Starting phenix.real_space_refine on Sun Mar 17 07:08:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6z_28893/03_2024/8f6z_28893_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6z_28893/03_2024/8f6z_28893.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6z_28893/03_2024/8f6z_28893.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6z_28893/03_2024/8f6z_28893.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6z_28893/03_2024/8f6z_28893_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6z_28893/03_2024/8f6z_28893_updated.pdb" } resolution = 2.7 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: 5 Type Number sf(0) Gaussians P 5 5.49 5 S 85 5.16 5 C 11129 2.51 5 N 2640 2.21 5 O 3138 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 23": "OE1" <-> "OE2" Residue "A GLU 390": "OE1" <-> "OE2" Residue "C GLU 272": "OE1" <-> "OE2" 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: 16997 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 3140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3140 Classifications: {'peptide': 387} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 366} Chain breaks: 1 Chain: "B" Number of atoms: 3456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3456 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: 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: "G" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: 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: "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: "K" 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: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 48 Unusual residues: {'CLR': 1, 'SCK': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Unusual residues: {'DD9': 1, 'NAG': 1, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 98 Unusual residues: {'CLR': 1, 'POV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'POV:plan-1': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'CLR': 1, 'POV': 1, 'SCK': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'NAG': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" C1 CLR A 502 " occ=0.80 ... (26 atoms not shown) pdb=" O1 CLR A 502 " occ=0.80 residue: pdb=" N POV B 602 " occ=0.75 ... (35 atoms not shown) pdb="C311 POV B 602 " occ=0.75 residue: pdb=" C1 CLR C 501 " occ=0.89 ... (26 atoms not shown) pdb=" O1 CLR C 501 " occ=0.89 residue: pdb=" C1 CLR D 503 " occ=0.75 ... (26 atoms not shown) pdb=" O1 CLR D 503 " occ=0.75 Time building chain proxies: 9.58, per 1000 atoms: 0.56 Number of scatterers: 16997 At special positions: 0 Unit cell: (99.4542, 111.218, 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 85 16.00 P 5 15.00 O 3138 8.00 N 2640 7.00 C 11129 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=2.04 Simple disulfide: pdb=" SG CYS B 130 " - pdb=" SG CYS B 144 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 142 " distance=2.03 Simple disulfide: pdb=" SG CYS D 128 " - pdb=" SG CYS D 142 " distance=2.02 Simple disulfide: pdb=" SG CYS D 192 " - pdb=" SG CYS D 193 " distance=2.04 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=0, symmetry=0 Links applied ALPHA1-6 " BMA F 3 " - " MAN F 4 " " MAN F 4 " - " MAN F 5 " " BMA G 3 " - " MAN G 4 " " BMA J 3 " - " MAN J 4 " " MAN J 4 " - " MAN J 5 " " BMA K 3 " - " MAN K 4 " " MAN K 4 " - " MAN K 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 K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " NAG-ASN " NAG B 601 " - " ASN B 70 " " NAG E 501 " - " ASN E 68 " " NAG F 1 " - " ASN A 141 " " NAG G 1 " - " ASN B 143 " " NAG H 1 " - " ASN B 208 " " NAG I 1 " - " ASN C 141 " " NAG J 1 " - " ASN D 141 " " NAG K 1 " - " ASN E 141 " Time building additional restraints: 7.98 Conformation dependent library (CDL) restraints added in 3.4 seconds 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3894 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 54 helices and 23 sheets defined 40.1% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.61 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 191 through 193 No H-bonds generated for 'chain 'A' and resid 191 through 193' Processing helix chain 'A' and resid 213 through 234 removed outlier: 4.680A pdb=" N ILE A 220 " --> pdb=" O VAL A 216 " (cutoff:3.500A) Proline residue: A 221 - end of helix removed outlier: 4.053A pdb=" N THR A 229 " --> pdb=" O PHE A 225 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N GLY A 230 " --> pdb=" O SER A 226 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU A 231 " --> pdb=" O PHE A 227 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N PHE A 233 " --> pdb=" O THR A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 239 No H-bonds generated for 'chain 'A' and resid 237 through 239' Processing helix chain 'A' and resid 242 through 263 Processing helix