Starting phenix.real_space_refine on Sun Mar 17 08:40:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2s_28826/03_2024/8f2s_28826_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2s_28826/03_2024/8f2s_28826.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2s_28826/03_2024/8f2s_28826_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2s_28826/03_2024/8f2s_28826_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2s_28826/03_2024/8f2s_28826_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2s_28826/03_2024/8f2s_28826.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2s_28826/03_2024/8f2s_28826.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2s_28826/03_2024/8f2s_28826_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2s_28826/03_2024/8f2s_28826_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= 0.002 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 86 5.16 5 C 11263 2.51 5 N 2653 2.21 5 O 3150 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17158 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3204 Classifications: {'peptide': 395} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 374} Chain breaks: 1 Chain: "B" Number of atoms: 3451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3451 Classifications: {'peptide': 425} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 397} Chain breaks: 1 Chain: "C" Number of atoms: 3294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3294 Classifications: {'peptide': 406} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 382} Chain breaks: 1 Chain: "D" Number of atoms: 3151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3151 Classifications: {'peptide': 388} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 367} Chain breaks: 1 Chain: "E" Number of atoms: 3317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3317 Classifications: {'peptide': 409} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 386} Chain breaks: 1 Chain: "F" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "G" 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: "H" 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: "I" 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: "J" 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: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 112 Unusual residues: {'CLR': 1, 'POV': 1, 'RBR': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "B" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 147 Unusual residues: {'DD9': 1, 'NAG': 2, 'POV': 2, 'RBR': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-1': 2} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 94 Unusual residues: {'CLR': 2, 'RBR': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {'NAG': 1, 'POV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 2} Unresolved non-hydrogen planarities: 6 Residues with excluded nonbonded symmetry interactions: 9 residue: pdb=" N POV A 502 " occ=0.75 ... (44 atoms not shown) pdb="C314 POV A 502 " occ=0.75 residue: pdb=" C1 CLR A 503 " occ=0.80 ... (26 atoms not shown) pdb=" O1 CLR A 503 " occ=0.80 residue: pdb=" N POV B 605 " occ=0.75 ... (33 atoms not shown) pdb="C311 POV B 605 " occ=0.75 residue: pdb=" N POV B 606 " occ=0.75 ... (35 atoms not shown) pdb="C311 POV B 606 " occ=0.75 residue: pdb=" N POV C 501 " occ=0.75 ... (30 atoms not shown) pdb=" P POV C 501 " occ=0.75 residue: pdb=" C1 CLR D 502 " occ=0.89 ... (26 atoms not shown) pdb=" O1 CLR D 502 " occ=0.89 residue: pdb=" C1 CLR D 503 " occ=0.75 ... (26 atoms not shown) pdb=" O1 CLR D 503 " occ=0.75 residue: pdb=" N POV E 502 " occ=0.75 ... (33 atoms not shown) pdb=" P POV E 502 " occ=0.75 residue: pdb=" N POV E 503 " occ=0.75 ... (33 atoms not shown) pdb="C311 POV E 503 " occ=0.75 Time building chain proxies: 9.61, per 1000 atoms: 0.56 Number of scatterers: 17158 At special positions: 0 Unit cell: (103.732, 119.773, 164.688, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 86 16.00 P 6 15.00 O 3150 8.00 N 2653 7.00 C 11263 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 193 " distance=2.05 Simple disulfide: pdb=" SG CYS B 130 " - pdb=" SG CYS B 144 " distance=2.04 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 142 " distance=2.04 Simple disulfide: pdb=" SG CYS D 128 " - pdb=" SG CYS D 142 " distance=2.03 Simple disulfide: pdb=" SG CYS D 192 " - pdb=" SG CYS D 193 " distance=2.05 Simple disulfide: pdb=" SG CYS E 128 " - pdb=" SG CYS E 142 " 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=1, symmetry=0 Links applied ALPHA1-3 " BMA F 3 " - " MAN F 7 " " MAN F 4 " - " MAN F 5 " ALPHA1-6 " BMA F 3 " - " MAN F 4 " " MAN F 4 " - " MAN F 6 " " BMA I 3 " - " MAN I 4 " " MAN I 4 " - " MAN I 5 " " BMA J 3 " - " MAN J 4 " " MAN J 4 " - " MAN J 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 I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG B 601 " - " ASN B 70 " " NAG B 602 " - " ASN B 208 " " NAG E 501 " - " ASN E 68 " " NAG F 1 " - " ASN A 141 " " NAG G 1 " - " ASN B 143 " " NAG H 1 " - " ASN C 141 " " NAG I 1 " - " ASN D 141 " " NAG J 1 " - " ASN E 141 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.49 Conformation dependent library (CDL) restraints added in 3.0 seconds 4006 Ramachandran restraints generated. 