Starting phenix.real_space_refine on Fri Feb 16 15:25:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qn9_14071/02_2024/7qn9_14071_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qn9_14071/02_2024/7qn9_14071.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qn9_14071/02_2024/7qn9_14071.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qn9_14071/02_2024/7qn9_14071.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qn9_14071/02_2024/7qn9_14071_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qn9_14071/02_2024/7qn9_14071_updated.pdb" } resolution = 2.9 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= -0.000 sd= 0.003 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 91 5.16 5 C 10194 2.51 5 N 2533 2.21 5 O 2878 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15696 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 2693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2693 Classifications: {'peptide': 333} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 315} Chain breaks: 1 Chain: "B" Number of atoms: 2720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2720 Classifications: {'peptide': 331} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 316} Chain breaks: 1 Chain: "C" Number of atoms: 2720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2720 Classifications: {'peptide': 331} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 316} Chain breaks: 1 Chain: "D" Number of atoms: 2720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2720 Classifications: {'peptide': 331} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 316} Chain breaks: 1 Chain: "E" Number of atoms: 2579 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 321, 2569 Classifications: {'peptide': 321} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 10, 'TRANS': 308} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 321, 2569 Classifications: {'peptide': 321} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 10, 'TRANS': 308} Chain breaks: 1 bond proxies already assigned to first conformer: 2627 Chain: "L" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "M" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" 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 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "d" 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 Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'HSM': 1, 'R16': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'HSM': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'D10': 1, 'HSM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N HSM C 501 " occ=0.70 ... (6 atoms not shown) pdb=" NE2 HSM C 501 " occ=0.70 residue: pdb=" N HSM D 502 " occ=0.70 ... (6 atoms not shown) pdb=" NE2 HSM D 502 " occ=0.70 Time building chain proxies: 10.10, per 1000 atoms: 0.64 Number of scatterers: 15696 At special positions: 0 Unit cell: (113.792, 116.48, 129.92, 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 91 16.00 O 2878 8.00 N 2533 7.00 C 10194 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 172 " - pdb=" SG CYS A 186 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 150 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 150 " distance=2.03 Simple disulfide: pdb=" SG CYS D 136 " - pdb=" SG CYS D 150 " distance=2.03 Simple disulfide: pdb=" SG CYS E 164 " - pdb=" SG CYS E 178 " distance=2.03 Simple disulfide: pdb=" SG CYS L 409 " - pdb=" SG CYS L 483 " distance=2.03 Simple disulfide: pdb=" SG CYS M 409 " - pdb=" SG CYS M 483 " 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 ALPHA1-3 " BMA F 3 " - " MAN F 4 " " BMA G 3 " - " MAN G 4 " " BMA H 3 " - " MAN H 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " " BMA G 3 " - " MAN G 5 " " BMA H 3 " - " MAN H 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " NAG-ASN " NAG A 601 " - " ASN A 157 " " NAG E 501 " - " ASN E 65 " " NAG F 1 " - " ASN B 149 " " NAG G 1 " - " ASN C 149 " " NAG H 1 " - " ASN D 149 " " NAG a 1 " - " ASN A 144 " " NAG b 1 " - " ASN B 80 " " NAG c 1 " - " ASN C 80 " " NAG d 1 " - " ASN D 80 " Time building additional restraints: 6.56 Conformation dependent library (CDL) restraints added in 3.1 seconds 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3564 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 51 helices and 24 sheets defined 33.6% alpha, 30.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.21 Creating SS restraints... Processing helix chain 'A' and resid 49 through 56 Processing helix chain 'A' and resid 106 through 108 No H-bonds generated for 'chain 'A' and resid 106 through 108' Processing helix chain 'A' and resid 121 through 126 removed outlier: 3.620A pdb=" N THR A 125 " --> pdb=" O MET A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 211 No H-bonds generated for 'chain 'A' and resid 208 through 211' Processing helix chain 'A' and resid 257 through 262 Processing helix chain 'A' and resid 264 through 279 removed outlier: 4.217A pdb=" N SER A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N PHE A 278 " --> pdb=" O SER A 274 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N TRP A 279 " --> pdb=" O GLN A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 309 removed outlier: 3.760A pdb=" N HIS A 308 " --> pdb=" O ILE A 304 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER A 309 " --> pdb=" O SER A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 347 Processing helix chain 'A' and resid 517 through 542 removed outlier: 3.682A pdb=" N ILE A 524 " --> pdb=" O LYS A 520 " (cutoff:3.500A) Proline residue: A 527 - end of helix Processing helix chain 'B' and resid 9 through 20 Processing helix chain 'B' and resid 70 through 72 No H-bonds generated for 'chain 'B' and resid 70 through 72' Processing helix chain 'B' and resid 85 through 90 Processing helix chain 'B' and resid 171 through 173 No H-bonds generated for 'chain 'B' and resid 171 through 173' Processing helix chain 'B' and resid 178 through 180 No H-bonds generated for 'chain 'B' and resid 178 through 180' Processing helix chain 'B' and resid 219 through 224 Processing helix chain 'B' and resid 226 through 241 removed outlier: 3.582A pdb=" N TRP B 237 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL B 238 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N SER B 239 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N PHE B 240 " --> pdb=" O SER B 236 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N TRP B 241 " --> pdb=" O TRP B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 271 removed outlier: 4.041A pdb=" N GLU B 270 " --> pdb=" O THR B 266 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N THR B 271 " --> pdb=" O HIS B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 305 Processing helix chain 'B' and resid 420 through 446 removed outlier: 3.507A pdb=" N ILE B 429 " --> pdb=" O ARG B 425 " (cutoff:3.500A) Proline residue: B 432 - end of helix Processing helix chain 'C' and resid 9 through 20 Processing helix chain 'C' and resid 70 through 72 No H-bonds generated for 'chain 'C' and resid 70 through 72' Processing helix chain 'C' and resid 85 through 90 Processing helix chain 'C' and resid 171 through 173 No H-bonds generated for 'chain 'C' and resid 171 through 173' Processing helix chain 'C' and resid 178 through 180 No H-bonds generated for 'chain 'C' and resid 178 through 180' Processing helix chain 'C' and resid 219 through 224 Processing helix chain 'C' and resid 226 through 241 removed outlier: 3.582A pdb=" N TRP C 237 " --> pdb=" O THR C 233 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL C 238 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N SER C 239 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N PHE C 240 " --> pdb=" O SER C 236 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N TRP C 241 " --> pdb=" O TRP C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 271 removed outlier: 4.042A pdb=" N GLU C 270 " --> pdb=" O THR C 266 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N THR C 271 " --> pdb=" O HIS C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 