chain 'A' and resid 273 through 299 Processing helix chain 'A' and resid 310 through 316 removed outlier: 3.726A pdb=" N ILE A 315 " --> pdb=" O TRP A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 323 No H-bonds generated for 'chain 'A' and resid 321 through 323' Processing helix chain 'A' and resid 372 through 425 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 226 through 231 Processing helix chain 'B' and resid 233 through 248 removed outlier: 3.713A pdb=" N ALA B 243 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER B 244 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N PHE B 247 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N TYR B 248 " --> pdb=" O SER B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 253 No H-bonds generated for 'chain 'B' and resid 251 through 253' Processing helix chain 'B' and resid 256 through 277 removed outlier: 3.586A pdb=" N ARG B 277 " --> pdb=" O LEU B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 313 Processing helix chain 'B' and resid 324 through 330 Processing helix chain 'B' and resid 333 through 337 Processing helix chain 'B' and resid 417 through 477 removed outlier: 3.653A pdb=" N SER B 421 " --> pdb=" O ASP B 417 " (cutoff:3.500A) Proline residue: B 463 - end of helix removed outlier: 3.811A pdb=" N ASN B 477 " --> pdb=" O PHE B 473 " (cutoff:3.500A) 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 177 through 179 No H-bonds generated for 'chain 'C' and resid 177 through 179' Processing helix chain 'C' and resid 218 through 240 removed outlier: 4.639A pdb=" N ILE C 226 " --> pdb=" O VAL C 222 " (cutoff:3.500A) Proline residue: C 227 - end of helix removed outlier: 4.487A pdb=" N PHE C 239 " --> pdb=" O ALA C 235 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N TYR C 240 " --> pdb=" O ILE C 236 " (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 Processing helix chain 'C' and resid 279 through 306 Processing helix chain 'C' and resid 316 through 323 Processing helix chain 'C' and resid 325 through 329 removed outlier: 4.163A pdb=" N PHE C 329 " --> pdb=" O THR C 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 325 through 329' 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 234 removed outlier: 4.302A pdb=" N ILE D 220 " --> pdb=" O VAL D 216 " (cutoff:3.500A) Proline residue: D 221 - end of helix removed outlier: 4.006A pdb=" N GLY D 230 " --> pdb=" O SER D 226 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU D 231 " --> pdb=" O PHE D 227 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL D 232 " --> pdb=" O LEU D 228 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N PHE D 233 " --> pdb=" O THR D 229 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N TYR D 234 " --> pdb=" O GLY D 230 " (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 261 Processing helix chain 'D' and resid 273 through 299 Processing helix chain 'D' and resid 310 through 316 Processing helix chain 'D' and resid 320 through 322 No H-bonds generated for 'chain 'D' and resid 320 through 322' Processing helix chain 'D' and resid 371 through 425 removed outlier: 3.678A pdb=" N VAL D 423 " --> pdb=" O ILE D 420 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL D 425 " --> pdb=" O THR D 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 12 Processing helix chain 'E' and resid 63 through 65 No H-bonds generated for 'chain 'E' and resid 63 through 65' 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 175 through 177 No H-bonds generated for 'chain 'E' and resid 175 through 177' Processing helix chain 'E' and resid 220 through 242 removed outlier: 4.650A pdb=" N ALA E 228 " --> pdb=" O ILE E 224 " (cutoff:3.500A) Proline residue: E 229 - end of helix removed outlier: 3.749A pdb=" N LEU E 236 " --> pdb=" O LEU E 232 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N VAL E 237 " --> pdb=" O ILE E 233 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N VAL E 238 " --> pdb=" O SER E 234 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N LEU E 239 " --> pdb=" O SER E 235 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL E 240 " --> pdb=" O LEU E 236 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N TYR E 241 " --> pdb=" O VAL E 237 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N PHE E 242 " --> pdb=" O VAL E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 271 removed outlier: 3.628A pdb=" N GLN E 271 " --> pdb=" O PHE E 267 " (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 Processing sheet with id= A, first strand: chain 'A' and resid 156 through 160 removed outlier: 6.073A pdb=" N VAL A 29 " --> pdb=" O SER A 157 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N SER A 159 " --> pdb=" O VAL A 29 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE A 31 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ASP