2003 Oldfield, 0 Emsley, 2003 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3908 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 49 helices and 22 sheets defined 39.6% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.29 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 Processing helix chain 'A' and resid 63 through 65 No H-bonds generated for 'chain 'A' and resid 63 through 65' Processing helix chain 'A' and resid 69 through 72 Processing helix chain 'A' and resid 82 through 84 No H-bonds generated for 'chain 'A' and resid 82 through 84' Processing helix chain 'A' and resid 213 through 234 removed outlier: 5.237A pdb=" N ILE A 220 " --> pdb=" O VAL A 216 " (cutoff:3.500A) Proline residue: A 221 - end of helix removed outlier: 3.661A pdb=" N VAL A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N PHE A 233 " --> pdb=" O THR A 229 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N TYR A 234 " --> pdb=" O GLY A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 263 removed outlier: 3.945A pdb=" N LEU A 258 " --> pdb=" O THR A 254 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL A 259 " --> pdb=" O VAL A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 299 Processing helix chain 'A' and resid 310 through 316 Processing helix chain 'A' and resid 320 through 323 Processing helix chain 'A' and resid 371 through 432 removed outlier: 4.249A pdb=" N GLY A 428 " --> pdb=" O SER A 424 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N ARG A 429 " --> pdb=" O VAL A 425 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLU A 432 " --> pdb=" O GLY A 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 12 Processing helix chain 'B' and resid 65 through 67 No H-bonds generated for 'chain 'B' and resid 65 through 67' Processing helix chain 'B' and resid 227 through 231 Processing helix chain 'B' and resid 233 through 247 removed outlier: 3.844A pdb=" N ALA B 243 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N SER B 244 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU B 245 " --> pdb=" O PHE B 241 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA B 246 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N PHE B 247 " --> pdb=" O ALA B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 277 Processing helix chain 'B' and resid 287 through 313 Processing helix chain 'B' and resid 324 through 331 Processing helix chain 'B' and resid 333 through 337 Processing helix chain 'B' and resid 417 through 477 Proline residue: B 463 - end of helix Processing helix chain 'C' and resid 2 through 11 Processing helix chain 'C' and resid 69 through 72 Processing helix chain 'C' and resid 82 through 84 No H-bonds generated for 'chain 'C' and resid 82 through 84' Processing helix chain 'C' and resid 218 through 239 Proline residue: C 227 - end of helix removed outlier: 4.529A pdb=" N PHE C 239 " --> pdb=" O ALA C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 245 No H-bonds generated for 'chain 'C' and resid 243 through 245' Processing helix chain 'C' and resid 248 through 266 removed outlier: 3.791A pdb=" N LEU C 266 " --> pdb=" O PHE C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 305 Processing helix chain 'C' and resid 316 through 322 Processing helix chain 'C' and resid 326 through 330 Processing helix chain 'C' and resid 399 through 459 Processing helix chain 'D' and resid 2 through 11 Processing helix chain 'D' and resid 63 through 65 No H-bonds generated for 'chain 'D' and resid 63 through 65' Processing helix chain 'D' and resid 69 through 72 Processing helix chain 'D' and resid 82 through 84 No H-bonds generated for 'chain 'D' and resid 82 through 84' Processing helix chain 'D' and resid 212 through 233 removed outlier: 4.497A pdb=" N ILE D 220 " --> pdb=" O VAL D 216 " (cutoff:3.500A) Proline residue: D 221 - end of helix removed outlier: 4.080A pdb=" N GLY D 230 " --> pdb=" O SER D 226 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU D 231 " --> pdb=" O PHE D 227 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N VAL D 232 " --> pdb=" O LEU D 228 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N PHE D 233 " --> pdb=" O THR D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 239 No H-bonds generated for 'chain 'D' and resid 237 through 239' Processing helix chain 'D' and resid 242 through 263 Processing helix chain 'D' and resid 273 through 299 Processing helix chain 'D' and resid 310 through 317 Processing helix chain 'D' and resid 320 through 323 No H-bonds generated for 'chain 'D' and resid 320 through 323' Processing helix chain 'D' and resid 372 through 424 removed outlier: 3.671A pdb=" N VAL D 423 " --> pdb=" O ILE D 419 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 12 Processing helix chain 'E' and resid 69 through 72 Processing helix chain 'E' and resid 82 through 84 No H-bonds generated for 'chain 'E' and resid 82 through 84' Processing helix chain 'E' and resid 132 through 134 No H-bonds generated for 'chain 'E' and resid 132 through 134' Processing helix chain 'E' and resid 220 through 242 removed outlier: 4.826A pdb=" N ALA E 228 " --> pdb=" O ILE E 224 " (cutoff:3.500A) Proline residue: E 229 - end of helix removed outlier: 3.829A pdb=" N LEU E 236 " --> pdb=" O LEU E 232 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N VAL E 237 " --> pdb=" O ILE E 233 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N VAL E 238 " --> pdb=" O SER E 234 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N LEU E 239 " --> pdb=" O SER E 235 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N VAL E 240 " --> pdb=" O LEU E 236 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N TYR E 241 " --> pdb=" O VAL E 237 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N PHE E 242 " --> pdb=" O VAL E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 272 removed outlier: 4.268A pdb=" N LYS E 272 " --> pdb=" O LEU E 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 308 Processing helix chain 'E' and resid 319 through 327 Processing helix chain 'E' and resid 412 through 471 removed outlier: 3.594A pdb=" N TRP E 453 " --> pdb=" O LYS E 449 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 