305 Processing helix chain 'C' and resid 420 through 446 removed outlier: 3.507A pdb=" N ILE C 429 " --> pdb=" O ARG C 425 " (cutoff:3.500A) Proline residue: C 432 - end of helix Processing helix chain 'D' and resid 9 through 20 Processing helix chain 'D' and resid 70 through 72 No H-bonds generated for 'chain 'D' and resid 70 through 72' Processing helix chain 'D' and resid 85 through 90 Processing helix chain 'D' and resid 171 through 173 No H-bonds generated for 'chain 'D' and resid 171 through 173' Processing helix chain 'D' and resid 178 through 180 No H-bonds generated for 'chain 'D' and resid 178 through 180' Processing helix chain 'D' and resid 219 through 224 Processing helix chain 'D' and resid 226 through 241 removed outlier: 3.583A pdb=" N TRP D 237 " --> pdb=" O THR D 233 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL D 238 " --> pdb=" O ILE D 234 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N SER D 239 " --> pdb=" O LEU D 235 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N PHE D 240 " --> pdb=" O SER D 236 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N TRP D 241 " --> pdb=" O TRP D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 271 removed outlier: 4.041A pdb=" N GLU D 270 " --> pdb=" O THR D 266 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N THR D 271 " --> pdb=" O HIS D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 305 Processing helix chain 'D' and resid 420 through 446 removed outlier: 3.509A pdb=" N ILE D 429 " --> pdb=" O ARG D 425 " (cutoff:3.500A) Proline residue: D 432 - end of helix Processing helix chain 'E' and resid 45 through 49 Processing helix chain 'E' and resid 98 through 100 No H-bonds generated for 'chain 'E' and resid 98 through 100' Processing helix chain 'E' and resid 113 through 118 removed outlier: 3.709A pdb=" N ASP E 117 " --> pdb=" O ARG E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 201 removed outlier: 3.762A pdb=" N GLU E 201 " --> pdb=" O GLU E 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 198 through 201' Processing helix chain 'E' and resid 250 through 270 Proline residue: E 257 - end of helix removed outlier: 4.262A pdb=" N SER E 268 " --> pdb=" O MET E 264 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N PHE E 269 " --> pdb=" O SER E 265 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N TRP E 270 " --> pdb=" O TRP E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 300 removed outlier: 3.698A pdb=" N ARG E 298 " --> pdb=" O MET E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 335 Processing helix chain 'E' and resid 425 through 450 removed outlier: 3.541A pdb=" N ALA E 433 " --> pdb=" O ILE E 429 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE E 435 " --> pdb=" O ALA E 431 " (cutoff:3.500A) Proline residue: E 436 - end of helix Processing helix chain 'L' and resid 449 through 451 No H-bonds generated for 'chain 'L' and resid 449 through 451' Processing helix chain 'L' and resid 496 through 498 No H-bonds generated for 'chain 'L' and resid 496 through 498' Processing helix chain 'M' and resid 449 through 451 No H-bonds generated for 'chain 'M' and resid 449 through 451' Processing helix chain 'M' and resid 496 through 498 No H-bonds generated for 'chain 'M' and resid 496 through 498' Processing sheet with id= A, first strand: chain 'A' and resid 200 through 204 removed outlier: 5.958A pdb=" N THR A 72 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N THR A 203 " --> pdb=" O THR A 72 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N VAL A 74 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLU A 73 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ILE A 104 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR A 79 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ASP A 96 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N PHE A 83 " --> pdb=" O THR A 94 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N THR A 94 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N THR A 159 " --> pdb=" O MET A 155 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N PHE A 152 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 132 through 134 removed outlier: 4.272A pdb=" N SER A 192 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE A 244 " --> pdb=" O SER A 192 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY A 228 " --> pdb=" O HIS A 251 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ARG A 253 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N LEU A 226 " --> pdb=" O ARG A 253 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 137 through 142 removed outlier: 6.773A pdb=" N SER A 169 " --> pdb=" O LYS A 138 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER A 140 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N THR A 167 " --> pdb=" O SER A 140 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 164 through 168 removed outlier: 6.220A pdb=" N VAL B 36 " --> pdb=" O GLU B 165 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N TYR B 167 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL B 38 " --> pdb=" O TYR B 167 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N CYS B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILE B 116 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 49 through 51 removed outlier: 3.789A pdb=" N MET B 49 " --> pdb=" O THR B 58 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.609A pdb=" N SER B 156 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU B 190 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LYS B 215 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ILE B 188 " --> pdb=" O LYS B 215 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 101 through 106 removed outlier: 6.691A pdb=" N THR B 133 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N SER B 104 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N THR B 131 " --> pdb=" O SER B 104 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 164 through 168 removed outlier: 6.220A pdb=" N VAL C 36 " --> pdb=" O GLU C 165 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N TYR C 167 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL C 38 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N CYS C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ARG C 68 " --> pdb=" O CYS C 37 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE C 116 " --> pdb=" O LEU C 83 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 49 through 51 removed outlier: 3.788A pdb=" N MET C 49 " --> pdb=" O THR C 58 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.609A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU C 190 " --> pdb=" O ARG C 213 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LYS C 215 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ILE C 188 " --> pdb=" O LYS C 215 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 101 through 106 removed outlier: 6.691A pdb=" N THR C 133 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N SER C 104 " --> pdb=" O THR C 131 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N THR C 131 " --> pdb=" O SER C 104 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 164 through 168 removed outlier: 6.220A pdb=" N VAL D 36 " --> pdb=" O GLU D 165 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N TYR D 167 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL D 38 " --> pdb=" O TYR D 167 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N CYS D 37 " --> pdb=" O ARG D 68 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ARG D 68 " --> pdb=" O CYS D 37 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N THR D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR D 58 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILE D 116 " --> pdb=" O LEU D 83 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 49 through 51 removed outlier: 3.789A pdb=" N MET D 49 " --> pdb=" O THR D 58 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 96 through 98 removed outlier: 3.609A pdb=" N SER D 156 " --> pdb=" O PRO D 206 