A 30 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ILE A 61 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ASN A 53 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N LEU A 40 " --> pdb=" O GLU A 51 " (cutoff:3.500A) removed outlier: 6.994A 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 80 Processing sheet with id= D, first strand: chain 'A' and resid 90 through 92 removed outlier: 3.716A pdb=" N CYS A 142 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE A 148 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N LEU A 199 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLN A 208 " --> pdb=" O MET A 178 " (cutoff:3.500A) removed outlier: 5.412A 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: 6.579A pdb=" N VAL B 31 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ASP B 161 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ILE B 33 " --> pdb=" O ASP B 161 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ASN B 32 " --> pdb=" O TYR B 63 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N TYR B 63 " --> pdb=" O ASN B 32 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ASN B 55 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N LEU B 42 " --> pdb=" O THR B 53 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N THR B 53 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 44 through 46 Processing sheet with id= G, first strand: chain 'B' and resid 80 through 82 Processing sheet with id= H, first strand: chain 'B' and resid 92 through 94 removed outlier: 4.686A pdb=" N ALA B 150 " --> pdb=" O GLN B 213 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N GLN B 213 " --> pdb=" O ALA B 150 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 164 through 166 Processing sheet with id= J, first strand: chain 'B' and resid 190 through 194 removed outlier: 6.821A pdb=" N ILE B 220 " --> pdb=" O ILE B 193 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 156 through 160 removed outlier: 6.415A pdb=" N VAL C 29 " --> pdb=" O THR C 157 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N GLN C 159 " --> pdb=" O VAL C 29 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N VAL C 31 " --> pdb=" O GLN C 159 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N THR C 30 " --> pdb=" O THR C 61 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N THR C 61 " --> pdb=" O THR C 30 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ASN C 53 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N LEU C 40 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N THR C 51 " --> pdb=" O LEU C 40 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 42 through 44 Processing sheet with id= M, first strand: chain 'C' and resid 77 through 80 Processing sheet with id= N, first strand: chain 'C' and resid 90 through 92 removed outlier: 6.622A pdb=" N GLN C 214 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N ILE C 188 " --> pdb=" O GLN C 214 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 193 through 198 removed outlier: 4.147A pdb=" N ARG C 198 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N TYR C 204 " --> pdb=" O ARG C 198 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 156 through 160 removed outlier: 6.036A pdb=" N VAL D 29 " --> pdb=" O SER D 157 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N SER D 159 " --> pdb=" O VAL D 29 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILE D 31 " --> pdb=" O SER D 159 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ASP D 30 " --> pdb=" O ILE D 61 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ILE D 61 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ASN D 53 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N LEU D 40 " --> pdb=" O GLU D 51 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N GLU D 51 " --> pdb=" O LEU D 40 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 42 through 44 Processing sheet with id= R, first strand: chain 'D' and resid 77 through 80 Processing sheet with id= S, first strand: chain 'D' and resid 90 through 92 removed outlier: 3.772A pdb=" N CYS D 142 " --> pdb=" O PHE D 205 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILE D 148 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N LEU D 199 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLN D 208 " --> pdb=" O MET D 178 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N MET D 178 " --> pdb=" O GLN D 208 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 156 through 160 removed outlier: 6.499A pdb=" N ILE E 29 " --> pdb=" O ASN E 157 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N GLN E 159 " --> pdb=" O ILE E 29 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N VAL E 31 " --> pdb=" O GLN E 159 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ASP