Starting phenix.real_space_refine on Fri Aug 9 05:55:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz3_41732/08_2024/8tz3_41732_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz3_41732/08_2024/8tz3_41732.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz3_41732/08_2024/8tz3_41732.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz3_41732/08_2024/8tz3_41732.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz3_41732/08_2024/8tz3_41732_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz3_41732/08_2024/8tz3_41732_trim.cif" } resolution = 2.31 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= 0.004 sd= 0.153 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: 7 Type Number sf(0) Gaussians P 12 5.49 5 S 87 5.16 5 Na 6 4.78 5 C 8412 2.51 5 N 1926 2.21 5 O 2202 1.98 5 H 12165 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 24810 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 8129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8129 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 18, 'TRANS': 514} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 69 Chain: "C" Number of atoms: 8129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8129 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 18, 'TRANS': 514} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 69 Chain: "B" Number of atoms: 8129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8129 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 18, 'TRANS': 514} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 69 Chain: "A" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 136 Unusual residues: {' NA': 2, 'LBN': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 74 Chain: "C" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 136 Unusual residues: {' NA': 2, 'LBN': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 74 Chain: "B" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 136 Unusual residues: {' NA': 2, 'LBN': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 74 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7934 SG CYS A 608 49.354 32.824 38.169 1.00 20.21 S ATOM 16063 SG CYS C 608 87.685 68.096 38.146 1.00 20.07 S ATOM 24192 SG CYS B 608 37.946 83.694 38.152 1.00 20.18 S Time building chain proxies: 11.36, per 1000 atoms: 0.46 Number of scatterers: 24810 At special positions: 0 Unit cell: (129.6, 127.44, 75.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 87 16.00 P 12 15.00 Na 6 11.00 O 2202 8.00 N 1926 7.00 C 8412 6.00 H 12165 1.00 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=0, symmetry=0 Time building additional restraints: 19.06 Conformation dependent library (CDL) restraints added in 2.4 seconds 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2946 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 3 sheets defined 89.7% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.68 Creating SS restraints... Processing helix chain 'A' and resid 90 through 103 Processing helix chain 'A' and resid 103 through 130 removed outlier: 3.619A pdb=" N ILE A 110 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 157 Proline residue: A 136 - end of helix Processing helix chain 'A' and resid 157 through 198 Proline residue: A 167 - end of helix removed outlier: 5.006A pdb=" N PHE A 177 " --> pdb=" O ASP A 173 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N TRP A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N TRP A 181 " --> pdb=" O PHE A 177 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N VAL A 182 " --> pdb=" O TRP A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 203 through 223 Processing helix chain 'A' and resid 232 through 252 removed outlier: 3.557A pdb=" N THR A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 270 Processing helix chain 'A' and resid 272 through 281 removed outlier: 4.173A pdb=" N GLY A 276 " --> pdb=" O TYR A 272 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE A 279 " --> pdb=" O ALA A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 287 Processing helix chain 'A' and resid 288 through 293 Processing helix chain 'A' and resid 294 through 311 removed outlier: 3.505A pdb=" N VAL A 298 " --> pdb=" O VAL A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 330 removed outlier: 3.524A pdb=" N TRP