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU D 190 " --> pdb=" O ARG D 213 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LYS D 215 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ILE D 188 " --> pdb=" O LYS D 215 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 101 through 106 removed outlier: 6.691A pdb=" N THR D 133 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N SER D 104 " --> pdb=" O THR D 131 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N THR D 131 " --> pdb=" O SER D 104 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 192 through 196 removed outlier: 6.047A pdb=" N VAL E 64 " --> pdb=" O VAL E 193 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N TYR E 195 " --> pdb=" O VAL E 64 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N VAL E 66 " --> pdb=" O TYR E 195 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ASN E 65 " --> pdb=" O ARG E 96 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ARG E 96 " --> pdb=" O ASN E 65 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N THR E 88 " --> pdb=" O ALA E 73 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ILE E 75 " --> pdb=" O THR E 86 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N THR E 86 " --> pdb=" O ILE E 75 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 124 through 126 removed outlier: 3.996A pdb=" N SER E 218 " --> pdb=" O HIS E 242 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ARG E 244 " --> pdb=" O ILE E 216 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N ILE E 216 " --> pdb=" O ARG E 244 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 129 through 134 removed outlier: 6.770A pdb=" N THR E 161 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ALA E 132 " --> pdb=" O THR E 159 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N THR E 159 " --> pdb=" O ALA E 132 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'L' and resid 2 through 7 Processing sheet with id= T, first strand: chain 'L' and resid 506 through 508 removed outlier: 3.506A pdb=" N ILE L 420 " --> pdb=" O LYS L 486 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ARG L 425 " --> pdb=" O PHE L 434 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N PHE L 434 " --> pdb=" O ARG L 425 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'L' and resid 484 through 486 removed outlier: 3.984A pdb=" N TYR L 501 " --> pdb=" O ALA L 485 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'M' and resid 2 through 7 Processing sheet with id= W, first strand: chain 'M' and resid 506 through 508 removed outlier: 3.506A pdb=" N ILE M 420 " --> pdb=" O LYS M 486 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ARG M 425 " --> pdb=" O PHE M 434 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N PHE M 434 " --> pdb=" O ARG M 425 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'M' and resid 484 through 486 removed outlier: 3.984A pdb=" N TYR M 501 " --> pdb=" O ALA M 485 " (cutoff:3.500A) 710 hydrogen bonds defined for protein. 2033 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: 5.07 Time building geometry restraints manager: 6.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4782 1.34 - 1.46: 4108 1.46 - 1.58: 7050 1.58 - 1.69: 0 1.69 - 1.81: 159 Bond restraints: 16099 Sorted by residual: bond pdb=" C1 BMA a 3 " pdb=" C2 BMA a 3 " ideal model delta sigma weight residual 1.519 1.548 -0.029 2.00e-02 2.50e+03 2.10e+00 bond pdb=" C1 MAN F 5 " pdb=" O5 MAN F 5 " ideal model delta sigma weight residual 1.399 1.428 -0.029 2.00e-02 2.50e+03 2.08e+00 bond pdb=" C1 MAN F 4 " pdb=" O5 MAN F 4 " ideal model delta sigma weight residual 1.399 1.428 -0.029 2.00e-02 2.50e+03 2.06e+00 bond pdb=" C1 MAN H 5 " pdb=" O5 MAN H 5 " ideal model delta sigma weight residual 1.399 1.428 -0.029 2.00e-02 2.50e+03 2.05e+00 bond pdb=" C1 MAN G 5 " pdb=" O5 MAN G 5 " ideal model delta sigma weight residual 1.399 1.428 -0.029 2.00e-02 2.50e+03 2.04e+00 ... (remaining 16094 not shown) Histogram of bond angle deviations from ideal: 99.32 - 106.25: 392 106.25 - 113.18: 8758 113.18 - 120.11: 5399 120.11 - 127.04: 7138 127.04 - 133.98: 185 Bond angle restraints: 21872 Sorted by residual: angle pdb=" C TYR B 304 " pdb=" N ILE B 305 " pdb=" CA ILE B 305 " ideal model delta sigma weight residual 121.85 116.69 5.16 1.19e+00 7.06e-01 1.88e+01 angle pdb=" C TYR C 304 " pdb=" N ILE C 305 " pdb=" CA ILE C 305 " ideal model delta sigma weight residual 121.85 116.71 5.14 1.19e+00 7.06e-01 1.87e+01 angle pdb=" C TYR D 304 " pdb=" N ILE D 305 " pdb=" CA ILE D 305 " ideal model delta sigma weight residual 121.85 116.71 5.14 1.19e+00 7.06e-01 1.86e+01 angle pdb=" C HIS B 267 " pdb=" N LEU B 268 " pdb=" CA LEU B 268 " ideal model delta sigma weight residual 120.38 125.22 -4.84 1.37e+00 5.33e-01 1.25e+01 angle pdb=" C HIS D 267 " pdb=" N LEU D 268 " pdb=" CA LEU D 268 " ideal model delta sigma weight residual 120.38 125.20 -4.82 1.37e+00 5.33e-01 1.24e+01 ... (remaining 21867 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.75: 9339 21.75 - 43.49: 325 43.49 - 65.24: 35 65.24 - 86.99: 35 86.99 - 108.73: 19 Dihedral angle restraints: 9753 sinusoidal: 4188 harmonic: 5565 Sorted by residual: dihedral pdb=" CA SER B 46 " pdb=" C SER B 46 " pdb=" N ILE B 47 " pdb=" CA ILE B 47 " ideal model delta harmonic sigma weight residual 180.00 154.79 25.21 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA SER D 46 " pdb=" C SER D 46 " pdb=" N ILE D 47 " pdb=" CA ILE D 47 " ideal model delta harmonic sigma weight residual 180.00 154.84 25.16 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA SER C 46 " pdb=" C SER C 46 " pdb=" N ILE C 47 " pdb=" CA ILE C 47 " ideal model delta harmonic sigma weight residual 180.00 154.88 25.12 0 5.00e+00 4.00e-02 2.52e+01 ... (remaining 9750 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 2091 0.058 - 0.116: 374 0.116 - 0.174: 33 0.174 - 0.231: 7 0.231 - 0.289: 5 Chirality restraints: 2510 Sorted by residual: chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-02 2.50e+03 8.63e+01 chirality pdb=" C1 BMA G 3 " pdb=" O4 NAG G 2 " pdb=" C2 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.51e+01 chirality pdb=" C1 BMA H 3 " pdb=" O4 NAG H 2 " pdb=" C2 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.52e+01 ... (remaining 2507 not shown) Planarity restraints: 2691 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 157 " 0.007 2.00e-02 2.50e+03 1.53e-02 4.68e+00 pdb=" CG TYR C 157 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR C 157 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR C 157 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C 157 " -0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR C 157 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR C 157 " -0.020 2.00e-02 2.50e+03 pdb=" OH TYR C 157 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 157 " -0.007 2.00e-02 2.50e+03 1.53e-02 4.66e+00 pdb=" CG TYR B 157 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR B 157 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR B 157 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR B 157 " 0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR B 157 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR B 157 " 0.020 2.00e-02 2.50e+03 pdb=" OH TYR B 157 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 157 " 0.006 2.00e-02 2.50e+03 1.52e-02 4.61e+00 pdb=" CG TYR D 157 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR D 157 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR D 157 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR D 157 " -0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR D 157 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR D 157 " -0.021 2.00e-02 2.50e+03 pdb=" OH TYR D 157 " 0.022 2.00e-02 2.50e+03 ... (remaining 2688 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 417 2.71 - 3.26: 15601 3.26 - 3.81: 26381 3.81 - 4.35: 34076 4.35 - 4.90: 56262 Nonbonded interactions: 132737 Sorted by model distance: nonbonded pdb=" O TRP M 440 " pdb=" NH1 ARG M 459 " model vdw 2.164 2.520 nonbonded pdb=" O TRP L 440 " pdb=" NH1 ARG L 459 " model vdw 2.165 2.520 nonbonded pdb=" OG1 THR E 215 " pdb=" OD1 ASN E 246 " model vdw 2.224 2.440 nonbonded pdb=" O VAL A 290 " pdb=" OG1 THR A 294 " model vdw 2.257 2.440 nonbonded pdb=" O SER A 305 " pdb=" ND1 HIS A 308 " model vdw 2.267 2.520 ... (remaining 132732 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B' and resid 8 through 447) selection = (chain 'C' and resid 8 through 447) selection = (chain 'D' and resid 8 through 447) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'L' selection = chain 'M' } ncs_group { reference = chain 'b' selection = chain 'c' selection = chain 'd' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 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: 0.020 Extract box with map and model: 5.900 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 45.810 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.120 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:12.