E 30 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ASN E 61 " --> pdb=" O ASP E 30 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ASN E 53 " --> pdb=" O THR E 38 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N LEU E 40 " --> pdb=" O THR E 51 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N THR E 51 " --> pdb=" O LEU E 40 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER E 115 " --> pdb=" O TYR E 111 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N LEU E 119 " --> pdb=" O ASN E 107 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ASN E 107 " --> pdb=" O LEU E 119 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 42 through 44 Processing sheet with id= V, first strand: chain 'E' and resid 90 through 92 removed outlier: 5.232A pdb=" N SER E 148 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N GLN E 207 " --> pdb=" O SER E 148 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 184 through 188 removed outlier: 6.889A pdb=" N ILE E 214 " --> pdb=" O ARG E 187 " (cutoff:3.500A) 788 hydrogen bonds defined for protein. 2148 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: 4.69 Time building geometry restraints manager: 8.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2644 1.31 - 1.44: 4786 1.44 - 1.58: 9853 1.58 - 1.71: 13 1.71 - 1.84: 139 Bond restraints: 17435 Sorted by residual: bond pdb=" C31 POV B 602 " pdb=" O31 POV B 602 " ideal model delta sigma weight residual 1.327 1.402 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C31 POV C 503 " pdb=" O31 POV C 503 " ideal model delta sigma weight residual 1.327 1.400 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" C31 POV C 502 " pdb=" O31 POV C 502 " ideal model delta sigma weight residual 1.327 1.400 -0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" C21 POV C 503 " pdb=" O21 POV C 503 " ideal model delta sigma weight residual 1.330 1.401 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" C21 POV B 602 " pdb=" O21 POV B 602 " ideal model delta sigma weight residual 1.330 1.400 -0.070 2.00e-02 2.50e+03 1.24e+01 ... (remaining 17430 not shown) Histogram of bond angle deviations from ideal: 98.78 - 105.83: 417 105.83 - 112.88: 9986 112.88 - 119.94: 5725 119.94 - 126.99: 7378 126.99 - 134.04: 275 Bond angle restraints: 23781 Sorted by residual: angle pdb=" O11 POV E 502 " pdb=" P POV E 502 " pdb=" O12 POV E 502 " ideal model delta sigma weight residual 97.67 110.79 -13.12 3.00e+00 1.11e-01 1.91e+01 angle pdb=" O11 POV C 502 " pdb=" P POV C 502 " pdb=" O12 POV C 502 " ideal model delta sigma weight residual 97.67 109.91 -12.24 3.00e+00 1.11e-01 1.66e+01 angle pdb=" O13 POV C 502 " pdb=" P POV C 502 " pdb=" O14 POV C 502 " ideal model delta sigma weight residual 121.11 109.06 12.05 3.00e+00 1.11e-01 1.61e+01 angle pdb=" O11 POV C 503 " pdb=" P POV C 503 " pdb=" O12 POV C 503 " ideal model delta sigma weight residual 97.67 109.61 -11.94 3.00e+00 1.11e-01 1.58e+01 angle pdb=" O11 POV B 602 " pdb=" P POV B 602 " pdb=" O12 POV B 602 " ideal model delta sigma weight residual 97.67 109.52 -11.85 3.00e+00 1.11e-01 1.56e+01 ... (remaining 23776 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.83: 10485 29.83 - 59.67: 281 59.67 - 89.50: 67 89.50 - 119.34: 20 119.34 - 149.17: 2 Dihedral angle restraints: 10855 sinusoidal: 4875 harmonic: 5980 Sorted by residual: 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 -150.93 -29.07 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA GLU B 418 " pdb=" C GLU B 418 " pdb=" N ILE B 419 " pdb=" CA ILE B 419 " ideal model delta harmonic sigma weight residual -180.00 -151.88 -28.12 0 5.00e+00 4.00e-02 3.16e+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 -153.50 -26.50 0 5.00e+00 4.00e-02 2.81e+01 ... (remaining 10852 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2353 0.059 - 0.118: 409 0.118 - 0.176: 44 0.176 - 0.235: 2 0.235 - 0.294: 7 Chirality restraints: 2815 Sorted by residual: chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" C5 BMA K 3 " pdb=" C4 BMA K 3 " pdb=" C6 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" C5 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C6 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 2812 not shown) Planarity restraints: 2881 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 483 " 0.037 5.00e-02 4.00e+02 5.61e-02 5.04e+00 pdb=" N PRO E 484 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO E 484 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 484 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 223 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.95e+00 pdb=" C ILE E 223 " -0.038 2.00e-02 2.50e+03 pdb=" O ILE E 223 " 0.015 2.00e-02 2.50e+03 pdb=" N ILE E 224 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 393 " 0.010 2.00e-02 2.50e+03 1.94e-02 3.78e+00 