156 through 160 removed outlier: 5.888A pdb=" N VAL A 29 " --> pdb=" O SER A 157 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N SER A 159 " --> pdb=" O VAL A 29 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ILE A 31 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ASP A 30 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ILE A 61 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ASN A 53 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N LEU A 40 " --> pdb=" O GLU A 51 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N GLU A 51 " --> pdb=" O LEU A 40 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 42 through 44 Processing sheet with id= C, first strand: chain 'A' and resid 77 through 81 Processing sheet with id= D, first strand: chain 'A' and resid 90 through 92 removed outlier: 3.581A pdb=" N CYS A 142 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ILE A 148 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU A 199 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLN A 208 " --> pdb=" O MET A 178 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N MET A 178 " --> pdb=" O GLN A 208 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 158 through 162 removed outlier: 6.311A pdb=" N VAL B 31 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N ASP B 161 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ILE B 33 " --> pdb=" O ASP B 161 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ASN B 32 " --> pdb=" O TYR B 63 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N TYR B 63 " --> pdb=" O ASN B 32 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ASN B 55 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N LEU B 42 " --> pdb=" O THR B 53 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N THR B 53 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 79 through 82 Processing sheet with id= G, first strand: chain 'B' and resid 92 through 94 Processing sheet with id= H, first strand: chain 'B' and resid 164 through 166 Processing sheet with id= I, first strand: chain 'B' and resid 190 through 194 removed outlier: 6.900A pdb=" N ILE B 220 " --> pdb=" O ILE B 193 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 156 through 160 removed outlier: 6.416A pdb=" N VAL C 29 " --> pdb=" O THR C 157 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N GLN C 159 " --> pdb=" O VAL C 29 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL C 31 " --> pdb=" O GLN C 159 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N THR C 30 " --> pdb=" O THR C 61 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N THR C 61 " --> pdb=" O THR C 30 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASN C 53 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N LEU C 40 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N THR C 51 " --> pdb=" O LEU C 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 42 through 44 Processing sheet with id= L, first strand: chain 'C' and resid 77 through 80 Processing sheet with id= M, first strand: chain 'C' and resid 90 through 92 Processing sheet with id= N, first strand: chain 'C' and resid 186 through 190 removed outlier: 6.890A pdb=" N ILE C 212 " --> pdb=" O GLU C 189 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 156 through 160 removed outlier: 6.035A pdb=" N VAL D 29 " --> pdb=" O SER D 157 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N SER D 159 " --> pdb=" O VAL D 29 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE D 31 " --> pdb=" O SER D 159 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ASP D 30 " --> pdb=" O ILE D 61 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ILE D 61 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ASN D 53 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N LEU D 40 " --> pdb=" O GLU D 51 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N GLU D 51 " --> pdb=" O LEU D 40 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 42 through 44 Processing sheet with id= Q, first strand: chain 'D' and resid 77 through 81 Processing sheet with id= R, first strand: chain 'D' and resid 90 through 92 removed outlier: 3.781A pdb=" N CYS D 142 " --> pdb=" O PHE D 205 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE D 205 " --> pdb=" O CYS D 142 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ILE D 148 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU D 199 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP D 180 " --> pdb=" O ILE D 206 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLN D 208 " --> pdb=" O MET D 178 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N MET D 178 " --> pdb=" O GLN D 208 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 156 through 160 removed outlier: 6.479A pdb=" N ILE E 29 " --> pdb=" O ASN E 157 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N GLN E 159 " --> pdb=" O ILE E 29 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL E 31 " --> pdb=" O GLN E 159 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ASP E 30 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ASN E 61 " --> pdb=" O ASP E 30 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASN E 53 " --> pdb=" O THR E 38 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N LEU E 40 " --> pdb=" O THR E 51 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N THR E 51 " --> pdb=" O LEU E 40 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER E 115 " --> pdb=" O TYR E 111 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N LEU E 119 " --> pdb=" O ASN E 107 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ASN E 107 " --> pdb=" O LEU E 119 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 42 through 44 Processing sheet with id= U, first strand: chain 'E' and resid 90 through 92 removed outlier: 5.269A pdb=" N SER E 148 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N GLN E 207 " --> pdb=" O SER E 148 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 184 through 188 removed outlier: 6.896A pdb=" N ILE E 214 " --> pdb=" O ARG E 187 " (cutoff:3.500A) 789 hydrogen bonds defined for protein. 