Starting phenix.real_space_refine on Sun Feb 18 06:51:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c82_16469/02_2024/8c82_16469_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c82_16469/02_2024/8c82_16469.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c82_16469/02_2024/8c82_16469_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c82_16469/02_2024/8c82_16469_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c82_16469/02_2024/8c82_16469_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c82_16469/02_2024/8c82_16469.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c82_16469/02_2024/8c82_16469.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c82_16469/02_2024/8c82_16469_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c82_16469/02_2024/8c82_16469_updated.pdb" } resolution = 3.4 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= 0.026 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 2 5.49 5 S 110 5.16 5 C 13534 2.51 5 N 3486 2.21 5 O 3938 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 236": "OD1" <-> "OD2" Residue "B TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 487": "OE1" <-> "OE2" Residue "B GLU 489": "OE1" <-> "OE2" Residue "C TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 146": "OE1" <-> "OE2" Residue "C PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 181": "OE1" <-> "OE2" Residue "C TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 246": "OD1" <-> "OD2" Residue "C PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 452": "OD1" <-> "OD2" Residue "C GLU 551": "OE1" <-> "OE2" Residue "D PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 94": "OD1" <-> "OD2" Residue "F GLU 98": "OE1" <-> "OE2" Residue "F GLU 166": "OE1" <-> "OE2" Residue "F GLU 270": "OE1" <-> "OE2" Residue "F GLU 273": "OE1" <-> "OE2" Residue "F GLU 321": "OE1" <-> "OE2" Residue "F ASP 404": "OD1" <-> "OD2" Residue "F TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 463": "OE1" <-> "OE2" Residue "F PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 467": "OE1" <-> "OE2" Residue "G GLU 25": "OE1" <-> "OE2" Residue "G TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 95": "OE1" <-> "OE2" Residue "G GLU 146": "OE1" <-> "OE2" Residue "G PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 246": "OD1" <-> "OD2" Residue "G PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 551": "OE1" <-> "OE2" Residue "G ASP 556": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 21070 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1496 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 10, 'TRANS': 172} Chain: "B" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3943 Classifications: {'peptide': 505} Link IDs: {'PTRANS': 25, 'TRANS': 479} Chain: "C" Number of atoms: 4382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4382 Classifications: {'peptide': 554} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 524} Chain: "D" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 569 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "E" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1496 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 10, 'TRANS': 172} Chain: "F" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3943 Classifications: {'peptide': 505} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 479} Chain: "G" Number of atoms: 4382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4382 Classifications: {'peptide': 554} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 524} Chain: "H" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 569 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'Z8A': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'PLP': 1, 'Q7G': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 130 Unusual residues: {'Q7G': 1, 'Z8A': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 11.25, per 1000 atoms: 0.53 Number of scatterers: 21070 At special positions: 0 Unit cell: (106.26, 175.56, 122.892, 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 110 16.00 P 2 15.00 O 3938 8.00 N 3486 7.00 C 13534 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.51 Conformation dependent library (CDL) restraints added in 3.9 seconds 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4932 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 106 helices and 16 sheets defined 45.6% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.48 Creating SS restraints... Processing helix chain 'A' and resid 63 through 71 Processing helix chain 'A' and resid 79 through 81 No H-bonds generated for 'chain 'A' and resid 79 through 81' Processing helix chain 'A' and resid 87 through 102 Processing helix chain 'A' and resid 108 through 127 Processing helix chain 'A' and resid 147 through 154 removed outlier: 6.276A pdb=" N ASP A 152 " --> pdb=" O TRP A 148 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N ASP A 153 " --> pdb=" O GLU A 149 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLU A 154 " --> pdb=" O GLN A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 178 Proline residue: A 168 - end of helix Processing helix chain 'A' and resid 183 through 197 removed outlier: 4.035A pdb=" N TRP A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 201 No H-bonds generated for 'chain 'A' and resid 199 through 201' Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'B' and resid 53 through 72 Processing helix chain 'B' and resid 82 through 85 removed outlier: 3.801A pdb=" N LYS B 85 " --> pdb=" O GLN B 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 82 through 85' Processing helix chain 'B' and resid 90 through 99 removed outlier: 3.662A pdb=" N ASP B 94 " --> pdb=" O PRO B 90 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA B 95 " --> pdb=" O GLN B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 119 removed outlier: 4.888A pdb=" N TRP B 116 " --> pdb=" O ASP B 112 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ARG B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N VAL B 118 " --> pdb=" O GLN B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 175 removed outlier: 3.586A pdb=" N GLU B 166 " --> pdb=" O GLU B 162 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL B 167 " --> pdb=" O PRO B 163 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS B 169 " --> pdb=" O LYS B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 203 Processing helix chain 'B' and resid 214 through 216 No H-bonds generated for 'chain 'B' and resid 214 through 216' Processing helix chain 'B' and resid 218 through 225 Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 240 through 249 Processing helix chain 'B' and resid 261 through 278 Processing helix chain 'B' and resid 303 through 313 Processing helix chain 'B' and resid 335 through 339 removed outlier: 3.669A pdb=" N PHE B 339 " --> pdb=" O LEU B 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 335 through 339' Processing helix chain 'B' and resid 343 through 346 No H-bonds generated for 'chain 'B' and resid 343 