pdb=" C SER A 393 " -0.034 2.00e-02 2.50e+03 pdb=" O SER A 393 " 0.013 2.00e-02 2.50e+03 pdb=" N ASN A 394 " 0.011 2.00e-02 2.50e+03 ... (remaining 2878 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 91 2.51 - 3.10: 12972 3.10 - 3.70: 26810 3.70 - 4.30: 41053 4.30 - 4.90: 67708 Nonbonded interactions: 148634 Sorted by model distance: nonbonded pdb=" OG SER B 244 " pdb=" OG1 THR B 462 " model vdw 1.907 2.440 nonbonded pdb=" OD1 ASN B 98 " pdb=" OG SER B 129 " model vdw 2.032 2.440 nonbonded pdb=" OD2 ASP A 152 " pdb=" OG1 THR A 154 " model vdw 2.070 2.440 nonbonded pdb=" OG SER A 82 " pdb=" O THR A 106 " model vdw 2.085 2.440 nonbonded pdb=" OD2 ASP D 138 " pdb=" NE2 GLN D 140 " model vdw 2.107 2.520 ... (remaining 148629 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)) selection = (chain 'D' and (resid 1 through 330 or resid 370 through 426 or resid 501)) } ncs_group { reference = chain 'F' selection = chain 'J' selection = chain 'K' } 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.680 Check model and map are aligned: 0.300 Set scattering table: 0.170 Process input model: 49.980 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.100 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:11.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 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 : 0.007 0.075 17435 Z= 0.446 Angle : 0.802 13.119 23781 Z= 0.368 Chirality : 0.047 0.294 2815 Planarity : 0.004 0.056 2873 Dihedral : 15.710 149.173 6940 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % 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: 0.31 (0.19), residues: 1995 helix: 1.84 (0.19), residues: 756 sheet: -0.92 (0.24), residues: 389 loop : -0.68 (0.21), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 118 HIS 0.004 0.001 HIS B 103 PHE 0.015 0.002 PHE C 12 TYR 0.015 0.002 TYR C 223 ARG 0.009 0.001 ARG E 147 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 1.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 1.5543 time to fit residues: 157.5393 Evaluate side-chains 74 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 2.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 0.0570 chunk 150 optimal weight: 0.1980 chunk 83 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 155 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 179 optimal weight: 0.8980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 HIS B 276 GLN B 305 ASN D 204 HIS D 322 ASN D 385 HIS E 172 HIS ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 ASN E 431 ASN E 437 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.0970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17435 Z= 0.190 Angle : 0.526 6.877 23781 Z= 0.270 Chirality : 0.043 0.182 2815 Planarity : 0.004 0.036 2873 Dihedral : 12.142 129.986 3031 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.70 % Allowed : 4.83 % Favored : 94.47 % 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: 0.60 (0.19), residues: 1995 helix: 2.03 (0.18), residues: 765 sheet: -0.82 (0.24), residues: 384 loop : -0.46 (0.22), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 187 HIS 0.004 0.001 HIS D 204 PHE 0.012 0.001 PHE E 467 TYR 0.014 0.001 TYR E 117 ARG 0.009 0.000 ARG C 168 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 83 time to evaluate : 2.009 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 ASP cc_start: 0.6715 (t0) cc_final: 0.6381 (t0) REVERT: A 373 LYS cc_start: 0.6964 (mmtt) cc_final: 0.6633 (mmtt) REVERT: D 404 MET cc_start: 0.8914 (tmm) cc_final: 0.8703 (tmt) REVERT: E 116 MET cc_start: 0.8621 (mmm) cc_final: 0.8135 (mmm) outliers start: 13 outliers final: 5 residues processed: 88 average time/residue: 1.4275 time to fit residues: 140.6596 Evaluate side-chains 76 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 71 time to evaluate : 2.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 282 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 99 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 149 optimal weight: 0.7980 chunk 122 optimal weight: 0.3980 chunk 49 optimal weight: 3.9990 chunk 180 optimal weight: 3.9990 chunk 194 optimal weight: 4.9990 chunk 160 optimal weight: 0.2980 chunk 178 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 144 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 276 GLN D 3 HIS D 48 GLN ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17435 Z= 0.174 Angle : 0.479 6.438 23781 Z= 0.244 Chirality : 0.042 0.174 2815 Planarity : 0.004 0.036 2873 Dihedral : 9.991 125.881 3031 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.97 % Allowed : 6.33 % Favored : 92.70 % 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: 0.82 (0.19), residues: 1995 helix: 2.23 (0.18), residues: 761 sheet: -0.71 (0.24), residues: 375 loop : -0.36 (0.22), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 