2304 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: 5.04 Time building geometry restraints manager: 7.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 2660 1.32 - 1.46: 5549 1.46 - 1.59: 9256 1.59 - 1.73: 12 1.73 - 1.87: 140 Bond restraints: 17617 Sorted by residual: bond pdb=" C1 RBR D 501 " pdb=" C14 RBR D 501 " ideal model delta sigma weight residual 1.045 1.531 -0.486 2.00e-02 2.50e+03 5.90e+02 bond pdb=" C1 RBR A 501 " pdb=" C14 RBR A 501 " ideal model delta sigma weight residual 1.045 1.529 -0.484 2.00e-02 2.50e+03 5.87e+02 bond pdb=" C1 RBR B 603 " pdb=" C14 RBR B 603 " ideal model delta sigma weight residual 1.045 1.528 -0.483 2.00e-02 2.50e+03 5.84e+02 bond pdb=" C14 RBR B 603 " pdb=" C15 RBR B 603 " ideal model delta sigma weight residual 1.185 1.531 -0.346 2.00e-02 2.50e+03 2.99e+02 bond pdb=" C14 RBR A 501 " pdb=" C15 RBR A 501 " ideal model delta sigma weight residual 1.185 1.529 -0.344 2.00e-02 2.50e+03 2.96e+02 ... (remaining 17612 not shown) Histogram of bond angle deviations from ideal: 95.70 - 103.37: 221 103.37 - 111.03: 7713 111.03 - 118.70: 6860 118.70 - 126.37: 8890 126.37 - 134.03: 360 Bond angle restraints: 24044 Sorted by residual: angle pdb=" O11 POV A 502 " pdb=" P POV A 502 " pdb=" O12 POV A 502 " ideal model delta sigma weight residual 97.67 109.78 -12.11 3.00e+00 1.11e-01 1.63e+01 angle pdb=" O11 POV C 501 " pdb=" P POV C 501 " pdb=" O12 POV C 501 " ideal model delta sigma weight residual 97.67 109.59 -11.92 3.00e+00 1.11e-01 1.58e+01 angle pdb=" O13 POV E 503 " pdb=" P POV E 503 " pdb=" O14 POV E 503 " ideal model delta sigma weight residual 121.11 109.32 11.79 3.00e+00 1.11e-01 1.54e+01 angle pdb=" O13 POV B 606 " pdb=" P POV B 606 " pdb=" O14 POV B 606 " ideal model delta sigma weight residual 121.11 109.35 11.76 3.00e+00 1.11e-01 1.54e+01 angle pdb=" O13 POV E 502 " pdb=" P POV E 502 " pdb=" O14 POV E 502 " ideal model delta sigma weight residual 121.11 109.39 11.72 3.00e+00 1.11e-01 1.53e+01 ... (remaining 24039 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.76: 10665 35.76 - 71.52: 231 71.52 - 107.28: 56 107.28 - 143.04: 24 143.04 - 178.80: 5 Dihedral angle restraints: 10981 sinusoidal: 4979 harmonic: 6002 Sorted by residual: dihedral pdb=" CA CYS D 142 " pdb=" C CYS D 142 " pdb=" N THR D 143 " pdb=" CA THR D 143 " ideal model delta harmonic sigma weight residual -180.00 -151.10 -28.90 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA CYS A 142 " pdb=" C CYS A 142 " pdb=" N THR A 143 " pdb=" CA THR A 143 " ideal model delta harmonic sigma weight residual -180.00 -151.80 -28.20 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA CYS D 192 " pdb=" C CYS D 192 " pdb=" N CYS D 193 " pdb=" CA CYS D 193 " ideal model delta harmonic sigma weight residual -180.00 -152.26 -27.74 0 5.00e+00 4.00e-02 3.08e+01 ... (remaining 10978 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.032: 2848 1.032 - 2.064: 3 2.064 - 3.096: 0 3.096 - 4.127: 0 4.127 - 5.159: 3 Chirality restraints: 2854 Sorted by residual: chirality pdb=" N31 RBR D 501 " pdb=" C3 RBR D 501 " pdb=" C35 RBR D 501 " pdb=" C38 RBR D 501 " both_signs ideal model delta sigma weight residual False -2.26 2.90 -5.16 2.00e-01 2.50e+01 6.65e+02 chirality pdb=" N31 RBR A 501 " pdb=" C3 RBR A 501 " pdb=" C35 RBR A 501 " pdb=" C38 RBR A 501 " both_signs ideal model delta sigma weight residual False -2.26 2.85 -5.11 2.00e-01 2.50e+01 6.53e+02 chirality pdb=" N31 RBR B 603 " pdb=" C3 RBR B 603 " pdb=" C35 RBR B 603 " pdb=" C38 RBR B 603 " both_signs ideal model delta sigma weight residual False -2.26 2.85 -5.11 2.00e-01 2.50e+01 6.53e+02 ... (remaining 2851 not shown) Planarity restraints: 2892 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 222 " 0.017 2.00e-02 2.50e+03 3.44e-02 1.19e+01 pdb=" C VAL C 222 " -0.060 2.00e-02 2.50e+03 pdb=" O VAL C 222 " 0.023 2.00e-02 2.50e+03 pdb=" N TYR C 223 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 141 " 0.024 2.00e-02 2.50e+03 2.45e-02 7.51e+00 pdb=" CG ASN D 141 " -0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN D 141 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN D 141 " -0.038 2.00e-02 2.50e+03 pdb=" C1 NAG I 1 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 141 " 0.019 2.00e-02 2.50e+03 1.99e-02 4.93e+00 pdb=" CG ASN A 141 " -0.006 2.00e-02 2.50e+03 pdb=" OD1 ASN A 141 " -0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN A 141 " -0.031 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " 0.024 2.00e-02 2.50e+03 ... (remaining 2889 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 271 2.68 - 3.24: 16411 3.24 - 3.79: 26041 3.79 - 4.35: 36099 4.35 - 4.90: 60348 Nonbonded interactions: 139170 Sorted by model distance: nonbonded pdb=" OE2 GLU D 45 " pdb=" NH2 ARG D 209 " model vdw 2.129 2.520 nonbonded pdb=" OD1 ASN B 305 " pdb=" OG SER B 457 " model vdw 2.205 2.440 nonbonded pdb=" OD2 ASP D 44 " pdb=" ND2 ASN D 47 " model vdw 2.222 2.520 nonbonded pdb=" O ASN B 27 " pdb=" OD1 ASN B 27 " model vdw 2.227 3.040 nonbonded pdb=" NH2 ARG E 147 " pdb=" OE1 GLU E 208 " model vdw 2.241 2.520 ... (remaining 139165 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 'A' and (resid 1 through 426 or resid 501 or resid 503)) selection = (chain 'D' and (resid 1 through 426 or resid 501 or