through 346' Processing helix chain 'B' and resid 369 through 378 removed outlier: 4.193A pdb=" N ILE B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 383 No H-bonds generated for 'chain 'B' and resid 380 through 383' Processing helix chain 'B' and resid 390 through 405 Processing helix chain 'B' and resid 408 through 425 removed outlier: 3.593A pdb=" N PHE B 424 " --> pdb=" O LEU B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 432 removed outlier: 4.040A pdb=" N SER B 432 " --> pdb=" O SER B 429 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 429 through 432' Processing helix chain 'B' and resid 451 through 457 Processing helix chain 'B' and resid 462 through 475 Processing helix chain 'B' and resid 483 through 502 Processing helix chain 'B' and resid 514 through 516 No H-bonds generated for 'chain 'B' and resid 514 through 516' Processing helix chain 'B' and resid 535 through 553 Processing helix chain 'C' and resid 20 through 27 Processing helix chain 'C' and resid 34 through 36 No H-bonds generated for 'chain 'C' and resid 34 through 36' Processing helix chain 'C' and resid 58 through 84 Processing helix chain 'C' and resid 109 through 113 Processing helix chain 'C' and resid 116 through 121 removed outlier: 5.360A pdb=" N ASP C 120 " --> pdb=" O ARG C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 185 Processing helix chain 'C' and resid 201 through 214 Processing helix chain 'C' and resid 225 through 235 removed outlier: 4.321A pdb=" N PHE C 233 " --> pdb=" O ASN C 229 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ASN C 234 " --> pdb=" O ALA C 230 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ALA C 235 " --> pdb=" O ASN C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 260 Processing helix chain 'C' and resid 273 through 285 Processing helix chain 'C' and resid 314 through 324 Processing helix chain 'C' and resid 346 through 349 No H-bonds generated for 'chain 'C' and resid 346 through 349' Processing helix chain 'C' and resid 379 through 388 removed outlier: 4.026A pdb=" N ARG C 384 " --> pdb=" O TRP C 380 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU C 387 " --> pdb=" O ASP C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 394 No H-bonds generated for 'chain 'C' and resid 391 through 394' Processing helix chain 'C' and resid 400 through 414 Processing helix chain 'C' and resid 422 through 443 Processing helix chain 'C' and resid 465 through 475 Processing helix chain 'C' and resid 505 through 522 Processing helix chain 'C' and resid 542 through 554 Proline residue: C 550 - end of helix removed outlier: 4.734A pdb=" N LYS C 554 " --> pdb=" O PRO C 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 21 Processing helix chain 'D' and resid 30 through 44 Processing helix chain 'D' and resid 53 through 68 Processing helix chain 'E' and resid 63 through 71 Processing helix chain 'E' and resid 87 through 102 Processing helix chain 'E' and resid 108 through 127 Processing helix chain 'E' and resid 147 through 154 removed outlier: 6.433A pdb=" N ASP E 152 " --> pdb=" O TRP E 148 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N ASP E 153 " --> pdb=" O GLU E 149 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLU E 154 " --> pdb=" O GLN E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 178 Proline residue: E 168 - end of helix Processing helix chain 'E' and resid 183 through 196 removed outlier: 3.556A pdb=" N TRP E 188 " --> pdb=" O LYS E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 201 No H-bonds generated for 'chain 'E' and resid 199 through 201' Processing helix chain 'F' and resid 54 through 72 removed outlier: 3.625A pdb=" N VAL F 59 " --> pdb=" O TYR F 55 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU F 60 " --> pdb=" O ARG F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 84 No H-bonds generated for 'chain 'F' and resid 82 through 84' Processing helix chain 'F' and resid 90 through 99 Processing helix chain 'F' and resid 111 through 119 removed outlier: 4.885A pdb=" N TRP F 116 " --> pdb=" O ASP F 112 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ARG F 117 " --> pdb=" O GLU F 113 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL F 118 " --> pdb=" O GLN F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 175 Processing helix chain 'F' and resid 190 through 203 Processing helix chain 'F' and resid 214 through 216 No H-bonds generated for 'chain 'F' and resid 214 through 216' Processing helix chain 'F' and resid 218 through 225 Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 240 through 249 Processing helix chain 'F' and resid 261 through 278 Processing helix chain 'F' and resid 303 through 313 Processing helix chain 'F' and resid 335 through 339 removed outlier: 3.677A pdb=" N PHE F 339 " --> pdb=" O LEU F 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 335 through 339' Processing helix chain 'F' and resid 343 through 346 No H-bonds generated for 'chain 'F' and resid 343 through 346' Processing helix chain 'F' and resid 369 through 378 removed outlier: 4.157A pdb=" N ILE F 377 " --> pdb=" O LEU F 373 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 383 No H-bonds generated for 'chain 'F' and resid 380 through 383' Processing helix chain 'F' and resid 390 through 405 Processing helix chain 'F' and resid 408 through 426 Processing helix chain 'F' and resid 451 through 458 Processing helix chain 'F' and resid 462 through 475 Processing helix chain 'F' and resid 483 through 502 removed outlier: 3.528A pdb=" N ASN F 502 " --> pdb=" O HIS F 498 " (cutoff:3.500A) Processing helix chain 'F' and resid 514 through 516 No H-bonds generated for 'chain 'F' and resid 514 through 516' Processing helix chain 'F' and resid 535 through 553 Processing helix chain 'G' and resid 20 through 27 Processing helix chain 'G' and resid 34 through 36 No H-bonds generated for 'chain 'G' and resid 34 through 36' Processing helix chain 'G' and resid 58 through 84 removed outlier: 3.501A pdb=" N TYR G 68 " --> pdb=" O THR G 64 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU G 71 " --> pdb=" O ASN G 67 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE G 72 " --> pdb=" O TYR G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 93 removed outlier: 3.731A pdb=" N LEU G 91 " --> pdb=" O ASN G 88 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N ASP G 92 " --> pdb=" O LYS G 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 113 Processing helix chain 'G' and resid 116 through 121 removed outlier: 5.395A pdb=" N ASP G 120 " --> pdb=" O ARG G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 174 through 185 Processing helix chain 'G' and resid 201 through 214 Processing helix chain 'G' and resid 225 through 235 removed outlier: 4.338A pdb=" N PHE G 233 " --> pdb=" O ASN G 229 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N ASN G 234 " --> pdb=" O ALA G 230 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ALA G 235 " --> pdb=" O ASN G 231 " (cutoff:3.500A) Processing helix chain 