187 HIS 0.003 0.001 HIS B 313 PHE 0.011 0.001 PHE E 467 TYR 0.011 0.001 TYR B 439 ARG 0.004 0.000 ARG C 168 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 81 time to evaluate : 2.036 Fit side-chains revert: symmetry clash REVERT: A 97 ASP cc_start: 0.6644 (t0) cc_final: 0.6329 (t0) REVERT: A 373 LYS cc_start: 0.6946 (mmtt) cc_final: 0.6645 (mmtt) REVERT: A 416 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8448 (mp) REVERT: E 116 MET cc_start: 0.8643 (mmm) cc_final: 0.8173 (mmm) outliers start: 18 outliers final: 4 residues processed: 91 average time/residue: 1.3873 time to fit residues: 141.7558 Evaluate side-chains 79 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 74 time to evaluate : 2.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain D residue 282 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 177 optimal weight: 0.9980 chunk 135 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 19 optimal weight: 0.0170 chunk 85 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 chunk 180 optimal weight: 4.9990 chunk 191 optimal weight: 10.0000 chunk 94 optimal weight: 0.8980 chunk 171 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.9820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN A 208 GLN B 20 HIS B 276 GLN ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 17435 Z= 0.212 Angle : 0.498 13.867 23781 Z= 0.251 Chirality : 0.042 0.190 2815 Planarity : 0.004 0.035 2873 Dihedral : 9.409 123.491 3031 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.18 % Allowed : 6.71 % Favored : 92.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.19), residues: 1995 helix: 2.26 (0.18), residues: 769 sheet: -0.65 (0.24), residues: 375 loop : -0.30 (0.22), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 311 HIS 0.003 0.000 HIS B 60 PHE 0.011 0.001 PHE E 467 TYR 0.012 0.001 TYR B 439 ARG 0.010 0.000 ARG C 168 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 81 time to evaluate : 1.905 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 ASP cc_start: 0.6653 (t0) cc_final: 0.6335 (t0) REVERT: A 373 LYS cc_start: 0.6861 (mmtt) cc_final: 0.6451 (mmtt) outliers start: 22 outliers final: 10 residues processed: 89 average time/residue: 1.3867 time to fit residues: 138.0361 Evaluate side-chains 85 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 75 time to evaluate : 1.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 308 MET Chi-restraints excluded: chain E residue 156 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 159 optimal weight: 4.9990 chunk 108 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 78 optimal weight: 0.0770 chunk 163 optimal weight: 0.7980 chunk 132 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 171 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 GLN B 276 GLN ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 17435 Z= 0.199 Angle : 0.487 13.991 23781 Z= 0.245 Chirality : 0.042 0.179 2815 Planarity : 0.004 0.034 2873 Dihedral : 8.932 122.188 3031 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.29 % Allowed : 7.46 % Favored : 91.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 1995 helix: 2.33 (0.18), residues: 769 sheet: -0.62 (0.25), residues: 370 loop : -0.27 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 311 HIS 0.003 0.000 HIS B 60 PHE 0.010 0.001 PHE A 256 TYR 0.011 0.001 TYR B 439 ARG 0.004 0.000 ARG C 168 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 81 time to evaluate : 2.041 Fit side-chains revert: symmetry clash REVERT: A 97 ASP cc_start: 0.6595 (t0) cc_final: 0.6292 (t0) REVERT: A 373 LYS cc_start: 0.6815 (mmtt) cc_final: 0.6426 (mmtt) outliers start: 24 outliers final: 11 residues processed: 94 average time/residue: 1.3804 time to fit residues: 145.5942 Evaluate side-chains 88 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 77 time to evaluate : 2.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 308 MET Chi-restraints excluded: chain D residue 407 ASP Chi-restraints excluded: chain D residue 418 CYS Chi-restraints excluded: chain E residue 156 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 64 optimal weight: 4.9990 chunk 172 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 191 optimal weight: 3.9990 chunk 159 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 GLN ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 17435 Z= 0.407 Angle : 0.567 14.932 23781 Z= 0.282 Chirality : 0.044 0.189 2815 Planarity : 0.004 0.044 2873 Dihedral : 9.031 123.874 3031 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.40 % Allowed : 8.00 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.86 (0.19), residues: 1995 helix: 2.23 (0.19), residues: 771 sheet: -0.69 (0.24), residues: 386 loop : -0.32 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 149 HIS 