resid 503)) } ncs_group { reference = chain 'I' selection = chain 'J' } 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=0.75 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: 2.040 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.980 Check model and map are aligned: 0.280 Set scattering table: 0.180 Process input model: 47.750 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 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 : 0.015 0.486 17617 Z= 0.954 Angle : 0.822 12.113 24044 Z= 0.358 Chirality : 0.182 5.159 2854 Planarity : 0.004 0.048 2884 Dihedral : 17.663 178.803 7052 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.19), residues: 2003 helix: 2.57 (0.19), residues: 751 sheet: 0.03 (0.25), residues: 414 loop : -0.82 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 60 HIS 0.005 0.001 HIS D 204 PHE 0.029 0.001 PHE C 443 TYR 0.010 0.001 TYR B 17 ARG 0.003 0.000 ARG B 222 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4006 Ramachandran restraints generated. 2003 Oldfield, 0 Emsley, 2003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4006 Ramachandran restraints generated. 2003 Oldfield, 0 Emsley, 2003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 1.930 Fit side-chains revert: symmetry clash REVERT: A 208 GLN cc_start: 0.8674 (tp40) cc_final: 0.8344 (tp40) REVERT: A 310 GLN cc_start: 0.8947 (tp-100) cc_final: 0.8680 (tp-100) REVERT: B 257 MET cc_start: 0.9077 (mmm) cc_final: 0.8875 (mmp) REVERT: B 475 MET cc_start: 0.8391 (ttp) cc_final: 0.8060 (ttt) REVERT: D 407 ASP cc_start: 0.8505 (m-30) cc_final: 0.8142 (t0) outliers start: 0 outliers final: 2 residues processed: 124 average time/residue: 1.2889 time to fit residues: 179.7783 Evaluate side-chains 84 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 82 time to evaluate : 1.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain D residue 195 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 168 optimal weight: 0.0870 chunk 150 optimal weight: 0.9990 chunk 83 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 180 optimal weight: 0.9980 overall best weight: 0.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 ASN B 95 GLN ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.0894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17617 Z= 0.182 Angle : 0.701 23.538 24044 Z= 0.301 Chirality : 0.088 2.407 2854 Planarity : 0.003 0.036 2884 Dihedral : 15.769 172.272 3133 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.86 % Allowed : 4.60 % Favored : 94.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.20), residues: 2003 helix: 3.06 (0.19), residues: 752 sheet: 0.22 (0.25), residues: 416 loop : -0.56 (0.22), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 60 HIS 0.004 0.000 HIS B 313 PHE 0.019 0.001 PHE E 267 TYR 0.010 0.001 TYR E 117 ARG 0.003 0.000 ARG A 66 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4006 Ramachandran restraints generated. 2003 Oldfield, 0 Emsley, 2003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4006 Ramachandran restraints generated. 2003 Oldfield, 0 Emsley, 2003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 93 time to evaluate : 2.035 Fit side-chains revert: symmetry clash REVERT: A 208 GLN cc_start: 0.8592 (tp40) cc_final: 0.8300 (tp40) REVERT: A 310 GLN cc_start: 0.8932 (tp-100) cc_final: 0.8594 (tp-100) REVERT: B 475 MET cc_start: 0.8190 (ttp) cc_final: 0.7972 (ttt) REVERT: D 117 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.7959 (ttm) REVERT: D 407 ASP cc_start: 0.8448 (m-30) cc_final: 0.8160 (t0) outliers start: 16 outliers final: 4 residues processed: 99 average time/residue: 1.2676 time to fit residues: 141.5038 Evaluate side-chains 90 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 85 time to evaluate : 1.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain D residue 117 MET Chi-restraints excluded: chain D residue 418 CYS Chi-restraints excluded: chain D residue 419 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 100 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 181 optimal weight: 0.9990 chunk 195 optimal weight: 0.9990 chunk 161 optimal weight: 0.8980 chunk 179 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 145 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 ASN B 95 GLN B 213 GLN ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 ASN D 408 HIS E 431 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17617 Z= 0.198 Angle : 0.669 22.869 24044 Z= 0.286 Chirality : 0.086 2.416 2854 Planarity : 0.003 0.038 2884 Dihedral : 14.593 177.326 3129 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.23 % Allowed : 6.05 % Favored : 92.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.20), residues: 2003 helix: 3.29 (0.18), residues: 750 sheet: 0.33 (0.25), residues: 416 loop : -0.50 (0.23), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 60 HIS 0.004 0.000 HIS B 313 PHE 0.017 0.001 PHE D 414 TYR 0.011 0.001 TYR E 117 ARG 0.006 0.000 ARG C 168 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4006 Ramachandran restraints generated. 2003 Oldfield, 0 Emsley, 2003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4006 Ramachandran restraints generated. 2003 Oldfield, 0 Emsley, 2003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 88 time to evaluate : 1.968 Fit side-chains REVERT: A 208 GLN cc_start: 0.8587 (tp40) cc_final: 0.8377 (tp40) REVERT: A 310 GLN cc_start: 0.8940 (tp-100) cc_final: 0.8602 (tp-100) REVERT: B 475 MET cc_start: 0.8200 (ttp) cc_final: 0.7973 (ttt) REVERT: D 117 MET cc_start: 0.8388 (OUTLIER) cc_final: 0.7958 (ttm) REVERT: D 200 ASP cc_start: 0.8598 (p0) cc_final: 0.8359 (p0) REVERT: D 407 ASP cc_start: 0.8431 (m-30) cc_final: 0.8154 (t0) outliers start: 23 outliers final: 7 residues processed: 101 average time/residue: 1.2912 time to fit residues: 147.1772 Evaluate side-chains 88 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 80 time to evaluate : 2.