'G' and resid 251 through 260 Processing helix chain 'G' and resid 273 through 285 Processing helix chain 'G' and resid 314 through 324 Processing helix chain 'G' and resid 346 through 349 No H-bonds generated for 'chain 'G' and resid 346 through 349' Processing helix chain 'G' and resid 379 through 388 removed outlier: 3.927A pdb=" N ARG G 384 " --> pdb=" O TRP G 380 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU G 387 " --> pdb=" O ASP G 383 " (cutoff:3.500A) Processing helix chain 'G' and resid 391 through 394 No H-bonds generated for 'chain 'G' and resid 391 through 394' Processing helix chain 'G' and resid 400 through 414 Processing helix chain 'G' and resid 422 through 443 Processing helix chain 'G' and resid 465 through 475 Processing helix chain 'G' and resid 505 through 522 Processing helix chain 'G' and resid 542 through 554 Proline residue: G 550 - end of helix removed outlier: 4.761A pdb=" N LYS G 554 " --> pdb=" O PRO G 550 " (cutoff:3.500A) Processing helix chain 'H' and resid 14 through 20 Processing helix chain 'H' and resid 26 through 44 removed outlier: 3.874A pdb=" N THR H 30 " --> pdb=" O GLY H 26 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N ILE H 31 " --> pdb=" O ILE H 27 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 68 Processing sheet with id= A, first strand: chain 'A' and resid 55 through 57 Processing sheet with id= B, first strand: chain 'B' and resid 135 through 137 Processing sheet with id= C, first strand: chain 'B' and resid 207 through 211 removed outlier: 3.516A pdb=" N ILE B 349 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL B 231 " --> pdb=" O PHE B 287 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N VAL B 289 " --> pdb=" O VAL B 231 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL B 233 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 8.826A pdb=" N GLU B 291 " --> pdb=" O VAL B 233 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N THR B 252 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N ALA B 234 " --> pdb=" O THR B 252 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N TYR B 254 " --> pdb=" O ALA B 234 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 434 through 436 Processing sheet with id= E, first strand: chain 'C' and resid 133 through 137 Processing sheet with id= F, first strand: chain 'C' and resid 139 through 142 removed outlier: 4.184A pdb=" N TYR C 147 " --> pdb=" O HIS C 142 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 218 through 222 removed outlier: 3.652A pdb=" N GLY C 362 " --> pdb=" O TYR C 374 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE C 359 " --> pdb=" O LEU C 328 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET C 361 " --> pdb=" O ILE C 330 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU C 242 " --> pdb=" O LEU C 298 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N CYS C 300 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILE C 244 " --> pdb=" O CYS C 300 " (cutoff:3.500A) removed outlier: 9.011A pdb=" N GLU C 302 " --> pdb=" O ILE C 244 " (cutoff:3.500A) removed outlier: 9.211A pdb=" N ASP C 246 " --> pdb=" O GLU C 302 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ALA C 263 " --> pdb=" O VAL C 243 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N SER C 245 " --> pdb=" O ALA C 263 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ARG C 265 " --> pdb=" O SER C 245 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 455 through 460 removed outlier: 3.563A pdb=" N ARG C 494 " --> pdb=" O VAL C 483 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N VAL C 481 " --> pdb=" O ARG C 496 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 55 through 57 Processing sheet with id= J, first strand: chain 'F' and resid 135 through 137 removed outlier: 3.576A pdb=" N GLU F 142 " --> pdb=" O ARG F 137 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 207 through 211 removed outlier: 3.513A pdb=" N ILE F 349 " --> pdb=" O LEU F 317 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL F 231 " --> pdb=" O PHE F 287 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N VAL F 289 " --> pdb=" O VAL F 231 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL F 233 " --> pdb=" O VAL F 289 " (cutoff:3.500A) removed outlier: 8.840A pdb=" N GLU F 291 " --> pdb=" O VAL F 233 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N THR F 252 " --> pdb=" O ILE F 232 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N ALA F 234 " --> pdb=" O THR F 252 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N TYR F 254 " --> pdb=" O ALA F 234 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 434 through 436 Processing sheet with id= M, first strand: chain 'G' and resid 133 through 137 Processing sheet with id= N, first strand: chain 'G' and resid 139 through 142 removed outlier: 4.180A pdb=" N TYR G 147 " --> pdb=" O HIS G 142 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 218 through 222 removed outlier: 3.705A pdb=" N GLY G 362 " --> pdb=" O TYR G 374 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE G 359 " --> pdb=" O LEU G 328 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N MET G 361 " --> pdb=" O ILE G 330 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LEU G 242 " --> pdb=" O LEU G 298 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N CYS G 300 " --> pdb=" O LEU G 242 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE G 244 " --> pdb=" O CYS G 300 " (cutoff:3.500A) removed outlier: 8.891A pdb=" N GLU G 302 " --> pdb=" O ILE G 244 " (cutoff:3.500A) removed outlier: 9.048A pdb=" N ASP G 246 " --> pdb=" O GLU G 302 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA G 263 " --> pdb=" O VAL G 243 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N SER G 245 " --> pdb=" O ALA G 263 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ARG G 265 " --> pdb=" O SER G 245 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 455 through 460 removed outlier: 3.684A pdb=" N ARG G 494 " --> pdb=" O VAL G 483 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N VAL G 481 " --> pdb=" O ARG G 496 " (cutoff:3.500A) 835 hydrogen bonds defined for protein. 2433 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: 6.56 Time building geometry restraints manager: 9.