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 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 : 0.003 0.034 16099 Z= 0.204 Angle : 0.636 6.387 21872 Z= 0.335 Chirality : 0.046 0.289 2510 Planarity : 0.005 0.058 2682 Dihedral : 13.258 108.734 6168 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.48 % Allowed : 3.60 % Favored : 95.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.28 % 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: 0.56 (0.19), residues: 1863 helix: 0.70 (0.20), residues: 573 sheet: 0.37 (0.24), residues: 453 loop : 0.33 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 440 HIS 0.004 0.001 HIS D 267 PHE 0.017 0.001 PHE D 306 TYR 0.022 0.004 TYR B 157 ARG 0.014 0.002 ARG D 28 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 427 time to evaluate : 1.799 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 TRP cc_start: 0.7080 (m-10) cc_final: 0.6471 (m100) REVERT: B 13 LYS cc_start: 0.9000 (tttt) cc_final: 0.8686 (ttpp) REVERT: B 215 LYS cc_start: 0.9016 (tttt) cc_final: 0.8781 (ttmm) REVERT: B 298 GLU cc_start: 0.8864 (tm-30) cc_final: 0.8568 (tm-30) REVERT: B 306 PHE cc_start: 0.7427 (t80) cc_final: 0.7067 (t80) REVERT: C 9 MET cc_start: 0.8505 (mtp) cc_final: 0.8185 (mtt) REVERT: C 90 GLN cc_start: 0.8970 (mp10) cc_final: 0.8271 (mp10) REVERT: C 230 ILE cc_start: 0.9663 (mt) cc_final: 0.9431 (mp) REVERT: D 13 LYS cc_start: 0.9103 (tttt) cc_final: 0.8671 (tmmt) REVERT: D 190 GLU cc_start: 0.8018 (tt0) cc_final: 0.7741 (tt0) REVERT: D 214 LEU cc_start: 0.8965 (mt) cc_final: 0.8748 (mt) REVERT: D 215 LYS cc_start: 0.8822 (tttt) cc_final: 0.8133 (ttmm) REVERT: D 223 LEU cc_start: 0.9025 (mt) cc_final: 0.8235 (tp) REVERT: D 230 ILE cc_start: 0.9604 (mt) cc_final: 0.9399 (mp) REVERT: D 306 PHE cc_start: 0.7580 (t80) cc_final: 0.7085 (t80) REVERT: D 433 PHE cc_start: 0.8640 (t80) cc_final: 0.8415 (t80) REVERT: E 203 ILE cc_start: 0.8721 (pp) cc_final: 0.8493 (pp) REVERT: E 250 TYR cc_start: 0.7105 (p90) cc_final: 0.6874 (p90) REVERT: E 334 ASN cc_start: 0.8913 (m-40) cc_final: 0.8631 (m110) REVERT: L 3 GLN cc_start: 0.8303 (mp10) cc_final: 0.6900 (mp10) REVERT: L 468 LEU cc_start: 0.8918 (tp) cc_final: 0.8582 (tt) REVERT: L 472 ASN cc_start: 0.8462 (t0) cc_final: 0.7939 (t0) REVERT: M 468 LEU cc_start: 0.8661 (tp) cc_final: 0.8450 (tp) REVERT: M 472 ASN cc_start: 0.8723 (t0) cc_final: 0.7843 (t0) REVERT: M 482 TYR cc_start: 0.8582 (m-80) cc_final: 0.8359 (m-80) outliers start: 8 outliers final: 3 residues processed: 431 average time/residue: 1.4208 time to fit residues: 667.4837 Evaluate side-chains 254 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 251 time to evaluate : 1.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain L residue 459 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 9.9990 chunk 142 optimal weight: 4.9990 chunk 79 optimal weight: 0.1980 chunk 48 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 147 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 chunk 109 optimal weight: 3.9990 chunk 170 optimal weight: 9.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN A 149 ASN A 345 ASN ** B 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 GLN D 185 GLN ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN E 77 HIS ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 GLN E 233 GLN E 240 HIS ** E 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 443 ASN ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 472 ASN M 3 GLN ** M 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 16099 Z= 0.363 Angle : 0.662 13.499 21872 Z= 0.346 Chirality : 0.045 0.159 2510 Planarity : 0.004 0.054 2682 Dihedral : 8.941 78.382 2673 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 3.84 % Allowed : 14.17 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.28 % 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: 1.31 (0.20), residues: 1863 helix: 1.79 (0.21), residues: 576 sheet: 0.38 (0.24), residues: 478 loop : 0.67 (0.23), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP E 315 HIS 0.008 0.002 HIS E 77 PHE 0.027 0.002 PHE B 293 TYR 0.027 0.002 TYR B 299 ARG 0.010 0.001 ARG E 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 262 time to evaluate : 1.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 MET cc_start: 0.8382 (mtm) cc_final: 0.8061 (mmm) REVERT: A 92 GLU cc_start: 0.8005 (pt0) cc_final: 0.7750 (pm20) REVERT: A 321 TRP cc_start: 0.7184 (m-10) cc_final: 0.6530 (m100) REVERT: A 335 ILE cc_start: 0.9452 (mm) cc_final: 0.9229 (mm) REVERT: B 13 LYS cc_start: 0.9024 (tttt) cc_final: 0.8698 (ttpp) REVERT: B 190 GLU cc_start: 0.7801 (tt0) cc_final: 0.7439 (pt0) REVERT: B 215 LYS cc_start: 0.9070 (tttt) cc_final: 0.8799 (ttmm) REVERT: B 269 ARG cc_start: 0.8333 (ptm160) cc_final: 0.8015 (ptm160) REVERT: B 298 GLU cc_start: 0.9042 (tm-30) cc_final: 0.8834 (tm-30) REVERT: B 306 PHE cc_start: 0.7733 (t80) cc_final: 0.7011 (t80) REVERT: C 9 MET cc_start: 0.8571 (mtp) cc_final: 0.8229 (mtt) REVERT: C 13 LYS cc_start: 0.9086 (tttp) cc_final: 0.8884 (ttpp) REVERT: C 90 GLN cc_start: 0.8959 (mp10) cc_final: 0.8209 (mp10) REVERT: C 230 ILE cc_start: 0.9627 (mt) cc_final: 0.9419 (mp) REVERT: C 286 MET cc_start: 0.8495 (mmp) cc_final: 0.8218 (mmm) REVERT: C 306 PHE cc_start: 0.7861 (t80) cc_final: 0.7566 (t80) REVERT: D 13 LYS cc_start: 0.9336 (tttt) cc_final: 0.8616 (tmmt) REVERT: D 21 LYS cc_start: 0.8285 (mmmm) cc_final: 0.7980 (mmmm) REVERT: D 147 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7239 (mm-30) REVERT: D 190 GLU cc_start: 0.8115 (tt0) cc_final: 0.7853 (tt0) REVERT: D 215 LYS cc_start: 0.8960 (tttt) cc_final: 0.8459 (ttmm) REVERT: D 243 ASN cc_start: 0.7953 (t0) cc_final: 0.7705 (t0) REVERT: D 306 PHE cc_start: 0.7466 (t80) cc_final: 0.6729 (t80) REVERT: E 118 LYS cc_start: 0.8930 (mmtm) cc_final: 0.8356 (mppt) REVERT: L 472 ASN cc_start: 0.8727 (t0) cc_final: 0.8262 (t0) REVERT: M 11 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.7265 (tm) REVERT: M 452 LYS cc_start: 0.8776 (ttmm) cc_final: 0.8494 (ttmm) REVERT: M 472 ASN cc_start: 0.8878 (t0) cc_final: 0.8295 (t0) REVERT: M 473 LEU cc_start: 0.9380 (mt) cc_final: 0.9088 (mm) REVERT: M 474 LYS cc_start: 0.8570 (mmmt) cc_final: 0.8304 (mmmt) outliers start: 64 outliers final: 21 residues processed: 297 average time/residue: 1.4174 time to fit residues: 460.4017 Evaluate side-chains 246 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 224 time to evaluate : 1.