0.006 0.001 HIS D 408 PHE 0.014 0.001 PHE E 467 TYR 0.015 0.001 TYR B 439 ARG 0.011 0.000 ARG C 168 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 77 time to evaluate : 2.127 Fit side-chains revert: symmetry clash REVERT: A 97 ASP cc_start: 0.6780 (t0) cc_final: 0.6480 (t0) REVERT: A 282 MET cc_start: 0.7979 (ttm) cc_final: 0.7668 (mtp) REVERT: A 373 LYS cc_start: 0.6860 (mmtt) cc_final: 0.6466 (mmtt) REVERT: A 404 MET cc_start: 0.7804 (tmm) cc_final: 0.7577 (tmt) REVERT: D 407 ASP cc_start: 0.8195 (OUTLIER) cc_final: 0.7906 (m-30) outliers start: 26 outliers final: 10 residues processed: 90 average time/residue: 1.4638 time to fit residues: 147.5010 Evaluate side-chains 83 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 72 time to evaluate : 1.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 308 MET Chi-restraints excluded: chain D residue 407 ASP Chi-restraints excluded: chain E residue 156 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 184 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 109 optimal weight: 0.6980 chunk 139 optimal weight: 0.6980 chunk 108 optimal weight: 0.6980 chunk 161 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 190 optimal weight: 8.9990 chunk 119 optimal weight: 4.9990 chunk 116 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 GLN ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 250 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 17435 Z= 0.184 Angle : 0.485 14.879 23781 Z= 0.245 Chirality : 0.042 0.173 2815 Planarity : 0.003 0.033 2873 Dihedral : 8.523 121.215 3031 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.29 % Allowed : 8.32 % Favored : 90.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.95 (0.19), residues: 1995 helix: 2.33 (0.19), residues: 770 sheet: -0.72 (0.24), residues: 391 loop : -0.25 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 311 HIS 0.004 0.001 HIS B 60 PHE 0.011 0.001 PHE E 467 TYR 0.011 0.001 TYR B 439 ARG 0.003 0.000 ARG C 168 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 76 time to evaluate : 2.148 Fit side-chains revert: symmetry clash REVERT: A 97 ASP cc_start: 0.6547 (t0) cc_final: 0.6292 (t0) REVERT: A 282 MET cc_start: 0.8014 (ttm) cc_final: 0.7742 (mtp) REVERT: A 373 LYS cc_start: 0.6776 (mmtt) cc_final: 0.6435 (mmtt) REVERT: A 416 LEU cc_start: 0.8758 (tt) cc_final: 0.8431 (mp) REVERT: D 326 PHE cc_start: 0.7696 (OUTLIER) cc_final: 0.7462 (p90) outliers start: 24 outliers final: 10 residues processed: 90 average time/residue: 1.5059 time to fit residues: 150.6610 Evaluate side-chains 85 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 74 time to evaluate : 1.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 308 MET Chi-restraints excluded: chain D residue 326 PHE Chi-restraints excluded: chain E residue 156 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 118 optimal weight: 0.8980 chunk 76 optimal weight: 6.9990 chunk 113 optimal weight: 6.9990 chunk 57 optimal weight: 0.0030 chunk 37 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 121 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 94 optimal weight: 0.6980 chunk 17 optimal weight: 5.9990 chunk 150 optimal weight: 0.0050 overall best weight: 0.4604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN B 95 GLN B 276 GLN ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.077 17435 Z= 0.158 Angle : 0.478 14.996 23781 Z= 0.240 Chirality : 0.041 0.169 2815 Planarity : 0.003 0.033 2873 Dihedral : 8.156 119.366 3031 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.23 % Allowed : 8.86 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 1.02 (0.19), residues: 1995 helix: 2.41 (0.19), residues: 766 sheet: -0.68 (0.24), residues: 390 loop : -0.21 (0.22), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 311 HIS 0.003 0.000 HIS B 60 PHE 0.010 0.001 PHE E 467 TYR 0.011 0.001 TYR B 439 ARG 0.005 0.000 ARG C 168 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 79 time to evaluate : 2.097 Fit side-chains revert: symmetry clash REVERT: A 97 ASP cc_start: 0.6583 (t0) cc_final: 0.6308 (t0) REVERT: A 282 MET cc_start: 0.8002 (ttm) cc_final: 0.7734 (mtp) REVERT: A 373 LYS cc_start: 0.6654 (mmtt) cc_final: 0.6379 (mmtt) REVERT: A 404 MET cc_start: 0.7652 (tmm) cc_final: 0.7380 (tmt) REVERT: A 416 LEU cc_start: 0.8772 (tt) cc_final: 0.8446 (mp) outliers start: 23 outliers final: 11 residues processed: 95 average time/residue: 1.3624 time to fit residues: 145.1280 Evaluate side-chains 85 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 74 time to evaluate : 2.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 308 MET Chi-restraints excluded: chain E residue 156 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 173 optimal weight: 2.9990 chunk 182 optimal weight: 0.8980 chunk 166 optimal weight: 0.9990 chunk 177 optimal weight: 0.3980 chunk 107 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 139 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 160 optimal weight: 0.1980 chunk 168 optimal weight: 0.1980 chunk 116 optimal weight: 4.