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5160 1.33 - 1.45: 4111 1.45 - 1.57: 12125 1.57 - 1.69: 2 1.69 - 1.81: 166 Bond restraints: 21564 Sorted by residual: bond pdb=" C04 Q7G E 302 " pdb=" C05 Q7G E 302 " ideal model delta sigma weight residual 1.836 1.531 0.305 2.00e-02 2.50e+03 2.32e+02 bond pdb=" C04 Q7G C 602 " pdb=" C05 Q7G C 602 " ideal model delta sigma weight residual 1.836 1.532 0.304 2.00e-02 2.50e+03 2.32e+02 bond pdb=" C13 Q7G C 602 " pdb=" C14 Q7G C 602 " ideal model delta sigma weight residual 1.599 1.325 0.274 2.00e-02 2.50e+03 1.88e+02 bond pdb=" C13 Q7G E 302 " pdb=" C14 Q7G E 302 " ideal model delta sigma weight residual 1.599 1.325 0.274 2.00e-02 2.50e+03 1.88e+02 bond pdb=" C07 Q7G C 602 " pdb=" C15 Q7G C 602 " ideal model delta sigma weight residual 1.779 1.525 0.254 2.00e-02 2.50e+03 1.61e+02 ... (remaining 21559 not shown) Histogram of bond angle deviations from ideal: 98.66 - 105.73: 541 105.73 - 112.79: 11539 112.79 - 119.86: 7182 119.86 - 126.93: 9744 126.93 - 133.99: 260 Bond angle restraints: 29266 Sorted by residual: angle pdb=" C GLN B 84 " pdb=" CA GLN B 84 " pdb=" CB GLN B 84 " ideal model delta sigma weight residual 110.88 104.00 6.88 1.57e+00 4.06e-01 1.92e+01 angle pdb=" N PHE D 48 " pdb=" CA PHE D 48 " pdb=" C PHE D 48 " ideal model delta sigma weight residual 114.31 109.01 5.30 1.29e+00 6.01e-01 1.69e+01 angle pdb=" CA LYS B 85 " pdb=" C LYS B 85 " pdb=" N PRO B 86 " ideal model delta sigma weight residual 118.44 124.52 -6.08 1.59e+00 3.96e-01 1.46e+01 angle pdb=" N PRO B 86 " pdb=" CA PRO B 86 " pdb=" CB PRO B 86 " ideal model delta sigma weight residual 103.25 107.00 -3.75 1.05e+00 9.07e-01 1.28e+01 angle pdb=" N PRO B 86 " pdb=" CA PRO B 86 " pdb=" C PRO B 86 " ideal model delta sigma weight residual 112.47 105.39 7.08 2.06e+00 2.36e-01 1.18e+01 ... (remaining 29261 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.93: 12476 28.93 - 57.86: 433 57.86 - 86.78: 55 86.78 - 115.71: 14 115.71 - 144.64: 2 Dihedral angle restraints: 12980 sinusoidal: 5324 harmonic: 7656 Sorted by residual: dihedral pdb=" CA LYS B 85 " pdb=" C LYS B 85 " pdb=" N PRO B 86 " pdb=" CA PRO B 86 " ideal model delta harmonic sigma weight residual -180.00 -53.94 -126.06 0 5.00e+00 4.00e-02 6.36e+02 dihedral pdb=" C4B Q7G C 602 " pdb=" C5B Q7G C 602 " pdb=" C6B Q7G C 602 " pdb=" O6B Q7G C 602 " ideal model delta sinusoidal sigma weight residual 143.94 -71.42 -144.64 1 3.00e+01 1.11e-03 1.94e+01 dihedral pdb=" CA TYR C 485 " pdb=" C TYR C 485 " pdb=" N PRO C 486 " pdb=" CA PRO C 486 " ideal model delta harmonic sigma weight residual 0.00 -20.05 20.05 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 12977 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.160: 3314 0.160 - 0.321: 11 0.321 - 0.481: 1 0.481 - 0.642: 0 0.642 - 0.802: 2 Chirality restraints: 3328 Sorted by residual: chirality pdb=" C02 Q7G C 602 " pdb=" C03 Q7G C 602 " pdb=" C06 Q7G C 602 " pdb=" C10 Q7G C 602 " both_signs ideal model delta sigma weight residual False 2.14 2.94 -0.80 2.00e-01 2.50e+01 1.61e+01 chirality pdb=" C02 Q7G E 302 " pdb=" C03 Q7G E 302 " pdb=" C06 Q7G E 302 " pdb=" C10 Q7G E 302 " both_signs ideal model delta sigma weight residual False 2.14 2.93 -0.79 2.00e-01 2.50e+01 1.57e+01 chirality pdb=" C2 Z8A E 301 " pdb=" C1 Z8A E 301 " pdb=" C3 Z8A E 301 " pdb=" N1 Z8A E 301 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.33 2.00e-01 2.50e+01 2.80e+00 ... (remaining 3325 not shown) Planarity restraints: 3688 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 Q7G E 302 " -0.016 2.00e-02 2.50e+03 5.76e-02 4.15e+01 pdb=" C13 Q7G E 302 " -0.009 2.00e-02 2.50e+03 pdb=" C14 Q7G E 302 " -0.095 2.00e-02 2.50e+03 pdb=" C15 Q7G E 302 " 0.069 2.00e-02 2.50e+03 pdb=" C16 Q7G E 302 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 212 " -0.029 5.00e-02 4.00e+02 4.44e-02 3.15e+00 pdb=" N PRO A 213 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 213 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 213 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP G 556 " -0.009 2.00e-02 2.50e+03 1.76e-02 3.11e+00 pdb=" C ASP G 556 " 0.031 2.00e-02 2.50e+03 pdb=" O ASP G 556 " -0.012 2.00e-02 2.50e+03 pdb=" N LYS G 557 " -0.010 2.00e-02 2.50e+03 ... (remaining 3685 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 206 2.67 - 3.22: 19138 3.22 - 3.78: 29454 3.78 - 4.34: 39088 4.34 - 4.90: 68898 Nonbonded interactions: 156784 Sorted by model distance: nonbonded pdb=" OD1 ASP C 238 " pdb=" N LYS C 239 " model vdw 2.108 2.520 nonbonded pdb=" OD1 ASP G 238 " pdb=" N LYS G 239 " model vdw 2.220 2.520 nonbonded pdb=" OH TYR F 460 " pdb=" OE1 GLU F 488 " model vdw 2.240 2.440 nonbonded pdb=" O PHE B 491 " pdb=" OG SER B 494 " model vdw 2.250 2.440 nonbonded pdb=" O GLN F 77 " pdb=" OG SER F 80 " model vdw 2.280 2.440 ... (remaining 156779 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' selection = (chain 'E' and (resid 39 through 221 or resid 301)) } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = (chain 'C' and (resid 8 through 561 or resid 601)) selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 17.660 Check model and map are aligned: 0.270 Set scattering table: 0.160 Process input model: 57.290 Find NCS groups from input model: 1.340 Set up NCS constraints: 0.160 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 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 : 0.008 0.305 21564 Z= 0.491 Angle : 0.666 10.193 29266 Z= 0.338 Chirality : 0.048 0.802 3328 Planarity : 0.004 0.058 3688 Dihedral : 15.026 144.639 8048 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.09 % Allowed : 0.17 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.76 % 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: 0.90 (0.16), residues: 2602 helix: 2.30 (0.16), residues: 1152 sheet: 0.69 (0.32), residues: 234 loop : -1.19 (0.16), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 112 HIS 0.006 0.001 HIS G 78 PHE 0.030 0.001 PHE E 163 TYR 0.018 0.001 TYR G 510 ARG 0.004 0.000 ARG B 456 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 338 time to evaluate : 2.571 Fit side-chains revert: symmetry clash REVERT: A 86 TRP cc_start: 0.7150 (m-10) cc_final: 0.4899 (m-90) REVERT: A 163 PHE cc_start: 0.8676 (t80) cc_final: 0.8151 (t80) REVERT: A 209 ARG cc_start: 0.6282 (mmt-90) cc_final: 0.5941 (mmt-90) REVERT: A 220 GLN cc_start: 0.8094 (mt0) cc_final: 0.7841 (mt0) REVERT: B 265 GLU cc_start: 0.6925 (tt0) cc_final: 0.6705 (tt0) REVERT: B 274 GLN cc_start: 0.8238 (tp40) cc_final: 0.7957 (tm-30) REVERT: C 409 SER cc_start: 0.8404 (m) cc_final: 0.8108 (m) REVERT: C 534 ASP cc_start: 0.8245 (m-30) cc_final: 0.7626 (p0) REVERT: D 7 SER cc_start: 0.8826 (t) cc_final: 0.8590 (p) REVERT: E 174 VAL cc_start: 0.8418 (t) cc_final: 0.7986 (p) REVERT: E 209 ARG cc_start: 0.6422 (mmt-90) cc_final: 0.5949 (mpt180) REVERT: F 99 ASP cc_start: 0.8604 (t0) cc_final: 0.8142 (t0) REVERT: F 274 GLN cc_start: 0.8202 (tp40) cc_final: 0.7920 (tm-30) REVERT: G 97 ASP cc_start: 0.7805 (t0) cc_final: 0.7228 (t70) REVERT: G 409 SER cc_start: 0.8671 (t) cc_final: 0.8458 (t) REVERT: G 548 ARG cc_start: 0.7367 (tpp80) cc_final: 0.6691 (mtp180) REVERT: H 5 LYS cc_start: 0.7966 (tppt) cc_final: 0.7703 (tttm) outliers start: 2 outliers final: 0 residues processed: 340 average time/residue: 0.3438 time to fit residues: 177.5282 Evaluate side-chains 218 residues out of total 2314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 2.