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain E residue 227 ASN Chi-restraints excluded: chain L residue 449 ASP Chi-restraints excluded: chain L residue 456 THR Chi-restraints excluded: chain L residue 477 ASP Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 445 THR Chi-restraints excluded: chain M residue 449 ASP Chi-restraints excluded: chain M residue 477 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 chunk 142 optimal weight: 0.2980 chunk 116 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 171 optimal weight: 6.9990 chunk 184 optimal weight: 3.9990 chunk 152 optimal weight: 0.0970 chunk 169 optimal weight: 9.9990 chunk 58 optimal weight: 0.8980 chunk 137 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 ASN B 303 ASN ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 141 ASN ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 GLN E 253 GLN L 1 GLN L 3 GLN M 3 GLN ** M 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16099 Z= 0.163 Angle : 0.577 10.218 21872 Z= 0.295 Chirality : 0.043 0.205 2510 Planarity : 0.003 0.034 2682 Dihedral : 7.260 69.725 2666 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.70 % Allowed : 15.43 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.28 % 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: 1.48 (0.20), residues: 1863 helix: 1.91 (0.22), residues: 570 sheet: 0.49 (0.23), residues: 482 loop : 0.79 (0.23), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP E 315 HIS 0.005 0.001 HIS A 308 PHE 0.016 0.001 PHE B 306 TYR 0.025 0.001 TYR B 299 ARG 0.008 0.000 ARG E 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 256 time to evaluate : 3.372 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 MET cc_start: 0.8403 (mtm) cc_final: 0.8127 (mmm) REVERT: A 262 GLN cc_start: 0.9040 (mm-40) cc_final: 0.8510 (mm-40) REVERT: A 282 LYS cc_start: 0.9206 (OUTLIER) cc_final: 0.8605 (ptpp) REVERT: A 321 TRP cc_start: 0.7139 (m-10) cc_final: 0.6478 (m100) REVERT: A 335 ILE cc_start: 0.9432 (mm) cc_final: 0.9223 (mm) REVERT: B 13 LYS cc_start: 0.9022 (tttt) cc_final: 0.8676 (ttpp) REVERT: B 48 ASP cc_start: 0.8572 (OUTLIER) cc_final: 0.8359 (m-30) REVERT: B 49 MET cc_start: 0.7983 (ttp) cc_final: 0.7694 (tmm) REVERT: B 215 LYS cc_start: 0.9034 (tttt) cc_final: 0.8750 (ttmm) REVERT: B 244 TYR cc_start: 0.8446 (p90) cc_final: 0.8202 (p90) REVERT: B 269 ARG cc_start: 0.8459 (ptm160) cc_final: 0.7672 (ttm-80) REVERT: B 274 LYS cc_start: 0.8810 (ttmm) cc_final: 0.8590 (ttmm) REVERT: B 306 PHE cc_start: 0.7546 (t80) cc_final: 0.7258 (t80) REVERT: C 9 MET cc_start: 0.8547 (mtp) cc_final: 0.8318 (ttm) REVERT: C 90 GLN cc_start: 0.8971 (mp10) cc_final: 0.8204 (mp10) REVERT: D 13 LYS cc_start: 0.9281 (tttt) cc_final: 0.8681 (tmmt) REVERT: D 21 LYS cc_start: 0.8473 (mmmm) cc_final: 0.8226 (mmmm) REVERT: D 147 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7379 (mm-30) REVERT: D 215 LYS cc_start: 0.8939 (tttt) cc_final: 0.8439 (tttp) REVERT: D 243 ASN cc_start: 0.8081 (t0) cc_final: 0.7707 (t0) REVERT: E 118 LYS cc_start: 0.9028 (mmtm) cc_final: 0.8629 (mmtp) REVERT: E 142 LYS cc_start: 0.8953 (mtmt) cc_final: 0.8703 (mtmm) REVERT: E 233 GLN cc_start: 0.7535 (OUTLIER) cc_final: 0.7296 (tp40) REVERT: L 3 GLN cc_start: 0.8118 (mp-120) cc_final: 0.7757 (mp10) REVERT: L 472 ASN cc_start: 0.8732 (t0) cc_final: 0.8348 (t0) REVERT: M 11 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.7010 (tm) REVERT: M 472 ASN cc_start: 0.8941 (t0) cc_final: 0.8352 (t0) REVERT: M 473 LEU cc_start: 0.9421 (mt) cc_final: 0.8996 (mm) REVERT: M 474 LYS cc_start: 0.8692 (mmmt) cc_final: 0.8456 (mmmt) outliers start: 45 outliers final: 13 residues processed: 281 average time/residue: 1.3433 time to fit residues: 415.0306 Evaluate side-chains 243 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 226 time to evaluate : 1.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain B residue 48 ASP Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain C residue 37 CYS Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain E residue 233 GLN Chi-restraints excluded: chain E residue 253 GLN Chi-restraints excluded: chain L residue 456 THR Chi-restraints excluded: chain L residue 477 ASP Chi-restraints excluded: chain M residue 11 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 6.9990 chunk 128 optimal weight: 6.9990 chunk 88 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 171 optimal weight: 6.9990 chunk 181 optimal weight: 9.9990 chunk 89 optimal weight: 0.8980 chunk 162 optimal weight: 4.9990 chunk 48 optimal weight: 7.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 ASN C 303 ASN ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 GLN E 253 GLN ** L 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 1 GLN M 3 GLN ** M 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 16099 Z= 0.332 Angle : 0.621 9.556 21872 Z= 0.319 Chirality : 0.044 0.215 2510 Planarity : 0.004 0.051 2682 Dihedral : 6.724 66.014 2666 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.00 % Allowed : 15.49 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.28 % 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: 1.38 (0.20), residues: 1863 helix: 1.81 (0.22), residues: 576 sheet: 0.41 (0.23), residues: 492 loop : 0.75 (0.24), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 315 HIS 0.004 0.001 HIS C 267 PHE 0.019 0.002 PHE C 293 TYR 0.030 0.002 TYR B 299 ARG 0.010 0.001 ARG E 114 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 247 time to evaluate : 1.816 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: symmetry clash revert: symmetry clash REVERT: A 282 LYS cc_start: 0.9211 (OUTLIER) cc_final: 0.8613 (ptpp) REVERT: A 321 TRP cc_start: 0.7159 (m-10) cc_final: 0.6485 (m100) REVERT: B 13 LYS cc_start: 0.9089 (tttt) cc_final: 0.8740 (ttpp) REVERT: B 49 MET cc_start: 0.8013 (ttp) cc_final: 0.7665 (tmm) REVERT: B 215 LYS cc_start: 0.9087 (tttt) cc_final: 0.8815 (ttmm) REVERT: B 244 TYR cc_start: 0.8638 (p90) cc_final: 0.8350 (p90) REVERT: B 269 ARG cc_start: 0.8419 (ptm160) cc_final: 0.7601 (ttm-80) REVERT: B 274 LYS cc_start: 0.8879 (ttmm) cc_final: 0.8618 (ttmm) REVERT: B 306 PHE cc_start: 0.7671 (t80) cc_final: 0.7344 (t80) REVERT: C 9 MET cc_start: 0.8585 (mtp) cc_final: 0.8306 (ttm) REVERT: C 84 ASP cc_start: 0.8051 (t70) cc_final: 0.7820 (t70) REVERT: C 90 GLN cc_start: 0.8934 (mp10) cc_final: 0.8094 (mp10) REVERT: D 13 LYS cc_start: 0.9280 (tttt) cc_final: 0.8658 (tmmt) REVERT: D 21 LYS cc_start: 0.8507 (mmmm) cc_final: 0.8278 (mmmm) REVERT: D 147 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7335 (mm-30) REVERT: D 215 LYS cc_start: 0.8979 (tttt) cc_final: 0.8582 (ttmm) REVERT: D 243 ASN cc_start: 0.8133 (t0) cc_final: 0.7699 (t0) REVERT: L 3 GLN cc_start: 0.8341 (mp-120) cc_final: 0.7823 (mp10) REVERT: L 472 ASN cc_start: 0.8839 (t0) cc_final: 0.8450 (t0) REVERT: M 11 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.7133 (tm) REVERT: M 472 ASN cc_start: 0.9059 (t0) cc_final: 0.8625 (t0) outliers start: 50 outliers final: 14 residues processed: 274 average time/residue: 1.4259 time to fit residues: 427.6644 Evaluate side-chains 240 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 224 time to evaluate : 1.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain E residue 253 GLN Chi-restraints excluded: chain L residue 456 THR Chi-restraints excluded: chain L residue 477 ASP Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 477 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 135 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 125 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 92 optimal weight: 0.2980 chunk 163 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 ASN ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN ** M 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 16099 Z= 0.202 Angle : 0.590 14.030 21872 Z= 0.299 Chirality : 0.043 0.221 2510 Planarity : 0.003 0.026 2682 Dihedral : 6.267 60.850 2666 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.76 % Allowed : 16.93 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.28 % 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: 1.42 (0.20), residues: 1863 helix: 1.83 (0.22), residues: 575 sheet: 0.51 (0.23), residues: 492 loop : 0.74 (0.24), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 315 HIS 0.003 0.001 HIS A 308 PHE 0.022 0.001 PHE C 306 TYR 0.026 0.001 TYR D 299 ARG 0.005 0.000 ARG L 459 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 246 time to evaluate : 1.