4520 (t80) cc_final: 0.4062 (t80) REVERT: A 302 TYR cc_start: 0.7301 (t80) cc_final: 0.6801 (t80) REVERT: A 346 ASN cc_start: 0.7957 (t0) cc_final: 0.7583 (t0) REVERT: B 37 ILE cc_start: 0.8421 (pt) cc_final: 0.8192 (pt) REVERT: B 57 LYS cc_start: 0.7968 (mmmt) cc_final: 0.7293 (mttt) REVERT: B 254 ASP cc_start: 0.7373 (t0) cc_final: 0.6839 (t0) REVERT: G 38 MET cc_start: 0.7580 (ppp) cc_final: 0.6907 (tpt) REVERT: L 64 SER cc_start: 0.7111 (m) cc_final: 0.6828 (p) outliers start: 2 outliers final: 0 residues processed: 195 average time/residue: 0.2307 time to fit residues: 66.5720 Evaluate side-chains 150 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 1.450 ------------------------------------------------------------------------------- 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: 0.9980 chunk 130 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 145 optimal weight: 0.0770 chunk 120 optimal weight: 8.9990 chunk 67 optimal weight: 0.2980 chunk 12 optimal weight: 0.5980 chunk 76 optimal weight: 2.9990 chunk 139 optimal weight: 7.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 237 GLN ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.4277 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= 0.158 Angle : 0.636 12.562 16412 Z= 0.322 Chirality : 0.043 0.174 1844 Planarity : 0.005 0.081 2089 Dihedral : 5.383 63.950 1685 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.08 % Allowed : 2.71 % Favored : 97.21 % 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: -0.98 (0.20), residues: 1504 helix: 0.27 (0.22), residues: 512 sheet: -0.32 (0.31), residues: 271 loop : -1.45 (0.21), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 339 HIS 0.010 0.001 HIS L 199 PHE 0.024 0.002 PHE R 91 TYR 0.020 0.001 TYR A 74 ARG 0.004 0.000 ARG B 68 *********************** 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 212 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 211 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 37 PHE cc_start: 0.8542 (p90) cc_final: 0.8080 (p90) REVERT: R 175 TRP cc_start: 0.4224 (t-100) cc_final: 0.3494 (t60) REVERT: R 312 GLN cc_start: 0.7856 (mt0) cc_final: 0.7313 (mm-40) REVERT: A 15 ARG cc_start: 0.5881 (mtm-85) cc_final: 0.5311 (ptm160) REVERT: A 88 MET cc_start: 0.8622 (ptt) cc_final: 0.8250 (ppp) REVERT: A 108 PHE cc_start: 0.8865 (m-80) cc_final: 0.8522 (m-80) REVERT: A 240 MET cc_start: 0.5886 (ttp) cc_final: 0.5277 (tmm) REVERT: A 290 TYR cc_start: 0.4582 (t80) cc_final: 0.3857 (t80) REVERT: A 302 TYR cc_start: 0.7308 (t80) cc_final: 0.6934 (t80) REVERT: A 341 ASP cc_start: 0.7907 (t70) cc_final: 0.7522 (p0) REVERT: A 347 ASN cc_start: 0.7907 (m110) cc_final: 0.7656 (m-40) REVERT: B 57 LYS cc_start: 0.7835 (mmpt) cc_final: 0.7258 (mttt) REVERT: B 254 ASP cc_start: 0.7443 (t0) cc_final: 0.6937 (t0) REVERT: B 331 SER cc_start: 0.8770 (t) cc_final: 0.8360 (m) REVERT: G 38 MET cc_start: 0.7553 (ppp) cc_final: 0.7047 (tpt) REVERT: L 64 SER cc_start: 0.7091 (m) cc_final: 0.6777 (p) REVERT: L 141 TYR cc_start: 0.6809 (m-80) cc_final: 0.6493 (m-80) outliers start: 1 outliers final: 0 residues processed: 212 average time/residue: 0.2070 time to fit residues: 65.3376 Evaluate side-chains 156 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 105 optimal weight: 0.0980 chunk 122 optimal weight: 0.3980 chunk 81 optimal weight: 5.9990 chunk 144 optimal weight: 0.0670 chunk 90 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 overall best weight: 0.4318 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 159 ASN L 199 