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 217 optimal weight: 2.9990 chunk 195 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 66 optimal weight: 0.2980 chunk 131 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 202 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 chunk 150 optimal weight: 6.9990 chunk 234 optimal weight: 0.2980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 GLN C 379 GLN E 69 GLN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 HIS F 477 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21564 Z= 0.220 Angle : 0.559 7.414 29266 Z= 0.284 Chirality : 0.043 0.215 3328 Planarity : 0.004 0.054 3688 Dihedral : 9.719 118.377 3040 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.25 % Allowed : 5.75 % Favored : 93.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.76 % 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: 0.88 (0.16), residues: 2602 helix: 2.40 (0.16), residues: 1144 sheet: 0.08 (0.32), residues: 234 loop : -1.15 (0.16), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 540 HIS 0.005 0.001 HIS G 203 PHE 0.019 0.002 PHE E 163 TYR 0.023 0.001 TYR G 510 ARG 0.006 0.000 ARG D 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 218 time to evaluate : 2.682 Fit side-chains REVERT: A 86 TRP cc_start: 0.7258 (m-10) cc_final: 0.4883 (m-90) REVERT: A 209 ARG cc_start: 0.6814 (mmt-90) cc_final: 0.6499 (mpt180) REVERT: A 220 GLN cc_start: 0.7956 (mt0) cc_final: 0.7684 (mt0) REVERT: B 99 ASP cc_start: 0.8650 (t0) cc_final: 0.8308 (t0) REVERT: B 274 GLN cc_start: 0.8194 (tp40) cc_final: 0.7893 (tm-30) REVERT: C 145 ASN cc_start: 0.8322 (m-40) cc_final: 0.8109 (m-40) REVERT: C 218 ASP cc_start: 0.6941 (OUTLIER) cc_final: 0.6723 (m-30) REVERT: C 361 MET cc_start: 0.7506 (tmm) cc_final: 0.7273 (tmm) REVERT: C 409 SER cc_start: 0.8404 (m) cc_final: 0.8131 (m) REVERT: C 534 ASP cc_start: 0.8603 (m-30) cc_final: 0.7615 (p0) REVERT: D 7 SER cc_start: 0.8908 (t) cc_final: 0.8581 (p) REVERT: E 174 VAL cc_start: 0.8550 (t) cc_final: 0.8243 (p) REVERT: E 177 HIS cc_start: 0.8176 (OUTLIER) cc_final: 0.7370 (t-90) REVERT: E 209 ARG cc_start: 0.6864 (mmt-90) cc_final: 0.6564 (mpt180) REVERT: F 99 ASP cc_start: 0.8564 (t0) cc_final: 0.8078 (t0) REVERT: F 265 GLU cc_start: 0.6961 (tt0) cc_final: 0.6725 (tt0) REVERT: F 274 GLN cc_start: 0.8186 (tp40) cc_final: 0.7888 (tm-30) REVERT: G 97 ASP cc_start: 0.7900 (t0) cc_final: 0.7332 (t70) REVERT: G 116 MET cc_start: 0.7424 (tpp) cc_final: 0.7134 (tpp) REVERT: G 409 SER cc_start: 0.8780 (t) cc_final: 0.8557 (t) REVERT: G 548 ARG cc_start: 0.7275 (tpp80) cc_final: 0.6869 (mtp180) REVERT: G 556 ASP cc_start: 0.7861 (t70) cc_final: 0.7243 (t70) REVERT: H 5 LYS cc_start: 0.8005 (tppt) cc_final: 0.7650 (tttm) outliers start: 29 outliers final: 20 residues processed: 236 average time/residue: 0.3399 time to fit residues: 123.9792 Evaluate side-chains 223 residues out of total 2314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 201 time to evaluate : 2.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain E residue 177 HIS Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 470 SER Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 260 SER Chi-restraints excluded: chain G residue 342 THR Chi-restraints excluded: chain G residue 417 ILE Chi-restraints excluded: chain G residue 500 SER Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 55 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 130 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 194 optimal weight: 0.8980 chunk 159 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 234 optimal weight: 0.7980 chunk 253 optimal weight: 3.9990 chunk 209 optimal weight: 0.9980 chunk 232 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 GLN E 69 GLN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21564 Z= 0.187 Angle : 0.514 6.950 29266 Z= 0.259 Chirality : 0.042 0.170 3328 Planarity : 0.004 0.081 3688 Dihedral : 9.250 114.713 3040 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.42 % Favored : 96.54 % Rotamer: Outliers : 1.43 % Allowed : 8.25 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.16), residues: 2602 helix: 2.53 (0.16), residues: 1128 sheet: 0.38 (0.31), residues: 258 loop : -1.20 (0.16), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 79 HIS 0.004 0.001 HIS G 203 PHE 0.021 0.001 PHE A 163 TYR 0.020 0.001 TYR G 510 ARG 0.004 0.000 ARG D 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 204 time to evaluate : 2.432 Fit side-chains REVERT: A 86 TRP cc_start: 0.7276 (m-10) cc_final: 0.4900 (m-90) REVERT: A 209 ARG cc_start: 0.6740 (mmt-90) cc_final: 0.6533 (mpt180) REVERT: B 99 ASP cc_start: 0.8540 (t0) cc_final: 0.8190 (t0) REVERT: B 274 GLN cc_start: 0.8143 (tp40) cc_final: 0.7800 (tm-30) REVERT: C 145 ASN cc_start: 0.8224 (m-40) cc_final: 0.7967 (m-40) REVERT: C 272 MET cc_start: 0.7200 (mmt) cc_final: 0.6715 (mmt) REVERT: C 409 SER cc_start: 0.8344 (m) cc_final: 0.8098 (m) REVERT: D 7 SER cc_start: 0.8884 (t) cc_final: 0.8520 (p) REVERT: D 51 MET cc_start: 0.8604 (mmm) cc_final: 0.8353 (mmm) REVERT: E 147 MET cc_start: 0.7676 (tpp) cc_final: 0.7461 (tpp) REVERT: E 174 VAL cc_start: 0.8574 (t) cc_final: 0.8248 (p) REVERT: E 209 ARG cc_start: 0.6859 (mmt-90) cc_final: 0.6602 (mpt180) REVERT: F 99 ASP cc_start: 0.8540 (t0) cc_final: 0.8057 (t0) REVERT: F 274 GLN cc_start: 0.8225 (tp40) cc_final: 0.7857 (tm-30) REVERT: F 424 PHE cc_start: 0.8186 (OUTLIER) cc_final: 0.7925 (t80) REVERT: G 97 ASP cc_start: 0.7950 (t0) cc_final: 0.7396 (t70) REVERT: G 116 MET cc_start: 0.7411 (tpp) cc_final: 0.7152 (tpp) REVERT: G 548 ARG cc_start: 0.7377 (tpp80) cc_final: 0.6835 (mtp180) REVERT: G 556 ASP cc_start: 0.7940 (t70) cc_final: 0.7360 (t70) REVERT: H 8 MET cc_start: 0.8344 (ttt) cc_final: 0.8033 (ttt) outliers start: 33 outliers final: 24 residues processed: 225 average time/residue: 0.3395 time to fit residues: 118.2692 Evaluate side-chains 212 residues out of total 2314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 187 time to evaluate : 2.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain D residue 49 TYR Chi-restraints excluded: chain E residue 177 HIS Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 424 PHE Chi-restraints excluded: chain F residue 494 SER Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 260 SER Chi-restraints excluded: chain G residue 342 THR Chi-restraints excluded: chain G residue 417 ILE Chi-restraints excluded: chain G residue 500 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 231 optimal weight: 4.9990 chunk 176 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 112 optimal weight: 0.8980 chunk 157 optimal weight: 0.8980 chunk 235 optimal weight: 3.9990 chunk 249 optimal weight: 0.9990 chunk 123 optimal weight: 5.9990 chunk 223 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN E 69 GLN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 237 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21564 Z= 0.225 Angle : 0.536 7.678 29266 Z= 0.272 Chirality : 0.043 0.173 3328 Planarity : 0.004 0.084 3688 Dihedral : 9.181 113.469 3040 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.12 % Allowed : 9.42 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.76 % 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: 0.92 (0.16), residues: 2602 helix: 2.51 (0.16), residues: 1128 