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 CYS cc_start: 0.8928 (m) cc_final: 0.8646 (m) REVERT: A 282 LYS cc_start: 0.9180 (OUTLIER) cc_final: 0.8598 (ptpp) REVERT: A 321 TRP cc_start: 0.7170 (m-10) cc_final: 0.6505 (m100) REVERT: B 49 MET cc_start: 0.8032 (ttp) cc_final: 0.7723 (tmm) REVERT: B 190 GLU cc_start: 0.7908 (tt0) cc_final: 0.7349 (pt0) REVERT: B 244 TYR cc_start: 0.8643 (p90) cc_final: 0.8342 (p90) REVERT: B 269 ARG cc_start: 0.8470 (ptm160) cc_final: 0.8254 (ttm-80) REVERT: B 274 LYS cc_start: 0.8797 (ttmm) cc_final: 0.8552 (tmtp) REVERT: B 306 PHE cc_start: 0.7573 (t80) cc_final: 0.7271 (t80) REVERT: C 9 MET cc_start: 0.8521 (mtp) cc_final: 0.8295 (ttm) REVERT: C 84 ASP cc_start: 0.8029 (t70) cc_final: 0.7794 (t70) REVERT: C 90 GLN cc_start: 0.8943 (mp10) cc_final: 0.8107 (mp10) REVERT: C 424 ASP cc_start: 0.9007 (m-30) cc_final: 0.8710 (m-30) REVERT: D 13 LYS cc_start: 0.9275 (tttt) cc_final: 0.8648 (tmmt) REVERT: D 21 LYS cc_start: 0.8508 (mmmm) cc_final: 0.8252 (mmmm) REVERT: D 102 LYS cc_start: 0.9213 (OUTLIER) cc_final: 0.8895 (mtmt) REVERT: D 147 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7306 (mm-30) REVERT: D 215 LYS cc_start: 0.8964 (tttt) cc_final: 0.8571 (ttmm) REVERT: D 243 ASN cc_start: 0.8121 (t0) cc_final: 0.7631 (t0) REVERT: D 269 ARG cc_start: 0.6568 (tmm160) cc_final: 0.5357 (tmt-80) REVERT: E 118 LYS cc_start: 0.9116 (mmtm) cc_final: 0.8800 (mmtm) REVERT: E 142 LYS cc_start: 0.8955 (mtmt) cc_final: 0.8719 (mtmm) REVERT: E 233 GLN cc_start: 0.7369 (tp40) cc_final: 0.6959 (tp-100) REVERT: L 3 GLN cc_start: 0.8357 (mp-120) cc_final: 0.7922 (mp10) REVERT: L 472 ASN cc_start: 0.8872 (t0) cc_final: 0.8543 (t0) REVERT: M 11 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.7145 (tm) REVERT: M 455 PHE cc_start: 0.8265 (m-10) cc_final: 0.7978 (m-10) REVERT: M 469 GLU cc_start: 0.7357 (mp0) cc_final: 0.7153 (mp0) REVERT: M 472 ASN cc_start: 0.9075 (t0) cc_final: 0.8716 (t0) outliers start: 46 outliers final: 14 residues processed: 270 average time/residue: 1.4190 time to fit residues: 419.3731 Evaluate side-chains 252 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 235 time to evaluate : 1.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain D residue 102 LYS Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain E residue 264 MET Chi-restraints excluded: chain L residue 456 THR Chi-restraints excluded: chain L residue 460 ASP Chi-restraints excluded: chain L residue 474 LYS Chi-restraints excluded: chain L residue 477 ASP Chi-restraints excluded: chain M residue 11 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 0.8980 chunk 163 optimal weight: 3.9990 chunk 35 optimal weight: 0.0000 chunk 106 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 181 optimal weight: 9.9990 chunk 150 optimal weight: 9.9990 chunk 84 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 ASN ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 1 GLN M 3 GLN ** M 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16099 Z= 0.259 Angle : 0.605 9.425 21872 Z= 0.309 Chirality : 0.043 0.220 2510 Planarity : 0.003 0.050 2682 Dihedral : 6.101 57.981 2666 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.52 % Allowed : 17.17 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.28 % 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: 1.35 (0.20), residues: 1863 helix: 1.75 (0.22), residues: 576 sheet: 0.41 (0.23), residues: 504 loop : 0.78 (0.24), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP L 440 HIS 0.004 0.001 HIS A 308 PHE 0.026 0.002 PHE C 293 TYR 0.028 0.002 TYR D 299 ARG 0.014 0.001 ARG E 114 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 241 time to evaluate : 1.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 CYS cc_start: 0.8906 (m) cc_final: 0.8616 (m) REVERT: A 282 LYS cc_start: 0.9184 (OUTLIER) cc_final: 0.8578 (ptpp) REVERT: A 321 TRP cc_start: 0.7218 (m-10) cc_final: 0.6523 (m100) REVERT: B 49 MET cc_start: 0.8048 (ttp) cc_final: 0.7760 (tmm) REVERT: B 190 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7331 (pt0) REVERT: B 244 TYR cc_start: 0.8676 (p90) cc_final: 0.8350 (p90) REVERT: B 269 ARG cc_start: 0.8475 (ptm160) cc_final: 0.7955 (ttm-80) REVERT: B 274 LYS cc_start: 0.8810 (ttmm) cc_final: 0.8561 (tmtp) REVERT: B 306 PHE cc_start: 0.7634 (t80) cc_final: 0.7372 (t80) REVERT: C 9 MET cc_start: 0.8490 (mtp) cc_final: 0.8233 (ttm) REVERT: C 84 ASP cc_start: 0.8069 (t70) cc_final: 0.7833 (t70) REVERT: C 90 GLN cc_start: 0.8929 (mp10) cc_final: 0.8076 (mp10) REVERT: C 102 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.8585 (mtmt) REVERT: C 297 LEU cc_start: 0.9400 (mp) cc_final: 0.9137 (mp) REVERT: C 424 ASP cc_start: 0.9003 (m-30) cc_final: 0.8717 (m-30) REVERT: D 13 LYS cc_start: 0.9277 (tttt) cc_final: 0.8636 (tmmt) REVERT: D 21 LYS cc_start: 0.8556 (mmmm) cc_final: 0.8304 (mmmm) REVERT: D 102 LYS cc_start: 0.9236 (OUTLIER) cc_final: 0.8909 (mtmt) REVERT: D 147 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7352 (mm-30) REVERT: D 182 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7372 (mm-30) REVERT: D 215 LYS cc_start: 0.8980 (tttt) cc_final: 0.8473 (ttmm) REVERT: D 243 ASN cc_start: 0.8130 (t0) cc_final: 0.7639 (t0) REVERT: E 142 LYS cc_start: 0.8939 (mtmt) cc_final: 0.8699 (mtmm) REVERT: E 233 GLN cc_start: 0.7423 (tp40) cc_final: 0.7036 (tp-100) REVERT: E 250 TYR cc_start: 0.7279 (p90) cc_final: 0.6487 (p90) REVERT: L 3 GLN cc_start: 0.8433 (mp-120) cc_final: 0.8025 (mp10) REVERT: L 472 ASN cc_start: 0.8893 (t0) cc_final: 0.8542 (t0) REVERT: M 11 LEU cc_start: 0.7632 (OUTLIER) cc_final: 0.7334 (tm) REVERT: M 455 PHE cc_start: 0.8302 (m-10) cc_final: 0.8100 (m-10) REVERT: M 460 ASP cc_start: 0.7660 (p0) cc_final: 0.6679 (p0) REVERT: M 469 GLU cc_start: 0.7473 (mp0) cc_final: 0.7172 (mp0) REVERT: M 472 ASN cc_start: 0.9102 (t0) cc_final: 0.7787 (t0) REVERT: M 474 LYS cc_start: 0.8378 (mmmt) cc_final: 0.8151 (mmpt) outliers start: 42 outliers final: 16 residues processed: 263 average time/residue: 1.3909 time to fit residues: 400.4364 Evaluate side-chains 253 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 232 time to evaluate : 1.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain C residue 102 LYS Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 102 LYS Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 118 LYS Chi-restraints excluded: chain L residue 456 THR Chi-restraints excluded: chain L residue 460 ASP Chi-restraints excluded: chain L residue 474 LYS Chi-restraints excluded: chain L residue 477 ASP Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 477 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 132 optimal weight: 9.9990 chunk 102 optimal weight: 5.9990 chunk 153 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 181 optimal weight: 8.9990 chunk 113 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN A 345 ASN B 224 GLN ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN ** M 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16099 Z= 0.274 Angle : 0.621 9.826 21872 Z= 0.315 Chirality : 0.044 0.220 2510 Planarity : 0.003 0.046 2682 Dihedral : 5.973 55.472 2666 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.58 % Allowed : 17.23 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.28 % 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: 1.30 (0.20), residues: 1863 helix: 1.72 (0.22), residues: 575 sheet: 0.51 (0.24), residues: 492 loop : 0.62 (0.24), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP L 440 HIS 0.004 0.001 HIS A 308 PHE 0.022 0.001 PHE D 306 TYR 0.028 0.002 TYR D 299 ARG 0.012 0.000 ARG A 307 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 239 time to evaluate : 1.