A 316 " --> pdb=" O GLY A 312 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE A 317 " --> pdb=" O LEU A 313 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS A 320 " --> pdb=" O TRP A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 343 removed outlier: 3.579A pdb=" N ILE A 343 " --> pdb=" O ALA A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 361 removed outlier: 3.557A pdb=" N ARG A 355 " --> pdb=" O LEU A 352 " (cutoff:3.500A) Proline residue: A 356 - end of helix Proline residue: A 359 - end of helix Processing helix chain 'A' and resid 362 through 376 removed outlier: 3.598A pdb=" N GLY A 373 " --> pdb=" O ILE A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 380 No H-bonds generated for 'chain 'A' and resid 378 through 380' Processing helix chain 'A' and resid 381 through 389 removed outlier: 3.529A pdb=" N TYR A 385 " --> pdb=" O VAL A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 414 removed outlier: 3.917A pdb=" N ALA A 403 " --> pdb=" O SER A 399 " (cutoff:3.500A) Proline residue: A 404 - end of helix Processing helix chain 'A' and resid 423 through 429 Processing helix chain 'A' and resid 437 through 479 removed outlier: 3.713A pdb=" N ILE A 450 " --> pdb=" O ALA A 446 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N SER A 451 " --> pdb=" O SER A 447 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU A 452 " --> pdb=" O SER A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 482 No H-bonds generated for 'chain 'A' and resid 480 through 482' Processing helix chain 'A' and resid 487 through 496 removed outlier: 3.675A pdb=" N TYR A 494 " --> pdb=" O VAL A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 503 Processing helix chain 'A' and resid 506 through 523 removed outlier: 3.920A pdb=" N PHE A 511 " --> pdb=" O TRP A 507 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N MET A 512 " --> pdb=" O GLN A 508 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS A 515 " --> pdb=" O PHE A 511 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU A 516 " --> pdb=" O MET A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 542 Processing helix chain 'A' and resid 555 through 566 Processing helix chain 'A' and resid 571 through 573 No H-bonds generated for 'chain 'A' and resid 571 through 573' Processing helix chain 'A' and resid 574 through 586 Processing helix chain 'A' and resid 589 through 619 removed outlier: 3.523A pdb=" N ALA A 595 " --> pdb=" O ARG A 591 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N MET A 598 " --> pdb=" O THR A 594 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N ARG A 599 " --> pdb=" O ALA A 595 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 103 Processing helix chain 'C' and resid 103 through 130 removed outlier: 3.619A pdb=" N ILE C 110 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 157 Proline residue: C 136 - end of helix Processing helix chain 'C' and resid 157 through 198 Proline residue: C 167 - end of helix removed outlier: 5.006A pdb=" N PHE C 177 " --> pdb=" O ASP C 173 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N TRP C 178 " --> pdb=" O SER C 174 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N TRP C 181 " --> pdb=" O PHE C 177 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N VAL C 182 " --> pdb=" O TRP C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 203 Processing helix chain 'C' and resid 203 through 223 Processing helix chain 'C' and resid 232 through 252 removed outlier: 3.557A pdb=" N THR C 252 " --> pdb=" O LEU C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 270 Processing helix chain 'C' and resid 272 through 281 removed outlier: 4.173A pdb=" N GLY C 276 " --> pdb=" O TYR C 272 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE C 279 " --> pdb=" O ALA C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 287 Processing helix chain 'C' and resid 288 through 293 Processing helix chain 'C' and resid 294 through 311 removed outlier: 3.505A pdb=" N VAL C 298 " --> pdb=" O VAL C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 330 removed outlier: 3.524A pdb=" N TRP C 316 " --> pdb=" O GLY C 312 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE C 317 " --> pdb=" O LEU C 313 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS C 320 " --> pdb=" O TRP C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 343 removed outlier: 3.580A pdb=" N ILE C 343 " --> pdb=" O ALA C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 361 removed outlier: 3.557A pdb=" N ARG C 355 " --> pdb=" O LEU C 352 " (cutoff:3.500A) Proline residue: C 356 - end of helix Proline residue: C 359 - end of helix Processing helix chain 'C' and resid 362 through 376 removed outlier: 3.599A pdb=" N GLY C 373 " --> pdb=" O ILE C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 380 No H-bonds generated for 'chain 'C' and resid 378 through 380' Processing helix chain 'C' and resid 381 through 389 removed outlier: 3.528A pdb=" N TYR C 385 " --> pdb=" O VAL C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 414 removed outlier: 3.917A pdb=" N ALA C 403 " --> pdb=" O SER C 399 " (cutoff:3.500A) Proline residue: C 404 - end of helix Processing helix chain 'C' and resid 423 through 429 Processing helix chain 'C' and resid 437 through 479 removed outlier: 3.712A pdb=" N ILE C 450 " --> pdb=" O ALA C 446 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N SER C 451 " --> pdb=" O SER C 447 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU C 452 " --> pdb=" O SER C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 482 No H-bonds generated for 'chain 'C' and resid 480 through 482' Processing helix chain 'C' and resid 487 through 496 removed outlier: 3.675A pdb=" N TYR C 494 " --> pdb=" O VAL C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 503 Processing helix chain 'C' and resid 506 through 523 removed outlier: 3.920A pdb=" N PHE C 511 " --> pdb=" O TRP C 507 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N MET C 512 " --> pdb=" O GLN C 508 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS C 515 " --> pdb=" O PHE C 511 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU C 516 " --> pdb=" O MET C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 542 Processing helix chain 'C' and resid 555 through 566 Processing helix chain 'C' and resid 571 through 573 No H-bonds generated for 'chain 'C' and resid 571 through 573' Processing helix chain 'C' and resid 574 through 586 Processing helix chain 'C' and resid 589 through 619 removed outlier: 3.523A pdb=" N ALA C 595 " --> pdb=" O ARG C 591 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N MET C 598 " --> pdb=" O THR C 594 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ARG C 599 " --> pdb=" O ALA C 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 103 Processing helix chain 'B' and resid 103 through 130 removed outlier: 3.619A pdb=" N ILE B 110 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 157 Proline residue: B 136 - end of helix Processing helix chain 'B' and resid 157 through 198 Proline residue: B 167 - end of helix removed outlier: 5.006A pdb=" N PHE B 177 " --> pdb=" O ASP B 173 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N TRP B 178 " --> pdb=" O SER B 174 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N TRP B 181 " --> pdb=" O PHE B 177 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N VAL B 182 " --> pdb=" O TRP B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 203 Processing helix chain 'B' and resid 203 through 223 Processing helix chain 'B' and resid 232 through 252 removed outlier: 3.558A pdb=" N THR B 252 " --> pdb=" O LEU B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 270 Processing helix chain 'B' and resid 272 through 281 removed outlier: 4.172A pdb=" N GLY B 276 " --> pdb=" O TYR B 272 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE B 279 " --> pdb=" O ALA B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 287 Processing helix chain 'B' and resid 288 through 293 Processing helix chain 'B' and resid 294 through 311 removed outlier: 3.505A pdb=" N VAL B 298 " --> pdb=" O VAL B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 330 removed outlier: 3.525A pdb=" N TRP B 316 " --> pdb=" O GLY B 312 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE B 317 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS B 320 " --> pdb=" O TRP B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 343 removed outlier: 3.579A pdb=" N ILE B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 361 removed outlier: 3.558A pdb=" N