sheet: 0.25 (0.31), residues: 254 loop : -1.23 (0.16), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 540 HIS 0.004 0.001 HIS G 203 PHE 0.021 0.002 PHE A 172 TYR 0.022 0.001 TYR C 510 ARG 0.003 0.000 ARG G 212 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 192 time to evaluate : 2.488 Fit side-chains REVERT: B 99 ASP cc_start: 0.8519 (t0) cc_final: 0.8145 (t0) REVERT: B 114 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.8167 (mp10) REVERT: B 274 GLN cc_start: 0.8159 (tp40) cc_final: 0.7781 (tm-30) REVERT: C 145 ASN cc_start: 0.8337 (m-40) cc_final: 0.8101 (m-40) REVERT: C 409 SER cc_start: 0.8369 (m) cc_final: 0.8114 (m) REVERT: D 7 SER cc_start: 0.8787 (t) cc_final: 0.8467 (p) REVERT: E 174 VAL cc_start: 0.8569 (t) cc_final: 0.8242 (p) REVERT: E 209 ARG cc_start: 0.6836 (mmt-90) cc_final: 0.6636 (mpt180) REVERT: F 99 ASP cc_start: 0.8510 (t0) cc_final: 0.8026 (t0) REVERT: F 114 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.8144 (mt0) REVERT: F 274 GLN cc_start: 0.8168 (tp40) cc_final: 0.7804 (tm-30) REVERT: G 97 ASP cc_start: 0.8006 (t0) cc_final: 0.7453 (t70) REVERT: G 116 MET cc_start: 0.7436 (tpp) cc_final: 0.7173 (tpp) REVERT: G 548 ARG cc_start: 0.7391 (tpp80) cc_final: 0.6818 (mtp180) REVERT: G 556 ASP cc_start: 0.7916 (t70) cc_final: 0.7381 (t70) REVERT: H 8 MET cc_start: 0.8394 (ttt) cc_final: 0.8089 (ttt) outliers start: 49 outliers final: 30 residues processed: 231 average time/residue: 0.3307 time to fit residues: 117.9031 Evaluate side-chains 220 residues out of total 2314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 188 time to evaluate : 2.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain D residue 49 TYR Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 470 SER Chi-restraints excluded: chain F residue 494 SER Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 260 SER Chi-restraints excluded: chain G residue 342 THR Chi-restraints excluded: chain G residue 375 ILE Chi-restraints excluded: chain G residue 409 SER Chi-restraints excluded: chain G residue 417 ILE Chi-restraints excluded: chain G residue 500 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 207 optimal weight: 0.5980 chunk 141 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 185 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 212 optimal weight: 2.9990 chunk 172 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 127 optimal weight: 3.9990 chunk 223 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 69 GLN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 21564 Z= 0.281 Angle : 0.567 7.482 29266 Z= 0.291 Chirality : 0.044 0.170 3328 Planarity : 0.004 0.086 3688 Dihedral : 9.222 113.279 3040 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.94 % Allowed : 10.85 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.76 % 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: 0.68 (0.16), residues: 2602 helix: 2.44 (0.16), residues: 1126 sheet: -0.38 (0.31), residues: 230 loop : -1.34 (0.16), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 86 HIS 0.004 0.001 HIS C 203 PHE 0.020 0.002 PHE E 172 TYR 0.024 0.002 TYR G 510 ARG 0.003 0.000 ARG G 258 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 193 time to evaluate : 2.484 Fit side-chains REVERT: B 99 ASP cc_start: 0.8514 (t0) cc_final: 0.8131 (t0) REVERT: B 114 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.8110 (mt0) REVERT: B 274 GLN cc_start: 0.8205 (tp40) cc_final: 0.7859 (tm-30) REVERT: C 145 ASN cc_start: 0.8415 (m-40) cc_final: 0.8156 (m-40) REVERT: C 409 SER cc_start: 0.8370 (m) cc_final: 0.8126 (m) REVERT: D 7 SER cc_start: 0.8802 (t) cc_final: 0.8446 (p) REVERT: E 174 VAL cc_start: 0.8594 (t) cc_final: 0.8281 (p) REVERT: F 99 ASP cc_start: 0.8527 (t0) cc_final: 0.8032 (t0) REVERT: F 114 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.8149 (mt0) REVERT: F 274 GLN cc_start: 0.8186 (tp40) cc_final: 0.7834 (tm-30) REVERT: F 279 LYS cc_start: 0.7583 (pttt) cc_final: 0.7026 (ttmm) REVERT: G 97 ASP cc_start: 0.8013 (t0) cc_final: 0.7505 (t70) REVERT: G 116 MET cc_start: 0.7469 (tpp) cc_final: 0.7212 (tpp) REVERT: G 548 ARG cc_start: 0.7384 (tpp80) cc_final: 0.6791 (mtp180) REVERT: H 8 MET cc_start: 0.8469 (ttt) cc_final: 0.8155 (ttt) outliers start: 45 outliers final: 33 residues processed: 228 average time/residue: 0.3478 time to fit residues: 124.4274 Evaluate side-chains 219 residues out of total 2314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 184 time to evaluate : 2.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 499 MET Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain D residue 49 TYR Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 470 SER Chi-restraints excluded: chain F residue 494 SER Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 260 SER Chi-restraints excluded: chain G residue 342 THR Chi-restraints excluded: chain G residue 375 ILE Chi-restraints excluded: chain G residue 409 SER Chi-restraints excluded: chain G residue 417 ILE Chi-restraints excluded: chain G residue 500 SER Chi-restraints excluded: chain H residue 49 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 83 optimal weight: 2.9990 chunk 224 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 146 optimal weight: 0.0170 chunk 61 optimal weight: 2.9990 chunk 249 optimal weight: 0.4980 chunk 207 optimal weight: 3.9990 chunk 115 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 131 optimal weight: 5.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 GLN E 69 GLN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 21564 Z= 0.148 Angle : 0.491 6.993 29266 Z= 0.247 Chirality : 0.042 0.444 3328 Planarity : 0.004 0.085 3688 Dihedral : 8.871 113.196 3040 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.69 % Allowed : 11.62 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.17), residues: 2602 helix: 2.52 (0.16), residues: 1138 sheet: 0.12 (0.30), residues: 282 loop : -1.19 (0.16), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 86 HIS 0.002 0.000 HIS C 514 PHE 0.016 0.001 PHE A 172 TYR 0.018 0.001 TYR F 71 ARG 0.002 0.000 ARG G 212 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 196 time to evaluate : 2.673 Fit side-chains REVERT: B 99 ASP cc_start: 0.8483 (t0) cc_final: 0.8104 (t0) REVERT: B 114 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.7906 (mt0) REVERT: B 274 GLN cc_start: 0.8152 (tp40) cc_final: 0.7762 (tm-30) REVERT: C 145 ASN cc_start: 0.8332 (m-40) cc_final: 0.8070 (m-40) REVERT: C 272 MET cc_start: 0.7409 (mmt) cc_final: 0.7021 (mmt) REVERT: D 7 SER cc_start: 0.8780 (t) cc_final: 0.8420 (p) REVERT: E 163 PHE cc_start: 0.8544 (t80) cc_final: 0.8186 (t80) REVERT: E 174 VAL cc_start: 0.8599 (t) cc_final: 0.8289 (p) REVERT: F 99 ASP cc_start: 0.8480 (t0) cc_final: 0.7993 (t0) REVERT: F 114 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.8157 (mt0) REVERT: F 274 GLN cc_start: 0.8147 (tp40) cc_final: 0.7739 (tm-30) REVERT: F 279 LYS cc_start: 0.7534 (pttt) cc_final: 0.7028 (ttmm) REVERT: G 97 ASP cc_start: 0.7988 (t0) cc_final: 0.7452 (t70) REVERT: G 116 MET cc_start: 0.7357 (tpp) cc_final: 0.7099 (tpp) REVERT: G 548 ARG cc_start: 0.7380 (tpp80) cc_final: 0.6776 (mtp180) REVERT: G 556 ASP cc_start: 0.7946 (t70) cc_final: 0.7438 (t70) REVERT: H 8 MET cc_start: 0.8376 (ttt) cc_final: 0.8059 (ttt) outliers start: 39 outliers final: 28 residues processed: 226 average time/residue: 0.4118 time to fit residues: 142.7239 Evaluate side-chains 216 residues out of total 2314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 186 time to evaluate : 2.