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 MET cc_start: 0.8378 (mtp) cc_final: 0.8157 (mmm) REVERT: A 262 GLN cc_start: 0.8873 (mt0) cc_final: 0.8579 (mt0) REVERT: A 267 CYS cc_start: 0.8905 (m) cc_final: 0.8640 (m) REVERT: A 273 LEU cc_start: 0.9577 (mt) cc_final: 0.9291 (mt) REVERT: A 282 LYS cc_start: 0.9181 (OUTLIER) cc_final: 0.8582 (ptpp) REVERT: A 321 TRP cc_start: 0.7207 (m-10) cc_final: 0.6501 (m100) REVERT: B 49 MET cc_start: 0.8050 (ttp) cc_final: 0.7767 (tmm) REVERT: B 190 GLU cc_start: 0.7929 (tt0) cc_final: 0.7374 (pt0) REVERT: B 269 ARG cc_start: 0.8438 (ptm160) cc_final: 0.8157 (ttm-80) REVERT: B 306 PHE cc_start: 0.7667 (t80) cc_final: 0.7438 (t80) REVERT: C 9 MET cc_start: 0.8501 (mtp) cc_final: 0.8218 (ttm) REVERT: C 84 ASP cc_start: 0.8077 (t70) cc_final: 0.7820 (t70) REVERT: C 90 GLN cc_start: 0.8924 (mp10) cc_final: 0.8008 (mp10) REVERT: C 102 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8537 (mtmt) REVERT: C 424 ASP cc_start: 0.8998 (m-30) cc_final: 0.8709 (m-30) REVERT: D 13 LYS cc_start: 0.9287 (tttt) cc_final: 0.8650 (tmmt) REVERT: D 21 LYS cc_start: 0.8581 (mmmm) cc_final: 0.8338 (mmmm) REVERT: D 102 LYS cc_start: 0.9242 (OUTLIER) cc_final: 0.8919 (mtmt) REVERT: D 147 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7369 (mm-30) REVERT: D 215 LYS cc_start: 0.8986 (tttt) cc_final: 0.8461 (ttmm) REVERT: D 243 ASN cc_start: 0.8142 (t0) cc_final: 0.7649 (t0) REVERT: E 142 LYS cc_start: 0.8933 (mtmt) cc_final: 0.8701 (mtmm) REVERT: E 233 GLN cc_start: 0.7390 (tp40) cc_final: 0.7038 (tp-100) REVERT: L 3 GLN cc_start: 0.8465 (mp-120) cc_final: 0.8051 (mp10) REVERT: L 472 ASN cc_start: 0.8963 (t0) cc_final: 0.8690 (t0) REVERT: M 11 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7355 (tm) REVERT: M 469 GLU cc_start: 0.7546 (mp0) cc_final: 0.7346 (mp0) REVERT: M 472 ASN cc_start: 0.9139 (t0) cc_final: 0.8477 (t0) REVERT: M 474 LYS cc_start: 0.8362 (mmmt) cc_final: 0.8060 (mtpp) outliers start: 43 outliers final: 18 residues processed: 262 average time/residue: 1.3945 time to fit residues: 400.3158 Evaluate side-chains 249 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 227 time to evaluate : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain C residue 102 LYS Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 102 LYS Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 264 MET Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 456 THR Chi-restraints excluded: chain L residue 460 ASP Chi-restraints excluded: chain L residue 474 LYS Chi-restraints excluded: chain L residue 477 ASP Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 477 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 54 optimal weight: 0.0670 chunk 35 optimal weight: 0.6980 chunk 115 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 142 optimal weight: 3.9990 chunk 164 optimal weight: 0.7980 overall best weight: 1.1122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN A 345 ASN B 224 GLN B 243 ASN ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 ASN ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN M 1 GLN M 3 GLN ** M 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16099 Z= 0.199 Angle : 0.621 9.570 21872 Z= 0.314 Chirality : 0.043 0.224 2510 Planarity : 0.004 0.068 2682 Dihedral : 5.777 52.486 2666 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.04 % Allowed : 17.71 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.28 % 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: 1.32 (0.20), residues: 1863 helix: 1.77 (0.22), residues: 572 sheet: 0.44 (0.24), residues: 498 loop : 0.68 (0.24), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP L 440 HIS 0.004 0.001 HIS A 308 PHE 0.024 0.001 PHE M 455 TYR 0.028 0.001 TYR B 299 ARG 0.015 0.000 ARG E 114 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 236 time to evaluate : 1.922 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: A 181 MET cc_start: 0.8441 (mtm) cc_final: 0.8218 (pmm) REVERT: A 262 GLN cc_start: 0.8819 (mt0) cc_final: 0.8600 (mt0) REVERT: A 267 CYS cc_start: 0.8853 (m) cc_final: 0.8605 (m) REVERT: A 282 LYS cc_start: 0.9167 (OUTLIER) cc_final: 0.8584 (ptpp) REVERT: A 321 TRP cc_start: 0.7191 (m-10) cc_final: 0.6489 (m100) REVERT: B 49 MET cc_start: 0.8029 (ttp) cc_final: 0.7757 (tmm) REVERT: B 190 GLU cc_start: 0.7928 (tt0) cc_final: 0.7368 (pt0) REVERT: B 269 ARG cc_start: 0.8395 (ptm160) cc_final: 0.8195 (ttm-80) REVERT: C 9 MET cc_start: 0.8496 (mtp) cc_final: 0.8211 (ttm) REVERT: C 84 ASP cc_start: 0.8036 (t70) cc_final: 0.7790 (t70) REVERT: C 90 GLN cc_start: 0.8918 (mp10) cc_final: 0.8069 (mp10) REVERT: C 102 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8493 (mtmt) REVERT: C 297 LEU cc_start: 0.9359 (mp) cc_final: 0.9111 (mp) REVERT: C 424 ASP cc_start: 0.8939 (m-30) cc_final: 0.8653 (m-30) REVERT: D 13 LYS cc_start: 0.9282 (tttt) cc_final: 0.8640 (tmmt) REVERT: D 21 LYS cc_start: 0.8584 (mmmm) cc_final: 0.8338 (mmmm) REVERT: D 147 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7367 (mm-30) REVERT: D 215 LYS cc_start: 0.8968 (tttt) cc_final: 0.8445 (ttmm) REVERT: D 243 ASN cc_start: 0.8125 (t0) cc_final: 0.7620 (t0) REVERT: E 82 ASN cc_start: 0.8888 (m-40) cc_final: 0.8671 (m-40) REVERT: E 142 LYS cc_start: 0.8906 (mtmt) cc_final: 0.8667 (mtmm) REVERT: E 233 GLN cc_start: 0.7406 (tp40) cc_final: 0.7040 (tp-100) REVERT: L 3 GLN cc_start: 0.8493 (mp10) cc_final: 0.8063 (mp10) REVERT: L 472 ASN cc_start: 0.8964 (t0) cc_final: 0.8687 (t0) REVERT: L 476 GLU cc_start: 0.8439 (mp0) cc_final: 0.8203 (pm20) REVERT: M 11 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7486 (tm) REVERT: M 454 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7592 (ttp80) REVERT: M 460 ASP cc_start: 0.7787 (p0) cc_final: 0.7529 (p0) REVERT: M 469 GLU cc_start: 0.7541 (mp0) cc_final: 0.7195 (mp0) REVERT: M 472 ASN cc_start: 0.9134 (t0) cc_final: 0.8549 (t0) REVERT: M 474 LYS cc_start: 0.8363 (mmmt) cc_final: 0.8137 (mtpp) outliers start: 34 outliers final: 17 residues processed: 257 average time/residue: 1.4097 time to fit residues: 397.9404 Evaluate side-chains 243 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 222 time to evaluate : 2.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain C residue 37 CYS Chi-restraints excluded: chain C residue 102 LYS Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 264 MET Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 456 THR Chi-restraints excluded: chain L residue 460 ASP Chi-restraints excluded: chain L residue 474 LYS Chi-restraints excluded: chain L residue 477 ASP Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 454 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 9.9990 chunk 158 optimal weight: 3.9990 chunk 168 optimal weight: 9.9990 chunk 101 optimal weight: 0.1980 chunk 73 optimal weight: 10.0000 chunk 132 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 152 optimal weight: 6.9990 chunk 159 optimal weight: 0.9980 chunk 110 optimal weight: 6.9990 chunk 178 optimal weight: 7.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN A 345 ASN B 224 GLN ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN ** M 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 16099 Z= 0.309 Angle : 0.645 10.320 21872 Z= 0.329 Chirality : 0.044 0.219 2510 Planarity : 0.003 0.057 2682 Dihedral : 5.833 51.700 2666 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.10 % Allowed : 18.25 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.28 % 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 (0.20), residues: 1863 helix: 1.69 (0.22), residues: 571 sheet: 0.39 (0.24), residues: 498 loop : 0.64 (0.24), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP L 440 HIS 0.003 0.001 HIS A 308 PHE 0.025 0.002 PHE C 307 TYR 0.030 0.002 TYR D 299 ARG 0.013 0.000 ARG A 307 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 227 time to evaluate : 1.