ARG B 355 " --> pdb=" O LEU B 352 " (cutoff:3.500A) Proline residue: B 356 - end of helix Proline residue: B 359 - end of helix Processing helix chain 'B' and resid 362 through 376 removed outlier: 3.599A pdb=" N GLY B 373 " --> pdb=" O ILE B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 380 No H-bonds generated for 'chain 'B' and resid 378 through 380' Processing helix chain 'B' and resid 381 through 389 removed outlier: 3.528A pdb=" N TYR B 385 " --> pdb=" O VAL B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 414 removed outlier: 3.916A pdb=" N ALA B 403 " --> pdb=" O SER B 399 " (cutoff:3.500A) Proline residue: B 404 - end of helix Processing helix chain 'B' and resid 423 through 429 Processing helix chain 'B' and resid 437 through 479 removed outlier: 3.713A pdb=" N ILE B 450 " --> pdb=" O ALA B 446 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N SER B 451 " --> pdb=" O SER B 447 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU B 452 " --> pdb=" O SER B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 482 No H-bonds generated for 'chain 'B' and resid 480 through 482' Processing helix chain 'B' and resid 487 through 496 removed outlier: 3.675A pdb=" N TYR B 494 " --> pdb=" O VAL B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 503 Processing helix chain 'B' and resid 506 through 523 removed outlier: 3.920A pdb=" N PHE B 511 " --> pdb=" O TRP B 507 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N MET B 512 " --> pdb=" O GLN B 508 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS B 515 " --> pdb=" O PHE B 511 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU B 516 " --> pdb=" O MET B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 542 Processing helix chain 'B' and resid 555 through 566 Processing helix chain 'B' and resid 571 through 573 No H-bonds generated for 'chain 'B' and resid 571 through 573' Processing helix chain 'B' and resid 574 through 586 Processing helix chain 'B' and resid 589 through 619 removed outlier: 3.524A pdb=" N ALA B 595 " --> pdb=" O ARG B 591 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N MET B 598 " --> pdb=" O THR B 594 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ARG B 599 " --> pdb=" O ALA B 595 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 546 through 547 Processing sheet with id=AA2, first strand: chain 'C' and resid 546 through 547 Processing sheet with id=AA3, first strand: chain 'B' and resid 546 through 547 967 hydrogen bonds defined for protein. 2856 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: 8.56 Time building geometry restraints manager: 20.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.02: 12147 1.02 - 1.22: 42 1.22 - 1.42: 5401 1.42 - 1.61: 7343 1.61 - 1.81: 180 Bond restraints: 25113 Sorted by residual: bond pdb=" O4 LBN C 804 " pdb=" P1 LBN C 804 " ideal model delta sigma weight residual 1.497 1.646 -0.149 2.00e-02 2.50e+03 5.56e+01 bond pdb=" O4 LBN A 804 " pdb=" P1 LBN A 804 " ideal model delta sigma weight residual 1.497 1.645 -0.148 2.00e-02 2.50e+03 5.51e+01 bond pdb=" O4 LBN A 805 " pdb=" P1 LBN A 805 " ideal model delta sigma weight residual 1.497 1.645 -0.148 2.00e-02 2.50e+03 5.49e+01 bond pdb=" O4 LBN B 804 " pdb=" P1 LBN B 804 " ideal model delta sigma weight residual 1.497 1.645 -0.148 2.00e-02 2.50e+03 5.48e+01 bond pdb=" O4 LBN C 805 " pdb=" P1 LBN C 805 " ideal model delta sigma weight residual 1.497 1.645 -0.148 2.00e-02 2.50e+03 5.48e+01 ... (remaining 25108 not shown) Histogram of bond angle deviations from ideal: 98.83 - 105.90: 271 105.90 - 112.97: 28614 112.97 - 120.04: 7432 120.04 - 127.10: 8593 127.10 - 134.17: 159 Bond angle restraints: 45069 Sorted by residual: angle pdb=" O1 LBN C 803 " pdb=" P1 LBN C 803 " pdb=" O2 LBN C 803 " ideal model delta sigma weight residual 93.45 110.16 -16.71 3.00e+00 1.11e-01 3.10e+01 angle pdb=" O1 LBN B 803 " pdb=" P1 LBN B 803 " pdb=" O2 LBN B 803 " ideal model delta sigma weight residual 93.45 110.16 -16.71 3.00e+00 1.11e-01 3.10e+01 angle pdb=" O1 LBN A 803 " pdb=" P1 LBN A 803 " pdb=" O2 LBN A 803 " ideal model delta sigma weight residual 93.45 110.14 -16.69 3.00e+00 1.11e-01 3.10e+01 angle pdb=" O1 LBN C 806 " pdb=" P1 LBN C 806 " pdb=" O2 LBN C 806 " ideal model delta sigma weight residual 93.45 110.10 -16.65 3.00e+00 1.11e-01 3.08e+01 angle pdb=" O1 LBN A 806 " pdb=" P1 LBN A 806 " pdb=" O2 LBN A 806 " ideal model delta sigma weight residual 93.45 110.06 -16.61 3.00e+00 1.11e-01 3.07e+01 ... (remaining 45064 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.64: 11584 35.64 - 71.29: 431 71.29 - 106.93: 18 106.93 - 142.57: 3 142.57 - 178.21: 6 Dihedral angle restraints: 12042 sinusoidal: 6312 harmonic: 5730 Sorted by residual: dihedral pdb=" O5 LBN A 803 " pdb=" C2 LBN A 803 " pdb=" C3 LBN A 803 " pdb=" O7 LBN A 803 " ideal model delta sinusoidal sigma weight residual 62.67 -119.12 -178.21 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O5 LBN B 803 " pdb=" C2 LBN B 803 " pdb=" C3 LBN B 803 " pdb=" O7 LBN B 803 " ideal model delta sinusoidal sigma weight residual 62.67 -119.14 -178.19 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O5 LBN C 803 " pdb=" C2 LBN C 803 " pdb=" C3 LBN C 803 " pdb=" O7 LBN C 803 " ideal model delta sinusoidal sigma weight residual 62.67 -119.15 -178.18 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 12039 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1183 0.039 - 0.078: 636 0.078 - 0.117: 147 0.117 - 0.156: 26 0.156 - 0.195: 3 Chirality restraints: 1995 Sorted by residual: chirality pdb=" C2 LBN A 805 " pdb=" C1 LBN A 805 " pdb=" C3 LBN A 805 " pdb=" O7 LBN A 805 " both_signs ideal model delta sigma weight residual False -2.36 -2.56 0.19 2.00e-01 2.50e+01 9.50e-01 chirality pdb=" C2 LBN C 805 " pdb=" C1 LBN C 805 " pdb=" C3 LBN C 805 " pdb=" O7 LBN C 805 " both_signs ideal model delta sigma weight residual False -2.36 -2.56 0.19 2.00e-01 2.50e+01 9.24e-01 chirality pdb=" C2 LBN B 805 " pdb=" C1 LBN B 805 " pdb=" C3 LBN B 805 " pdb=" O7 LBN B 805 " both_signs ideal model delta sigma weight residual False -2.36 -2.56 0.19 2.00e-01 2.50e+01 9.24e-01 ... (remaining 1992 not shown) Planarity restraints: 3657 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 295 " 0.041 5.00e-02 4.00e+02 6.24e-02 6.22e+00 pdb=" N PRO A 296 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 296 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 296 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 295 " -0.041 5.00e-02 4.00e+02 6.23e-02 6.20e+00 pdb=" N PRO C 296 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO C 296 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 296 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 295 " -0.041 5.00e-02 4.00e+02 6.22e-02 6.20e+00 pdb=" N PRO B 296 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO B 296 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 296 " -0.035 5.00e-02 4.00e+02 ... (remaining 3654 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.14: 694 2.14 - 2.76: 44243 2.76 - 3.37: 68493 3.37 - 3.99: 90622 3.99 - 4.60: 143127 Nonbonded interactions: 347179 Sorted by model distance: nonbonded pdb=" O PHE C 223 " pdb="HH22 ARG C 599 " model vdw 1.530 2.450 nonbonded pdb=" O PHE B 223 " pdb="HH22 ARG B 599 " model vdw 1.532 2.450 nonbonded pdb=" O PHE A 223 " pdb="HH22 ARG A 599 " model vdw 1.532 2.450 nonbonded pdb=" O VAL C 298 " pdb=" HG SER C 302 " model vdw 1.540 2.450 nonbonded pdb=" O VAL B 298 " pdb=" HG SER B 302 " model vdw 1.564 2.450 ... (remaining 347174 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 0.760 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: 0.410 Extract box with map and model: 0.830 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 73.690 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 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 : 0.011 0.149 12948 Z= 0.735 Angle : 0.991 16.712 17547 Z= 0.438 Chirality : 0.048 0.195 1995 Planarity : 0.006 0.062 2115 Dihedral : 16.560 178.214 4548 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.82 % Favored : 96.99 % Rotamer: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.08 (0.17), residues: 1593 helix: -1.96 (0.11), residues: 1323 sheet: None (None), residues: 0 loop : -1.07 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 476 HIS 0.004 0.001 HIS B 367 PHE 0.022 0.002 PHE C 279 TYR 0.012 0.002 TYR A 285 ARG 0.002 0.001 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 229 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 1.833 Fit side-chains revert: symmetry clash REVERT: A 129 