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain E residue 177 HIS Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 205 THR Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 494 SER Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 260 SER Chi-restraints excluded: chain G residue 342 THR Chi-restraints excluded: chain G residue 417 ILE Chi-restraints excluded: chain G residue 500 SER Chi-restraints excluded: chain H residue 49 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 240 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 182 optimal weight: 0.8980 chunk 141 optimal weight: 0.7980 chunk 210 optimal weight: 0.7980 chunk 139 optimal weight: 10.0000 chunk 248 optimal weight: 0.8980 chunk 155 optimal weight: 3.9990 chunk 151 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21564 Z= 0.183 Angle : 0.509 7.339 29266 Z= 0.258 Chirality : 0.043 0.466 3328 Planarity : 0.004 0.085 3688 Dihedral : 8.799 113.385 3040 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.69 % Allowed : 12.06 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.17), residues: 2602 helix: 2.59 (0.16), residues: 1128 sheet: 0.15 (0.30), residues: 282 loop : -1.19 (0.16), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 294 HIS 0.002 0.001 HIS G 203 PHE 0.023 0.001 PHE E 172 TYR 0.018 0.001 TYR G 510 ARG 0.004 0.000 ARG C 212 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 188 time to evaluate : 2.367 Fit side-chains REVERT: B 99 ASP cc_start: 0.8480 (t0) cc_final: 0.8093 (t0) REVERT: B 114 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.8153 (mp10) REVERT: B 274 GLN cc_start: 0.8181 (tp40) cc_final: 0.7750 (tm-30) REVERT: C 145 ASN cc_start: 0.8214 (m-40) cc_final: 0.7921 (m-40) REVERT: D 7 SER cc_start: 0.8770 (t) cc_final: 0.8399 (p) REVERT: E 163 PHE cc_start: 0.8582 (t80) cc_final: 0.8236 (t80) REVERT: E 174 VAL cc_start: 0.8614 (t) cc_final: 0.8303 (p) REVERT: F 99 ASP cc_start: 0.8499 (t0) cc_final: 0.8016 (t0) REVERT: F 114 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.8156 (mt0) REVERT: F 274 GLN cc_start: 0.8144 (tp40) cc_final: 0.7734 (tm-30) REVERT: F 279 LYS cc_start: 0.7463 (pttt) cc_final: 0.6992 (ttmm) REVERT: G 97 ASP cc_start: 0.8003 (t0) cc_final: 0.7464 (t70) REVERT: G 116 MET cc_start: 0.7329 (tpp) cc_final: 0.7074 (tpp) REVERT: G 548 ARG cc_start: 0.7329 (tpp80) cc_final: 0.6719 (mtp180) REVERT: H 8 MET cc_start: 0.8343 (ttt) cc_final: 0.8080 (ttt) outliers start: 39 outliers final: 35 residues processed: 220 average time/residue: 0.3343 time to fit residues: 113.1352 Evaluate side-chains 222 residues out of total 2314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 185 time to evaluate : 2.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 205 THR Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain F residue 494 SER Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 260 SER Chi-restraints excluded: chain G residue 342 THR Chi-restraints excluded: chain G residue 375 ILE Chi-restraints excluded: chain G residue 417 ILE Chi-restraints excluded: chain G residue 481 VAL Chi-restraints excluded: chain G residue 500 SER Chi-restraints excluded: chain H residue 49 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 153 optimal weight: 3.9990 chunk 99 optimal weight: 0.5980 chunk 148 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 158 optimal weight: 0.3980 chunk 169 optimal weight: 0.9990 chunk 122 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 195 optimal weight: 4.9990 chunk 226 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 21564 Z= 0.156 Angle : 0.489 7.170 29266 Z= 0.247 Chirality : 0.042 0.432 3328 Planarity : 0.004 0.084 3688 Dihedral : 8.510 112.271 3040 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.82 % Allowed : 12.19 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.76 % 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: 1.09 (0.17), residues: 2602 helix: 2.65 (0.16), residues: 1126 sheet: 0.21 (0.30), residues: 282 loop : -1.12 (0.16), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 294 HIS 0.002 0.000 HIS G 203 PHE 0.036 0.001 PHE A 172 TYR 0.017 0.001 TYR F 71 ARG 0.004 0.000 ARG G 212 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 194 time to evaluate : 2.457 Fit side-chains REVERT: A 163 PHE cc_start: 0.8321 (t80) cc_final: 0.8076 (t80) REVERT: B 99 ASP cc_start: 0.8512 (t0) cc_final: 0.8127 (t0) REVERT: B 114 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.7909 (mt0) REVERT: B 274 GLN cc_start: 0.8139 (tp40) cc_final: 0.7714 (tm-30) REVERT: C 97 ASP cc_start: 0.8272 (t0) cc_final: 0.7935 (p0) REVERT: C 145 ASN cc_start: 0.8159 (m-40) cc_final: 0.7893 (m-40) REVERT: C 272 MET cc_start: 0.7454 (mmt) cc_final: 0.7070 (mmt) REVERT: D 7 SER cc_start: 0.8780 (t) cc_final: 0.8413 (p) REVERT: E 163 PHE cc_start: 0.8591 (t80) cc_final: 0.8281 (t80) REVERT: E 174 VAL cc_start: 0.8615 (t) cc_final: 0.8304 (p) REVERT: F 99 ASP cc_start: 0.8481 (t0) cc_final: 0.8007 (t0) REVERT: F 114 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.8218 (mp10) REVERT: F 274 GLN cc_start: 0.8122 (tp40) cc_final: 0.7693 (tm-30) REVERT: F 279 LYS cc_start: 0.7433 (pttt) cc_final: 0.6955 (ttmm) REVERT: G 97 ASP cc_start: 0.7996 (t0) cc_final: 0.7457 (t70) REVERT: G 116 MET cc_start: 0.7293 (tpp) cc_final: 0.7044 (tpp) REVERT: G 272 MET cc_start: 0.7493 (mmt) cc_final: 0.7058 (mmt) REVERT: G 548 ARG cc_start: 0.7308 (tpp80) cc_final: 0.6678 (mtp180) REVERT: G 556 ASP cc_start: 0.7951 (t70) cc_final: 0.7437 (t70) REVERT: H 8 MET cc_start: 0.8283 (ttt) cc_final: 0.8029 (ttt) outliers start: 42 outliers final: 36 residues processed: 228 average time/residue: 0.3504 time to fit residues: 122.9469 Evaluate side-chains 225 residues out of total 2314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 187 time to evaluate : 2.