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain D residue 117 MET Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 323 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 178 optimal weight: 5.9990 chunk 136 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 181 optimal weight: 3.9990 chunk 192 optimal weight: 7.9990 chunk 94 optimal weight: 0.7980 chunk 172 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 ASN B 60 HIS B 95 GLN B 213 GLN B 267 GLN E 431 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17617 Z= 0.255 Angle : 0.678 22.859 24044 Z= 0.291 Chirality : 0.086 2.301 2854 Planarity : 0.003 0.036 2884 Dihedral : 14.025 159.698 3129 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.34 % Allowed : 6.69 % Favored : 91.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.20), residues: 2003 helix: 3.27 (0.18), residues: 749 sheet: 0.37 (0.25), residues: 411 loop : -0.47 (0.22), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 60 HIS 0.003 0.001 HIS B 313 PHE 0.020 0.001 PHE D 414 TYR 0.010 0.001 TYR E 117 ARG 0.002 0.000 ARG C 168 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4006 Ramachandran restraints generated. 2003 Oldfield, 0 Emsley, 2003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4006 Ramachandran restraints generated. 2003 Oldfield, 0 Emsley, 2003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 84 time to evaluate : 2.079 Fit side-chains revert: symmetry clash REVERT: A 208 GLN cc_start: 0.8627 (tp40) cc_final: 0.8417 (tp40) REVERT: A 310 GLN cc_start: 0.8944 (tp-100) cc_final: 0.8613 (tp-100) REVERT: B 454 ASP cc_start: 0.8128 (t0) cc_final: 0.7922 (t0) REVERT: B 475 MET cc_start: 0.8215 (ttp) cc_final: 0.7970 (ttt) REVERT: D 117 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.7968 (ttm) REVERT: D 200 ASP cc_start: 0.8577 (p0) cc_final: 0.8353 (p0) REVERT: D 407 ASP cc_start: 0.8428 (m-30) cc_final: 0.8147 (t0) outliers start: 25 outliers final: 11 residues processed: 98 average time/residue: 1.2740 time to fit residues: 140.7351 Evaluate side-chains 93 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 81 time to evaluate : 1.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain D residue 117 MET Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 418 CYS Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 323 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 160 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 143 optimal weight: 0.5980 chunk 79 optimal weight: 5.9990 chunk 164 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 172 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 GLN B 305 ASN D 408 HIS E 431 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17617 Z= 0.271 Angle : 0.681 21.965 24044 Z= 0.293 Chirality : 0.085 2.271 2854 Planarity : 0.003 0.037 2884 Dihedral : 13.532 158.954 3129 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.18 % Allowed : 8.08 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.20), residues: 2003 helix: 3.29 (0.18), residues: 749 sheet: 0.37 (0.25), residues: 412 loop : -0.45 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 60 HIS 0.004 0.001 HIS B 60 PHE 0.021 0.001 PHE D 414 TYR 0.011 0.001 TYR E 117 ARG 0.002 0.000 ARG E 217 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4006 Ramachandran restraints generated. 2003 Oldfield, 0 Emsley, 2003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4006 Ramachandran restraints generated. 2003 Oldfield, 0 Emsley, 2003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 83 time to evaluate : 2.144 Fit side-chains revert: symmetry clash REVERT: A 208 GLN cc_start: 0.8640 (tp40) cc_final: 0.8425 (tp40) REVERT: A 310 GLN cc_start: 0.8930 (tp-100) cc_final: 0.8611 (tp-100) REVERT: B 475 MET cc_start: 0.8245 (ttp) cc_final: 0.8017 (ttt) REVERT: D 117 MET cc_start: 0.8388 (OUTLIER) cc_final: 0.7965 (ttm) REVERT: D 200 ASP cc_start: 0.8580 (p0) cc_final: 0.8354 (p0) REVERT: D 407 ASP cc_start: 0.8452 (m-30) cc_final: 0.8186 (t0) outliers start: 22 outliers final: 12 residues processed: 94 average time/residue: 1.3023 time to fit residues: 138.4000 Evaluate side-chains 92 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 79 time to evaluate : 2.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain D residue 117 MET Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 418 CYS Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 323 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 64 optimal weight: 7.9990 chunk 173 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 192 optimal weight: 0.9990 chunk 159 optimal weight: 5.9990 chunk 89 optimal weight: 0.2980 chunk 16 optimal weight: 0.3980 chunk 63 optimal weight: 0.6980 chunk 101 optimal weight: 4.9990 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 59 GLN A 134 HIS B 213 GLN D 48 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 17617 Z= 0.143 Angle : 0.663 21.432 24044 Z= 0.280 Chirality : 0.085 2.277 2854 Planarity : 0.003 0.040 2884 Dihedral : 13.192 159.683 3129 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.96 % Allowed : 8.61 % Favored : 90.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.20), residues: 2003 helix: 3.34 (0.18), residues: 749 sheet: 0.45 (0.25), residues: 409 loop : -0.39 (0.23), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 60 HIS 0.003 0.000 HIS B 313 PHE 0.020 0.001 PHE D 414 TYR 0.012 0.001 TYR E 117 ARG 0.001 0.000 ARG A 66 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4006 Ramachandran restraints generated. 