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 0.4356 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= 0.153 Angle : 0.629 16.063 16412 Z= 0.317 Chirality : 0.043 0.169 1844 Planarity : 0.004 0.068 2089 Dihedral : 5.073 60.339 1685 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % 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: -0.84 (0.21), residues: 1504 helix: 0.36 (0.23), residues: 512 sheet: -0.17 (0.32), residues: 275 loop : -1.39 (0.21), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 339 HIS 0.011 0.001 HIS L 199 PHE 0.025 0.002 PHE R 91 TYR 0.030 0.001 TYR A 69 ARG 0.004 0.000 ARG A 176 *********************** 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 226 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 226 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 25 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7183 (mm-30) REVERT: R 33 GLU cc_start: 0.7023 (tp30) cc_final: 0.6315 (mp0) REVERT: R 37 PHE cc_start: 0.8588 (p90) cc_final: 0.8064 (p90) REVERT: R 85 PHE cc_start: 0.7678 (t80) cc_final: 0.7318 (t80) REVERT: R 175 TRP cc_start: 0.4114 (t-100) cc_final: 0.3374 (t60) REVERT: R 201 GLU cc_start: 0.8478 (mp0) cc_final: 0.7913 (pp20) REVERT: R 312 GLN cc_start: 0.7905 (mt0) cc_final: 0.7262 (mm-40) REVERT: A 15 ARG cc_start: 0.5788 (mtm-85) cc_final: 0.5222 (ptm160) REVERT: A 88 MET cc_start: 0.8520 (ptt) cc_final: 0.8124 (ppp) REVERT: A 108 PHE cc_start: 0.8859 (m-80) cc_final: 0.8514 (m-80) REVERT: A 115 GLU cc_start: 0.6475 (mp0) cc_final: 0.6251 (mp0) REVERT: A 119 MET cc_start: 0.4331 (ttt) cc_final: 0.3667 (ttt) REVERT: A 178 ARG cc_start: 0.6710 (tpt170) cc_final: 0.6343 (ttm110) REVERT: A 240 MET cc_start: 0.5749 (ttp) cc_final: 0.5202 (tmm) REVERT: A 290 TYR cc_start: 0.4417 (t80) cc_final: 0.3872 (t80) REVERT: A 302 TYR cc_start: 0.7482 (t80) cc_final: 0.7003 (t80) REVERT: B 186 ASP cc_start: 0.8769 (t0) cc_final: 0.8280 (t70) REVERT: B 254 ASP cc_start: 0.7292 (t0) cc_final: 0.6899 (t0) REVERT: B 331 SER cc_start: 0.8788 (t) cc_final: 0.8539 (m) REVERT: G 38 MET cc_start: 0.7617 (ppp) cc_final: 0.7118 (tpt) REVERT: L 64 SER cc_start: 0.6981 (m) cc_final: 0.6717 (p) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.2414 time to fit residues: 78.7498 Evaluate side-chains 160 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 113 optimal weight: 0.7980 chunk 131 optimal weight: 0.0040 chunk 138 optimal weight: 0.9990 chunk 126 optimal weight: 10.0000 overall best weight: 0.6594 ------------------------------------------------------------------------------- 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 237 GLN B 156 GLN B 225 HIS ** L 38 GLN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 moved from start: 0.4493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12099 Z= 0.156 Angle : 0.629 13.971 16412 Z= 0.316 Chirality : 0.043 0.177 1844 Planarity : 0.004 0.069 2089 Dihedral : 4.863 56.945 1685 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.08 % Allowed : 1.63 % 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: -0.78 (0.21), residues: 1504 helix: 0.35 (0.22), residues: 513 sheet: -0.11 (0.31), residues: 275 loop : -1.31 (0.21), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 339 HIS 0.012 0.001 HIS L 199 PHE 0.026 0.002 PHE R 159 TYR 0.022 0.001 TYR A 74 ARG 0.003 0.000 ARG G 62 *********************** 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 212 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 211 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 37 PHE cc_start: 0.8656 (p90) cc_final: 