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 GLN B 437 ASN ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.076 17435 Z= 0.161 Angle : 0.475 15.450 23781 Z= 0.238 Chirality : 0.041 0.172 2815 Planarity : 0.003 0.033 2873 Dihedral : 7.932 117.511 3031 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.91 % Allowed : 9.34 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 1.05 (0.19), residues: 1995 helix: 2.41 (0.19), residues: 771 sheet: -0.69 (0.24), residues: 397 loop : -0.17 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 311 HIS 0.012 0.001 HIS E 323 PHE 0.020 0.001 PHE A 227 TYR 0.011 0.001 TYR B 439 ARG 0.004 0.000 ARG C 168 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 80 time to evaluate : 2.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 ASP cc_start: 0.6548 (t0) cc_final: 0.6292 (t0) REVERT: A 282 MET cc_start: 0.8011 (ttm) cc_final: 0.7748 (mtp) REVERT: A 373 LYS cc_start: 0.6723 (mmtt) cc_final: 0.6475 (mmtt) REVERT: A 416 LEU cc_start: 0.8752 (tt) cc_final: 0.8445 (mp) outliers start: 17 outliers final: 14 residues processed: 92 average time/residue: 1.3978 time to fit residues: 144.2065 Evaluate side-chains 91 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 77 time to evaluate : 2.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 308 MET Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 448 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 188 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 89 optimal weight: 0.3980 chunk 130 optimal weight: 0.7980 chunk 197 optimal weight: 0.4980 chunk 181 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 16 optimal weight: 0.3980 chunk 121 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 HIS A 408 HIS B 95 GLN B 276 GLN B 437 ASN ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.075 17435 Z= 0.168 Angle : 0.485 15.589 23781 Z= 0.242 Chirality : 0.041 0.169 2815 Planarity : 0.003 0.033 2873 Dihedral : 7.799 116.266 3031 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.75 % Allowed : 9.72 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 1.07 (0.19), residues: 1995 helix: 2.43 (0.19), residues: 765 sheet: -0.68 (0.24), residues: 398 loop : -0.13 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 311 HIS 0.009 0.001 HIS E 323 PHE 0.025 0.001 PHE C 468 TYR 0.011 0.001 TYR B 439 ARG 0.004 0.000 ARG C 168 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 76 time to evaluate : 1.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 ASP cc_start: 0.6507 (t0) cc_final: 0.6251 (t0) REVERT: A 282 MET cc_start: 0.8013 (ttm) cc_final: 0.7754 (mtp) REVERT: A 373 LYS cc_start: 0.6609 (mmtt) cc_final: 0.6354 (mmtt) REVERT: A 416 LEU cc_start: 0.8765 (tt) cc_final: 0.8457 (mp) outliers start: 14 outliers final: 13 residues processed: 85 average time/residue: 1.5382 time to fit residues: 146.1871 Evaluate side-chains 88 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 75 time to evaluate : 2.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 308 MET Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 448 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 157 optimal weight: 0.0980 chunk 65 optimal weight: 0.4980 chunk 161 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 138 optimal weight: 3.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 HIS B 276 GLN ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.066997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.051694 restraints weight = 39446.978| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 2.80 r_work: 0.2627 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2623 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2623 r_free = 0.2623 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2623 r_free = 0.2623 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2623 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 17435 Z= 0.171 Angle : 0.479 15.711 23781 Z= 0.240 Chirality : 0.041 0.169 2815 Planarity : 0.003 0.033 2873 Dihedral : 7.668 114.859 3031 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.97 % Allowed : 9.39 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 1.10 (0.19), residues: 1995 helix: 2.43 (0.19), residues: 766 sheet: -0.66 (0.24), residues: 398 loop : -0.10 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 311 HIS 0.009 0.001 HIS E 323 PHE 0.023 0.001 PHE A 227 TYR 0.011 0.001 TYR B 439 ARG 0.004 0.000 ARG C 168 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3958.99 seconds wall clock time: 72 minutes 5.64 seconds (4325.64 seconds total)