MET cc_start: 0.7105 (mtp) cc_final: 0.6829 (mtp) REVERT: A 228 THR cc_start: 0.8253 (p) cc_final: 0.8035 (p) REVERT: A 248 LEU cc_start: 0.8141 (tp) cc_final: 0.7831 (mp) REVERT: A 421 LYS cc_start: 0.7891 (mttt) cc_final: 0.7514 (mmtt) REVERT: A 483 TYR cc_start: 0.8200 (t80) cc_final: 0.7737 (t80) REVERT: A 508 GLN cc_start: 0.7509 (mt0) cc_final: 0.7051 (mp10) REVERT: A 590 LYS cc_start: 0.8215 (tttt) cc_final: 0.8007 (ttmt) REVERT: C 129 MET cc_start: 0.6650 (mtp) cc_final: 0.6326 (mtp) REVERT: C 231 TYR cc_start: 0.7955 (t80) cc_final: 0.7543 (t80) REVERT: C 248 LEU cc_start: 0.7823 (tp) cc_final: 0.7592 (mp) REVERT: C 317 ILE cc_start: 0.8435 (mt) cc_final: 0.8159 (tp) REVERT: C 325 MET cc_start: 0.8319 (mtm) cc_final: 0.8106 (mtm) REVERT: C 355 ARG cc_start: 0.7716 (ttt180) cc_final: 0.7341 (ttp80) REVERT: C 370 MET cc_start: 0.8699 (mtm) cc_final: 0.8373 (mtm) REVERT: C 421 LYS cc_start: 0.7873 (mttt) cc_final: 0.7668 (mmtp) REVERT: B 129 MET cc_start: 0.6740 (mtp) cc_final: 0.6533 (mtp) REVERT: B 151 ASP cc_start: 0.7696 (m-30) cc_final: 0.7422 (m-30) REVERT: B 231 TYR cc_start: 0.8021 (t80) cc_final: 0.7588 (t80) REVERT: B 248 LEU cc_start: 0.7926 (tp) cc_final: 0.7718 (mp) REVERT: B 325 MET cc_start: 0.8169 (mtm) cc_final: 0.7925 (mtm) REVERT: B 421 LYS cc_start: 0.7846 (mttt) cc_final: 0.7392 (mmtt) REVERT: B 440 GLU cc_start: 0.8230 (tt0) cc_final: 0.7934 (tt0) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 1.9755 time to fit residues: 505.4680 Evaluate side-chains 183 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 1.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 92 optimal weight: 0.6980 chunk 144 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 ASN C 204 GLN C 426 ASN B 423 ASN B 426 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 12948 Z= 0.158 Angle : 0.525 4.492 17547 Z= 0.288 Chirality : 0.036 0.126 1995 Planarity : 0.005 0.048 2115 Dihedral : 14.765 146.961 1998 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.16 % Allowed : 7.68 % Favored : 92.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.20), residues: 1593 helix: 1.20 (0.14), residues: 1326 sheet: None (None), residues: 0 loop : -0.50 (0.39), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 323 HIS 0.004 0.001 HIS C 288 PHE 0.016 0.001 PHE B 279 TYR 0.010 0.001 TYR B 519 ARG 0.002 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 186 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 184 time to evaluate : 1.804 Fit side-chains REVERT: A 129 MET cc_start: 0.6689 (mtp) cc_final: 0.6442 (mtp) REVERT: A 189 LEU cc_start: 0.7515 (tp) cc_final: 0.7044 (tm) REVERT: A 231 TYR cc_start: 0.7819 (t80) cc_final: 0.7437 (t80) REVERT: A 248 LEU cc_start: 0.7948 (tp) cc_final: 0.7547 (mp) REVERT: A 317 ILE cc_start: 0.8463 (mt) cc_final: 0.8209 (tp) REVERT: A 325 MET cc_start: 0.8478 (mtm) cc_final: 0.8106 (mtm) REVERT: A 483 TYR cc_start: 0.8157 (t80) cc_final: 0.7750 (t80) REVERT: C 129 MET cc_start: 0.6650 (mtp) cc_final: 0.6402 (mtp) REVERT: C 231 TYR cc_start: 0.7686 (t80) cc_final: 0.7472 (t80) REVERT: C 317 ILE cc_start: 0.8466 (mt) cc_final: 0.8124 (tp) REVERT: C 355 ARG cc_start: 0.7671 (ttt180) cc_final: 0.7323 (ttp80) REVERT: C 421 LYS cc_start: 0.7877 (mttt) cc_final: 0.7641 (mmtp) REVERT: B 142 VAL cc_start: 0.7529 (t) cc_final: 0.7135 (p) REVERT: B 154 MET cc_start: 0.6773 (mmt) cc_final: 0.6506 (mmm) REVERT: B 231 TYR cc_start: 0.7756 (t80) cc_final: 0.7378 (t80) REVERT: B 248 LEU cc_start: 0.7843 (tp) cc_final: 0.7555 (mp) REVERT: B 325 MET cc_start: 0.8439 (mtm) cc_final: 0.7914 (mtm) REVERT: B 421 LYS cc_start: 0.7835 (mttt) cc_final: 0.7366 (mmtp) REVERT: B 440 GLU cc_start: 0.7893 (tt0) cc_final: 0.7634 (tt0) outliers start: 2 outliers final: 0 residues processed: 184 average time/residue: 1.8084 time to fit residues: 375.4766 Evaluate side-chains 174 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 1.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 120 optimal weight: 0.5980 chunk 98 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 chunk 156 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 ASN C 204 GLN B 426 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12948 Z= 0.226 Angle : 0.546 5.777 17547 Z= 0.297 Chirality : 0.038 0.125 1995 Planarity : 0.004 0.048 2115 Dihedral : 13.742 145.910 1998 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.87 % Allowed : 7.21 % Favored : 91.