0.8082 (p90) REVERT: R 85 PHE cc_start: 0.7776 (t80) cc_final: 0.7325 (t80) REVERT: R 175 TRP cc_start: 0.4157 (t-100) cc_final: 0.3445 (t60) REVERT: R 312 GLN cc_start: 0.7864 (mt0) cc_final: 0.7234 (mm-40) REVERT: A 88 MET cc_start: 0.8570 (ptt) cc_final: 0.8187 (ppp) REVERT: A 108 PHE cc_start: 0.8875 (m-80) cc_final: 0.8514 (m-80) REVERT: A 115 GLU cc_start: 0.6416 (mp0) cc_final: 0.6171 (mp0) REVERT: A 119 MET cc_start: 0.4680 (ttt) cc_final: 0.4039 (ttt) REVERT: A 240 MET cc_start: 0.5991 (ttp) cc_final: 0.5490 (tmm) REVERT: A 290 TYR cc_start: 0.4443 (t80) cc_final: 0.3940 (t80) REVERT: A 302 TYR cc_start: 0.7398 (t80) cc_final: 0.7154 (t80) REVERT: B 76 ASP cc_start: 0.7445 (p0) cc_final: 0.6909 (p0) REVERT: B 254 ASP cc_start: 0.7460 (t0) cc_final: 0.6936 (t0) REVERT: G 38 MET cc_start: 0.7532 (ppp) cc_final: 0.6992 (tpt) REVERT: L 64 SER cc_start: 0.6976 (m) cc_final: 0.6724 (p) outliers start: 1 outliers final: 0 residues processed: 212 average time/residue: 0.2146 time to fit residues: 66.7202 Evaluate side-chains 148 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 10.0000 chunk 138 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 105 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 chunk 121 optimal weight: 20.0000 chunk 127 optimal weight: 10.0000 chunk 88 optimal weight: 0.9990 chunk 142 optimal weight: 10.0000 chunk 86 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 199 ASN ** R 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 237 GLN B 225 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.4799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12099 Z= 0.289 Angle : 0.721 11.158 16412 Z= 0.377 Chirality : 0.046 0.236 1844 Planarity : 0.005 0.071 2089 Dihedral : 5.483 54.512 1685 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 0.08 % Allowed : 1.01 % 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: -1.23 (0.20), residues: 1504 helix: -0.13 (0.22), residues: 520 sheet: -0.37 (0.31), residues: 277 loop : -1.48 (0.21), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 339 HIS 0.006 0.002 HIS B 62 PHE 0.030 0.003 PHE R 91 TYR 0.023 0.002 TYR A 74 ARG 0.003 0.001 ARG R 69 *********************** 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 202 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 201 time to evaluate : 1.279 Fit side-chains revert: symmetry clash REVERT: R 37 PHE cc_start: 0.8761 (p90) cc_final: 0.8428 (p90) REVERT: R 85 PHE cc_start: 0.7740 (t80) cc_final: 0.7297 (t80) REVERT: R 126 TRP cc_start: 0.7835 (m100) cc_final: 0.7561 (m100) REVERT: R 312 GLN cc_start: 0.7950 (mt0) cc_final: 0.7324 (mm-40) REVERT: A 88 MET cc_start: 0.8614 (ptt) cc_final: 0.8171 (ppp) REVERT: A 108 PHE cc_start: 0.8895 (m-80) cc_final: 0.8562 (m-80) REVERT: A 115 GLU cc_start: 0.6522 (mp0) cc_final: 0.6289 (mp0) REVERT: A 240 MET cc_start: 0.5895 (ttp) cc_final: 0.5639 (ttp) REVERT: A 290 TYR cc_start: 0.4686 (t80) cc_final: 0.3869 (t80) REVERT: A 341 ASP cc_start: 0.8128 (t70) cc_final: 0.7496 (p0) REVERT: B 37 ILE cc_start: 0.8258 (pt) cc_final: 0.8008 (pt) REVERT: B 254 ASP cc_start: 0.7418 (t0) cc_final: 0.7003 (t0) REVERT: G 38 MET cc_start: 0.7645 (ppp) cc_final: 0.7008 (tpt) REVERT: L 141 TYR cc_start: 0.6962 (m-80) cc_final: 0.6614 (m-80) outliers start: 1 outliers final: 1 residues processed: 202 average time/residue: 0.2055 time to fit residues: 61.8794 Evaluate side-chains 149 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 148 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 1.9990 chunk 99 optimal weight: 0.0000 