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 MET cc_start: 0.8406 (mtm) cc_final: 0.8156 (pmm) REVERT: A 262 GLN cc_start: 0.8753 (mt0) cc_final: 0.8535 (mt0) REVERT: A 267 CYS cc_start: 0.8798 (m) cc_final: 0.8543 (m) REVERT: A 282 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8597 (ptpp) REVERT: A 321 TRP cc_start: 0.7184 (m-10) cc_final: 0.6484 (m100) REVERT: B 49 MET cc_start: 0.8050 (ttp) cc_final: 0.7673 (tmm) REVERT: B 190 GLU cc_start: 0.7943 (tt0) cc_final: 0.7305 (pt0) REVERT: B 269 ARG cc_start: 0.8416 (ptm160) cc_final: 0.8046 (ttm-80) REVERT: C 9 MET cc_start: 0.8502 (mtp) cc_final: 0.8182 (ttm) REVERT: C 90 GLN cc_start: 0.8906 (mp10) cc_final: 0.7986 (mp10) REVERT: C 102 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8577 (mtmt) REVERT: C 297 LEU cc_start: 0.9380 (mp) cc_final: 0.9147 (mp) REVERT: C 424 ASP cc_start: 0.8953 (m-30) cc_final: 0.8645 (m-30) REVERT: D 13 LYS cc_start: 0.9289 (tttt) cc_final: 0.8651 (tmmt) REVERT: D 21 LYS cc_start: 0.8618 (mmmm) cc_final: 0.8367 (mmmm) REVERT: D 147 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7413 (mm-30) REVERT: D 190 GLU cc_start: 0.8115 (tt0) cc_final: 0.7784 (tt0) REVERT: D 215 LYS cc_start: 0.8991 (tttt) cc_final: 0.8458 (ttmm) REVERT: D 243 ASN cc_start: 0.8128 (t0) cc_final: 0.7651 (t0) REVERT: D 426 TRP cc_start: 0.8161 (OUTLIER) cc_final: 0.7845 (m-90) REVERT: E 82 ASN cc_start: 0.8852 (m-40) cc_final: 0.8597 (m-40) REVERT: E 142 LYS cc_start: 0.8935 (mtmt) cc_final: 0.8709 (mtmm) REVERT: E 233 GLN cc_start: 0.7368 (tp40) cc_final: 0.7001 (tp-100) REVERT: E 298 ARG cc_start: 0.7574 (OUTLIER) cc_final: 0.6743 (ptt180) REVERT: L 3 GLN cc_start: 0.8429 (mp10) cc_final: 0.8071 (mp10) REVERT: L 472 ASN cc_start: 0.9065 (t0) cc_final: 0.8820 (t0) REVERT: L 476 GLU cc_start: 0.8441 (mp0) cc_final: 0.8217 (pm20) REVERT: M 454 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7674 (ttp80) REVERT: M 460 ASP cc_start: 0.7704 (p0) cc_final: 0.6776 (p0) REVERT: M 469 GLU cc_start: 0.7560 (mp0) cc_final: 0.7198 (mp0) REVERT: M 472 ASN cc_start: 0.9159 (t0) cc_final: 0.8798 (t0) outliers start: 35 outliers final: 14 residues processed: 244 average time/residue: 1.4143 time to fit residues: 377.6246 Evaluate side-chains 240 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 221 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain C residue 102 LYS Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 426 TRP Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain E residue 264 MET Chi-restraints excluded: chain E residue 298 ARG Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 456 THR Chi-restraints excluded: chain L residue 474 LYS Chi-restraints excluded: chain L residue 477 ASP Chi-restraints excluded: chain M residue 454 ARG Chi-restraints excluded: chain M residue 477 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 187 optimal weight: 2.9990 chunk 172 optimal weight: 7.9990 chunk 149 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 118 optimal weight: 0.5980 chunk 158 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN A 345 ASN B 217 ASN ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 ASN ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN D 224 GLN ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 1 GLN M 3 GLN M 472 ASN ** M 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 16099 Z= 0.230 Angle : 0.647 11.089 21872 Z= 0.327 Chirality : 0.044 0.225 2510 Planarity : 0.003 0.061 2682 Dihedral : 5.663 48.811 2666 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.74 % Allowed : 18.97 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.28 % 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: 1.27 (0.20), residues: 1863 helix: 1.65 (0.22), residues: 577 sheet: 0.38 (0.24), residues: 494 loop : 0.72 (0.24), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP L 440 HIS 0.004 0.001 HIS A 308 PHE 0.027 0.001 PHE B 306 TYR 0.040 0.002 TYR D 220 ARG 0.015 0.000 ARG E 114 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 234 time to evaluate : 1.791 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: A 181 MET cc_start: 0.8374 (mtm) cc_final: 0.8156 (pmm) REVERT: A 262 GLN cc_start: 0.8689 (mt0) cc_final: 0.7705 (mt0) REVERT: A 267 CYS cc_start: 0.8738 (m) cc_final: 0.8526 (m) REVERT: A 282 LYS cc_start: 0.9191 (OUTLIER) cc_final: 0.8602 (ptpp) REVERT: A 321 TRP cc_start: 0.7172 (m-10) cc_final: 0.6519 (m100) REVERT: B 49 MET cc_start: 0.8009 (ttp) cc_final: 0.7747 (tmm) REVERT: B 55 MET cc_start: 0.8959 (ttm) cc_final: 0.8711 (mmm) REVERT: B 190 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7234 (pt0) REVERT: B 269 ARG cc_start: 0.8071 (ptm160) cc_final: 0.7357 (ttm170) REVERT: C 9 MET cc_start: 0.8482 (mtp) cc_final: 0.8168 (ttm) REVERT: C 90 GLN cc_start: 0.8911 (mp10) cc_final: 0.7979 (mp10) REVERT: C 102 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8483 (mtmt) REVERT: C 424 ASP cc_start: 0.8891 (m-30) cc_final: 0.8583 (m-30) REVERT: D 13 LYS cc_start: 0.9277 (tttt) cc_final: 0.8634 (tmmt) REVERT: D 21 LYS cc_start: 0.8574 (mmmm) cc_final: 0.8334 (mmmm) REVERT: D 147 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7345 (mm-30) REVERT: D 181 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8078 (mm) REVERT: D 182 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7335 (mm-30) REVERT: D 190 GLU cc_start: 0.8129 (tt0) cc_final: 0.7781 (tt0) REVERT: D 215 LYS cc_start: 0.8972 (tttt) cc_final: 0.8436 (ttmm) REVERT: D 227 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.8298 (tpp) REVERT: D 243 ASN cc_start: 0.8123 (t0) cc_final: 0.7640 (t0) REVERT: E 82 ASN cc_start: 0.8661 (m-40) cc_final: 0.8398 (m-40) REVERT: E 142 LYS cc_start: 0.8912 (mtmt) cc_final: 0.8674 (mtmm) REVERT: E 233 GLN cc_start: 0.7373 (tp40) cc_final: 0.7004 (tp-100) REVERT: E 298 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.6696 (ptt180) REVERT: E 334 ASN cc_start: 0.8860 (m-40) cc_final: 0.8590 (m110) REVERT: L 3 GLN cc_start: 0.8454 (mp10) cc_final: 0.8086 (mp10) REVERT: L 476 GLU cc_start: 0.8412 (mp0) cc_final: 0.8197 (pm20) REVERT: M 430 LYS cc_start: 0.8649 (pmmt) cc_final: 0.8410 (pptt) REVERT: M 454 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7585 (ttp80) REVERT: M 460 ASP cc_start: 0.8049 (p0) cc_final: 0.7566 (p0) REVERT: M 469 GLU cc_start: 0.7620 (mp0) cc_final: 0.7276 (mp0) REVERT: M 472 ASN cc_start: 0.9099 (t0) cc_final: 0.8849 (t0) outliers start: 29 outliers final: 14 residues processed: 249 average time/residue: 1.3747 time to fit residues: 374.9619 Evaluate side-chains 242 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 221 time to evaluate : 1.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain C residue 102 LYS Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain E residue 264 MET Chi-restraints excluded: chain E residue 298 ARG Chi-restraints excluded: chain L residue 456 THR Chi-restraints excluded: chain L residue 474 LYS Chi-restraints excluded: chain L residue 477 ASP Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 454 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 6.9990 chunk 137 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 149 optimal weight: 8.9990 chunk 62 optimal weight: 6.9990 chunk 153 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 27 optimal weight: 0.2980 chunk 131 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN A 345 ASN B 224 GLN ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 ASN ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN D 224 GLN ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN M 472 ASN ** M 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.083179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.061701 restraints weight = 52641.151| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 3.63 r_work: 0.2785 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2791 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2791 r_free = 0.2791 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2790 r_free = 0.2790 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2790 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 16099 Z= 0.204 Angle : 0.647 11.696 21872 Z= 0.328 Chirality : 0.044 0.229 2510 Planarity : 0.003 0.046 2682 Dihedral : 5.453 45.708 2666 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.86 % Allowed : 19.09 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.28 % 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: 1.33 (0.20), residues: 1863 helix: 1.74 (0.22), residues: 571 sheet: 0.44 (0.24), residues: 493 loop : 0.73 (0.24), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP L 440 HIS 0.003 0.001 HIS A 308 PHE 0.019 0.001 PHE C 307 TYR 0.035 0.002 TYR D 220 ARG 0.014 0.000 ARG A 307 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6799.32 seconds wall clock time: 121 minutes 23.78 seconds (7283.78 seconds total)