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.21), residues: 1593 helix: 1.97 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -0.48 (0.36), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 323 HIS 0.005 0.001 HIS C 288 PHE 0.026 0.002 PHE A 279 TYR 0.010 0.002 TYR C 310 ARG 0.004 0.001 ARG A 599 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 191 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 180 time to evaluate : 1.817 Fit side-chains REVERT: A 129 MET cc_start: 0.6675 (mtp) cc_final: 0.6450 (mtp) REVERT: A 193 LEU cc_start: 0.8206 (mt) cc_final: 0.7937 (mm) REVERT: A 248 LEU cc_start: 0.8135 (tp) cc_final: 0.7679 (mp) REVERT: A 325 MET cc_start: 0.8535 (mtm) cc_final: 0.8142 (mtm) REVERT: A 483 TYR cc_start: 0.8181 (t80) cc_final: 0.7723 (t80) REVERT: A 497 MET cc_start: 0.8613 (tmm) cc_final: 0.8283 (tmm) REVERT: A 506 ASP cc_start: 0.7672 (p0) cc_final: 0.7322 (p0) REVERT: C 129 MET cc_start: 0.6756 (mtp) cc_final: 0.6453 (mtp) REVERT: C 231 TYR cc_start: 0.7987 (t80) cc_final: 0.7593 (t80) REVERT: C 355 ARG cc_start: 0.7726 (ttt180) cc_final: 0.7306 (ttp80) REVERT: B 142 VAL cc_start: 0.7567 (t) cc_final: 0.7170 (p) REVERT: B 231 TYR cc_start: 0.7837 (t80) cc_final: 0.7450 (t80) REVERT: B 248 LEU cc_start: 0.8120 (tp) cc_final: 0.7730 (mp) REVERT: B 305 MET cc_start: 0.8304 (mmm) cc_final: 0.8069 (mmm) REVERT: B 325 MET cc_start: 0.8528 (mtm) cc_final: 0.7850 (mtm) REVERT: B 421 LYS cc_start: 0.7888 (mttt) cc_final: 0.7402 (mmtt) REVERT: B 440 GLU cc_start: 0.8148 (tt0) cc_final: 0.7876 (tt0) outliers start: 11 outliers final: 5 residues processed: 187 average time/residue: 1.8313 time to fit residues: 392.5290 Evaluate side-chains 173 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 168 time to evaluate : 1.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 413 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 142 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 69 optimal weight: 0.4980 chunk 97 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 153 optimal weight: 4.9990 chunk 137 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 ASN C 204 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12948 Z= 0.276 Angle : 0.598 6.179 17547 Z= 0.324 Chirality : 0.040 0.133 1995 Planarity : 0.004 0.047 2115 Dihedral : 14.311 149.424 1998 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.50 % Allowed : 6.81 % Favored : 91.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.21), residues: 1593 helix: 1.96 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -0.42 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 323 HIS 0.005 0.001 HIS C 288 PHE 0.029 0.002 PHE A 279 TYR 0.011 0.002 TYR C 310 ARG 0.005 0.001 ARG A 599 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 187 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 168 time to evaluate : 1.930 Fit side-chains REVERT: A 193 LEU cc_start: 0.8285 (mt) cc_final: 0.8017 (mm) REVERT: A 231 TYR cc_start: 0.7983 (t80) cc_final: 0.7489 (t80) REVERT: A 248 LEU cc_start: 0.8239 (tp) cc_final: 0.7798 (mm) REVERT: A 483 TYR cc_start: 0.8161 (t80) cc_final: 0.7693 (t80) REVERT: C 355 ARG cc_start: 0.7774 (ttt180) cc_final: 0.7439 (ttp80) REVERT: B 142 VAL cc_start: 0.7573 (t) cc_final: 0.7174 (p) REVERT: B 231 TYR cc_start: 0.7931 (t80) cc_final: 0.7423 (t80) REVERT: B 248 LEU cc_start: 0.8215 (tp) cc_final: 0.7788 (mp) REVERT: B 305 MET cc_start: 0.8314 (mmm) cc_final: 0.8012 (mmm) REVERT: B 325 MET cc_start: 0.8599 (mtm) cc_final: 0.7828 (mtm) REVERT: B 421 LYS cc_start: 0.7898 (mttt) cc_final: 0.7381 (mmtp) outliers start: 19 outliers final: 12 residues processed: 179 average time/residue: 1.7880 time to fit residues: 362.2918 Evaluate side-chains 179 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 167 time to evaluate : 1.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 444 GLN Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 506 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 87 optimal weight: 0.0770 chunk 2 optimal weight: 20.0000 chunk 114 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 106 optimal weight: 50.0000 chunk 0 optimal weight: 50.0000 chunk 78 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 overall best weight: 3.