2003 Oldfield, 0 Emsley, 2003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4006 Ramachandran restraints generated. 2003 Oldfield, 0 Emsley, 2003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 84 time to evaluate : 2.063 Fit side-chains revert: symmetry clash REVERT: A 310 GLN cc_start: 0.8915 (tp-100) cc_final: 0.8576 (tp-100) REVERT: A 407 ASP cc_start: 0.8352 (t0) cc_final: 0.7932 (t0) REVERT: B 475 MET cc_start: 0.8214 (ttp) cc_final: 0.7995 (ttt) REVERT: D 117 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.7924 (ttm) REVERT: D 324 MET cc_start: 0.8068 (mmp) cc_final: 0.7785 (mtp) REVERT: D 407 ASP cc_start: 0.8407 (m-30) cc_final: 0.8139 (t0) outliers start: 18 outliers final: 6 residues processed: 93 average time/residue: 1.2376 time to fit residues: 130.6663 Evaluate side-chains 85 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 78 time to evaluate : 2.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain D residue 117 MET Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 418 CYS Chi-restraints excluded: chain D residue 419 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 185 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 109 optimal weight: 3.9990 chunk 140 optimal weight: 0.1980 chunk 108 optimal weight: 2.9990 chunk 162 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 191 optimal weight: 4.9990 chunk 120 optimal weight: 0.0020 chunk 116 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 overall best weight: 1.2394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 GLN B 305 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17617 Z= 0.199 Angle : 0.664 21.548 24044 Z= 0.283 Chirality : 0.084 2.262 2854 Planarity : 0.003 0.039 2884 Dihedral : 12.951 158.211 3129 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.02 % Allowed : 9.31 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.20), residues: 2003 helix: 3.38 (0.18), residues: 748 sheet: 0.48 (0.25), residues: 408 loop : -0.37 (0.23), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 60 HIS 0.003 0.000 HIS A 186 PHE 0.013 0.001 PHE E 467 TYR 0.012 0.001 TYR E 117 ARG 0.001 0.000 ARG E 217 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4006 Ramachandran restraints generated. 2003 Oldfield, 0 Emsley, 2003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4006 Ramachandran restraints generated. 2003 Oldfield, 0 Emsley, 2003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 77 time to evaluate : 2.060 Fit side-chains REVERT: A 310 GLN cc_start: 0.8927 (tp-100) cc_final: 0.8587 (tp-100) REVERT: A 407 ASP cc_start: 0.8358 (t0) cc_final: 0.7923 (t0) REVERT: B 475 MET cc_start: 0.8165 (ttp) cc_final: 0.7955 (ttt) REVERT: D 117 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.7939 (ttm) REVERT: D 324 MET cc_start: 0.8057 (mmp) cc_final: 0.7748 (mtp) REVERT: D 407 ASP cc_start: 0.8467 (m-30) cc_final: 0.8199 (t0) outliers start: 19 outliers final: 10 residues processed: 87 average time/residue: 1.3461 time to fit residues: 132.4955 Evaluate side-chains 86 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 75 time to evaluate : 2.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain D residue 117 MET Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 418 CYS Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain E residue 323 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 118 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 121 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 chunk 17 optimal weight: 0.0970 chunk 150 optimal weight: 0.9990 chunk 174 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17617 Z= 0.199 Angle : 0.670 21.502 24044 Z= 0.284 Chirality : 0.084 2.260 2854 Planarity : 0.003 0.040 2884 Dihedral : 12.846 158.413 3129 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.07 % Allowed : 9.42 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.20), residues: 2003 helix: 3.41 (0.18), residues: 748 sheet: 0.48 (0.25), residues: 413 loop : -0.35 (0.23), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 60 HIS 0.003 0.000 HIS B 60 PHE 0.024 0.001 PHE D 414 TYR 0.012 0.001 TYR E 117 ARG 0.001 0.000 ARG E 217 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4006 Ramachandran restraints generated. 2003 Oldfield, 0 Emsley, 2003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4006 Ramachandran restraints generated. 2003 Oldfield, 0 Emsley, 2003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 75 time to evaluate : 2.108 Fit side-chains REVERT: A 310 GLN cc_start: 0.8921 (tp-100) cc_final: 0.8583 (tp-100) REVERT: A 407 ASP cc_start: 0.8354 (t0) cc_final: 0.7919 (t0) REVERT: B 475 MET cc_start: 0.8185 (ttp) cc_final: 0.7982 (ttt) REVERT: D 117 MET cc_start: 0.8374 (OUTLIER) cc_final: 0.7938 (ttm) REVERT: D 324 MET cc_start: 0.8048 (mmp) cc_final: 0.7746 (mtp) REVERT: D 407 ASP cc_start: 0.8476 (m-30) cc_final: 0.8218 (t0) outliers start: 20 outliers final: 12 residues processed: 86 average time/residue: 1.3594 time to fit residues: 131.7853 Evaluate side-chains 88 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 75 time to evaluate : 2.