chunk 149 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 118 optimal weight: 10.0000 chunk 12 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 126 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 200 ASN ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.4779 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= 0.174 Angle : 0.656 13.365 16412 Z= 0.333 Chirality : 0.044 0.201 1844 Planarity : 0.005 0.083 2089 Dihedral : 5.171 58.042 1685 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % 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: -0.97 (0.21), residues: 1504 helix: 0.17 (0.22), residues: 513 sheet: -0.33 (0.31), residues: 280 loop : -1.34 (0.21), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 339 HIS 0.014 0.001 HIS L 199 PHE 0.027 0.002 PHE R 91 TYR 0.026 0.001 TYR A 302 ARG 0.006 0.000 ARG A 176 ********************** 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 207 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 37 PHE cc_start: 0.8742 (p90) cc_final: 0.8402 (p90) REVERT: R 83 ASP cc_start: 0.7081 (p0) cc_final: 0.6640 (t0) REVERT: R 85 PHE cc_start: 0.7891 (t80) cc_final: 0.7545 (t80) REVERT: R 86 MET cc_start: 0.8147 (tmm) cc_final: 0.7571 (ttt) REVERT: R 184 GLN cc_start: 0.8918 (mm110) cc_final: 0.8471 (mm110) REVERT: R 309 MET cc_start: 0.5305 (mtt) cc_final: 0.4927 (mpp) REVERT: R 312 GLN cc_start: 0.7935 (mt0) cc_final: 0.7276 (mm-40) REVERT: A 52 GLN cc_start: 0.6943 (pt0) cc_final: 0.6740 (pt0) REVERT: A 88 MET cc_start: 0.8631 (ptt) cc_final: 0.8245 (ppp) REVERT: A 108 PHE cc_start: 0.8848 (m-80) cc_final: 0.8515 (m-80) REVERT: A 240 MET cc_start: 0.5861 (ttp) cc_final: 0.5324 (tmm) REVERT: A 290 TYR cc_start: 0.3892 (t80) cc_final: 0.2957 (t80) REVERT: A 302 TYR cc_start: 0.7307 (t80) cc_final: 0.6892 (t80) REVERT: A 327 THR cc_start: 0.6915 (m) cc_final: 0.6712 (p) REVERT: B 37 ILE cc_start: 0.8248 (pt) cc_final: 0.8010 (pt) REVERT: B 57 LYS cc_start: 0.7644 (mmmt) cc_final: 0.6998 (mttt) REVERT: B 254 ASP cc_start: 0.7423 (t0) cc_final: 0.6946 (t0) REVERT: G 38 MET cc_start: 0.7591 (ppp) cc_final: 0.6992 (tpt) REVERT: L 64 SER cc_start: 0.7080 (m) cc_final: 0.6790 (p) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.2105 time to fit residues: 64.7953 Evaluate side-chains 156 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 119 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 237 GLN ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.125342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.106048 restraints weight = 32203.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.104938 restraints weight = 40145.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.105750 restraints weight = 35475.343| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6777 moved from start: 0.4873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12099 Z= 0.182 Angle : 0.650 13.279 16412 Z= 0.331 Chirality : 0.043 0.193 1844 Planarity : 0.005 0.078 2089 Dihedral : 5.016 53.031 1685 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.08 % Allowed : 0.23 % Favored : 99.69 % 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: -0.94 (0.21), residues: 1504 helix: 0.18 (0.22), residues: 514 sheet: -0.37 (0.31), residues: 280 loop : -1.30 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 339 HIS 0.005 0.001 HIS G 44 PHE 0.027 0.002 PHE R 159 TYR 0.027 0.001 TYR R 257 ARG 0.004 0.000 ARG R 177 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2434.92 seconds wall clock time: 45 minutes 29.24 seconds (2729.24 seconds total)