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain D residue 63 PHE Chi-restraints excluded: chain E residue 177 HIS Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 205 THR Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain F residue 494 SER Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 260 SER Chi-restraints excluded: chain G residue 342 THR Chi-restraints excluded: chain G residue 375 ILE Chi-restraints excluded: chain G residue 417 ILE Chi-restraints excluded: chain G residue 481 VAL Chi-restraints excluded: chain G residue 500 SER Chi-restraints excluded: chain H residue 49 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 238 optimal weight: 3.9990 chunk 217 optimal weight: 0.6980 chunk 231 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 181 optimal weight: 0.0970 chunk 71 optimal weight: 0.9980 chunk 209 optimal weight: 0.2980 chunk 219 optimal weight: 0.5980 chunk 230 optimal weight: 0.6980 chunk 152 optimal weight: 0.6980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 21564 Z= 0.135 Angle : 0.476 6.921 29266 Z= 0.238 Chirality : 0.041 0.428 3328 Planarity : 0.004 0.084 3688 Dihedral : 8.160 109.005 3040 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.64 % Allowed : 12.49 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.76 % 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: 1.21 (0.17), residues: 2602 helix: 2.73 (0.16), residues: 1126 sheet: 0.32 (0.31), residues: 282 loop : -1.04 (0.16), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 540 HIS 0.002 0.000 HIS G 514 PHE 0.034 0.001 PHE A 172 TYR 0.018 0.001 TYR F 71 ARG 0.004 0.000 ARG G 212 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 192 time to evaluate : 2.559 Fit side-chains REVERT: B 99 ASP cc_start: 0.8495 (t0) cc_final: 0.8112 (t0) REVERT: B 114 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.8207 (mp10) REVERT: B 274 GLN cc_start: 0.8102 (tp40) cc_final: 0.7662 (mt0) REVERT: C 97 ASP cc_start: 0.8307 (t0) cc_final: 0.8018 (p0) REVERT: C 145 ASN cc_start: 0.7928 (m-40) cc_final: 0.7720 (m-40) REVERT: C 272 MET cc_start: 0.7417 (mmt) cc_final: 0.7106 (mmt) REVERT: D 7 SER cc_start: 0.8761 (t) cc_final: 0.8391 (p) REVERT: E 174 VAL cc_start: 0.8525 (t) cc_final: 0.8179 (p) REVERT: F 99 ASP cc_start: 0.8498 (t0) cc_final: 0.8090 (t0) REVERT: F 274 GLN cc_start: 0.8081 (tp40) cc_final: 0.7615 (tm-30) REVERT: G 97 ASP cc_start: 0.7964 (t0) cc_final: 0.7441 (t70) REVERT: G 116 MET cc_start: 0.7245 (tpp) cc_final: 0.6880 (tpp) REVERT: G 272 MET cc_start: 0.7348 (mmt) cc_final: 0.6964 (mmt) REVERT: G 548 ARG cc_start: 0.7303 (tpp80) cc_final: 0.6647 (mtp180) REVERT: H 8 MET cc_start: 0.8143 (ttt) cc_final: 0.7935 (ttt) outliers start: 38 outliers final: 32 residues processed: 226 average time/residue: 0.3545 time to fit residues: 122.7581 Evaluate side-chains 222 residues out of total 2314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 189 time to evaluate : 2.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain D residue 63 PHE Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain F residue 494 SER Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 260 SER Chi-restraints excluded: chain G residue 342 THR Chi-restraints excluded: chain G residue 375 ILE Chi-restraints excluded: chain G residue 417 ILE Chi-restraints excluded: chain G residue 481 VAL Chi-restraints excluded: chain G residue 500 SER Chi-restraints excluded: chain H residue 49 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 245 optimal weight: 0.5980 chunk 149 optimal weight: 7.9990 chunk 116 optimal weight: 0.9980 chunk 170 optimal weight: 0.4980 chunk 257 optimal weight: 9.9990 chunk 236 optimal weight: 0.9990 chunk 204 optimal weight: 0.0870 chunk 21 optimal weight: 5.9990 chunk 158 optimal weight: 0.0050 chunk 125 optimal weight: 6.9990 chunk 162 optimal weight: 1.9990 overall best weight: 0.4372 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 375 GLN C 291 ASN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 213 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 21564 Z= 0.131 Angle : 0.475 6.764 29266 Z= 0.237 Chirality : 0.042 0.418 3328 Planarity : 0.004 0.084 3688 Dihedral : 7.959 104.219 3040 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.43 % Allowed : 12.88 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.76 % 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: 1.29 (0.17), residues: 2602 helix: 2.78 (0.16), residues: 1126 sheet: 0.39 (0.31), residues: 282 loop : -0.99 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 540 HIS 0.002 0.000 HIS C 514 PHE 0.042 0.001 PHE A 172 TYR 0.017 0.001 TYR F 71 ARG 0.004 0.000 ARG G 212 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 200 time to evaluate : 2.359 Fit side-chains REVERT: B 274 GLN cc_start: 0.8050 (tp40) cc_final: 0.7607 (mt0) REVERT: C 97 ASP cc_start: 0.8301 (t0) cc_final: 0.7978 (p0) REVERT: D 7 SER cc_start: 0.8766 (t) cc_final: 0.8412 (p) REVERT: E 163 PHE cc_start: 0.8612 (t80) cc_final: 0.8309 (t80) REVERT: E 174 VAL cc_start: 0.8474 (t) cc_final: 0.8159 (p) REVERT: F 99 ASP cc_start: 0.8496 (t0) cc_final: 0.8098 (t0) REVERT: F 274 GLN cc_start: 0.8081 (tp40) cc_final: 0.7618 (tm-30) REVERT: G 97 ASP cc_start: 0.7964 (t0) cc_final: 0.7424 (t70) REVERT: G 116 MET cc_start: 0.7190 (tpp) cc_final: 0.6861 (tpp) REVERT: G 272 MET cc_start: 0.7381 (mmt) cc_final: 0.7038 (mmt) REVERT: G 548 ARG cc_start: 0.7305 (tpp80) cc_final: 0.6472 (mtp180) REVERT: G 552 ASP cc_start: 0.8277 (m-30) cc_final: 0.7907 (m-30) REVERT: G 556 ASP cc_start: 0.7922 (t70) cc_final: 0.7383 (t70) outliers start: 33 outliers final: 31 residues processed: 229 average time/residue: 0.3391 time to fit residues: 118.9473 Evaluate side-chains 223 residues out of total 2314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 192 time to evaluate : 2.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain D residue 63 PHE Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain F residue 494 SER Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 260 SER Chi-restraints excluded: chain G residue 342 THR Chi-restraints excluded: chain G residue 375 ILE Chi-restraints excluded: chain G residue 417 ILE Chi-restraints excluded: chain G residue 481 VAL Chi-restraints excluded: chain G residue 500 SER Chi-restraints excluded: chain H residue 49 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 218 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 188 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 205 optimal weight: 7.9990 chunk 85 optimal weight: 2.9990 chunk 210 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 179 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 375 GLN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.192268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.145836 restraints weight = 26703.785| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 2.54 r_work: 0.3661 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3516 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21564 Z= 0.184 Angle : 0.502 7.230 29266 Z= 0.254 Chirality : 0.043 0.426 3328 Planarity : 0.004 0.084 3688 Dihedral : 7.994 103.363 3040 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.38 % Allowed : 12.96 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.17), residues: 2602 helix: 2.74 (0.16), residues: 1128 sheet: 0.34 (0.31), residues: 282 loop : -1.04 (0.17), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 540 HIS 0.003 0.001 HIS G 203 PHE 0.039 0.001 PHE A 172 TYR 0.019 0.001 TYR G 510 ARG 0.004 0.000 ARG C 212 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4294.68 seconds wall clock time: 79 minutes 11.52 seconds (4751.52 seconds total)