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain D residue 117 MET Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 418 CYS Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain E residue 323 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 183 optimal weight: 7.9990 chunk 167 optimal weight: 1.9990 chunk 178 optimal weight: 4.9990 chunk 107 optimal weight: 0.5980 chunk 77 optimal weight: 3.9990 chunk 140 optimal weight: 0.0670 chunk 54 optimal weight: 2.9990 chunk 161 optimal weight: 5.9990 chunk 169 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 chunk 189 optimal weight: 0.8980 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 GLN B 305 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17617 Z= 0.166 Angle : 0.656 21.343 24044 Z= 0.278 Chirality : 0.084 2.258 2854 Planarity : 0.003 0.041 2884 Dihedral : 12.654 158.538 3129 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.86 % Allowed : 9.58 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.20), residues: 2003 helix: 3.46 (0.18), residues: 748 sheet: 0.49 (0.25), residues: 413 loop : -0.31 (0.23), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 60 HIS 0.005 0.000 HIS B 60 PHE 0.023 0.001 PHE D 414 TYR 0.013 0.001 TYR E 117 ARG 0.001 0.000 ARG A 66 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4006 Ramachandran restraints generated. 2003 Oldfield, 0 Emsley, 2003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4006 Ramachandran restraints generated. 2003 Oldfield, 0 Emsley, 2003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 76 time to evaluate : 2.163 Fit side-chains REVERT: A 310 GLN cc_start: 0.8906 (tp-100) cc_final: 0.8563 (tp-100) REVERT: A 407 ASP cc_start: 0.8312 (t0) cc_final: 0.7889 (t0) REVERT: D 117 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.7904 (ttm) REVERT: D 324 MET cc_start: 0.8009 (mmp) cc_final: 0.7756 (mtp) REVERT: D 407 ASP cc_start: 0.8457 (m-30) cc_final: 0.8210 (t0) REVERT: E 467 PHE cc_start: 0.7951 (m-10) cc_final: 0.7391 (t80) outliers start: 16 outliers final: 8 residues processed: 87 average time/residue: 1.3635 time to fit residues: 134.6801 Evaluate side-chains 83 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 74 time to evaluate : 2.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain D residue 117 MET Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 418 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 115 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 131 optimal weight: 4.9990 chunk 198 optimal weight: 0.6980 chunk 182 optimal weight: 0.9990 chunk 157 optimal weight: 3.9990 chunk 16 optimal weight: 0.0980 chunk 121 optimal weight: 4.9990 chunk 96 optimal weight: 0.7980 chunk 125 optimal weight: 7.9990 chunk 168 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 GLN B 305 ASN D 408 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 17617 Z= 0.153 Angle : 0.664 21.291 24044 Z= 0.280 Chirality : 0.084 2.257 2854 Planarity : 0.003 0.082 2884 Dihedral : 12.567 158.181 3129 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.59 % Allowed : 10.01 % Favored : 89.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.20), residues: 2003 helix: 3.47 (0.18), residues: 748 sheet: 0.46 (0.25), residues: 412 loop : -0.25 (0.23), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 60 HIS 0.004 0.000 HIS B 60 PHE 0.021 0.001 PHE D 414 TYR 0.013 0.001 TYR E 117 ARG 0.001 0.000 ARG A 66 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4006 Ramachandran restraints generated. 2003 Oldfield, 0 Emsley, 2003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4006 Ramachandran restraints generated. 2003 Oldfield, 0 Emsley, 2003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 76 time to evaluate : 2.029 Fit side-chains REVERT: A 310 GLN cc_start: 0.8885 (tp-100) cc_final: 0.8552 (tp-100) REVERT: A 407 ASP cc_start: 0.8303 (t0) cc_final: 0.7884 (t0) REVERT: D 117 MET cc_start: 0.8321 (OUTLIER) cc_final: 0.7880 (ttm) REVERT: D 324 MET cc_start: 0.7980 (mmp) cc_final: 0.7736 (mtp) REVERT: D 407 ASP cc_start: 0.8466 (m-30) cc_final: 0.8210 (t0) REVERT: E 467 PHE cc_start: 0.7927 (m-10) cc_final: 0.7463 (t80) outliers start: 11 outliers final: 6 residues processed: 83 average time/residue: 1.3620 time to fit residues: 127.3946 Evaluate side-chains 83 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 76 time to evaluate : 2.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain D residue 117 MET Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 418 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 48 optimal weight: 5.9990 chunk 145 optimal weight: 0.9990 chunk 23 optimal weight: 0.0060 chunk 43 optimal weight: 7.9990 chunk 158 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 138 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 overall best weight: 1.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 GLN B 305 ASN D 408 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.060803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.046852 restraints weight = 45282.119| |-----------------------------------------------------------------------------| r_work (start): 0.2627 rms_B_bonded: 3.13 r_work: 0.2466 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2466 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2470 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2470 r_free = 0.2470 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2470 r_free = 0.2470 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2470 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17617 Z= 0.194 Angle : 0.666 21.399 24044 Z= 0.282 Chirality : 0.084 2.254 2854 Planarity : 0.003 0.078 2884 Dihedral : 12.478 157.732 3129 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.80 % Allowed : 10.06 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.20), residues: 2003 helix: 3.47 (0.18), residues: 748 sheet: 0.46 (0.25), residues: 410 loop : -0.27 (0.23), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 60 HIS 0.006 0.000 HIS C 105 PHE 0.021 0.001 PHE D 414 TYR 0.013 0.001 TYR E 117 ARG 0.001 0.000 ARG E 217 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3878.90 seconds wall clock time: 70 minutes 43.09 seconds (4243.09 seconds total)