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 ASN C 204 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12948 Z= 0.283 Angle : 0.596 6.360 17547 Z= 0.322 Chirality : 0.040 0.132 1995 Planarity : 0.004 0.046 2115 Dihedral : 14.303 150.117 1998 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.66 % Allowed : 7.28 % Favored : 91.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.21), residues: 1593 helix: 1.96 (0.14), residues: 1320 sheet: None (None), residues: 0 loop : -0.33 (0.35), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 323 HIS 0.006 0.001 HIS C 288 PHE 0.029 0.002 PHE A 279 TYR 0.011 0.002 TYR C 310 ARG 0.005 0.001 ARG B 589 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 189 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 168 time to evaluate : 1.825 Fit side-chains REVERT: A 193 LEU cc_start: 0.8267 (mt) cc_final: 0.8009 (mm) REVERT: A 231 TYR cc_start: 0.7984 (t80) cc_final: 0.7568 (t80) REVERT: A 248 LEU cc_start: 0.8272 (tp) cc_final: 0.7821 (mm) REVERT: A 483 TYR cc_start: 0.8153 (t80) cc_final: 0.7693 (t80) REVERT: C 222 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7959 (tt) REVERT: C 355 ARG cc_start: 0.7792 (ttt180) cc_final: 0.7454 (ttp80) REVERT: B 142 VAL cc_start: 0.7538 (t) cc_final: 0.7175 (p) REVERT: B 231 TYR cc_start: 0.7917 (t80) cc_final: 0.7455 (t80) REVERT: B 248 LEU cc_start: 0.8216 (tp) cc_final: 0.7827 (mm) REVERT: B 305 MET cc_start: 0.8305 (mmm) cc_final: 0.8015 (mmm) REVERT: B 325 MET cc_start: 0.8555 (mtm) cc_final: 0.7687 (mtm) REVERT: B 421 LYS cc_start: 0.7903 (mttt) cc_final: 0.7384 (mmtp) outliers start: 21 outliers final: 16 residues processed: 181 average time/residue: 1.7043 time to fit residues: 349.5727 Evaluate side-chains 182 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 165 time to evaluate : 1.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 444 GLN Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 506 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 138 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 ASN C 204 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12948 Z= 0.218 Angle : 0.537 5.422 17547 Z= 0.290 Chirality : 0.038 0.125 1995 Planarity : 0.004 0.044 2115 Dihedral : 13.706 150.474 1998 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.95 % Allowed : 8.00 % Favored : 91.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.67 (0.21), residues: 1593 helix: 2.20 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -0.32 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 323 HIS 0.004 0.001 HIS C 288 PHE 0.025 0.002 PHE C 279 TYR 0.009 0.002 TYR C 310 ARG 0.003 0.001 ARG B 599 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 177 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 165 time to evaluate : 1.929 Fit side-chains REVERT: A 193 LEU cc_start: 0.8178 (mt) cc_final: 0.7919 (mm) REVERT: A 231 TYR cc_start: 0.7933 (t80) cc_final: 0.7556 (t80) REVERT: A 248 LEU cc_start: 0.8219 (tp) cc_final: 0.7791 (mm) REVERT: A 483 TYR cc_start: 0.8177 (t80) cc_final: 0.7668 (t80) REVERT: C 355 ARG cc_start: 0.7777 (ttt180) cc_final: 0.7436 (ttp80) REVERT: C 472 SER cc_start: 0.8585 (OUTLIER) cc_final: 0.8288 (t) REVERT: B 142 VAL cc_start: 0.7567 (t) cc_final: 0.7219 (p) REVERT: B 231 TYR cc_start: 0.7869 (t80) cc_final: 0.7416 (t80) REVERT: B 248 LEU cc_start: 0.8136 (tp) cc_final: 0.7758 (mm) REVERT: B 305 MET cc_start: 0.8297 (mmm) cc_final: 0.7996 (mmm) REVERT: B 325 MET cc_start: 0.8602 (mtm) cc_final: 0.7768 (mtm) REVERT: B 421 LYS cc_start: 0.7899 (mttt) cc_final: 0.7404 (mmtt) outliers start: 12 outliers final: 10 residues processed: 172 average time/residue: 1.8449 time to fit residues: 358.3327 Evaluate side-chains 176 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 165 time to evaluate : 1.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 620 ASN Chi-restraints excluded: chain C residue 444 GLN Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 506 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 17 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 112 optimal weight: 7.9990 chunk 129 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 chunk 61 optimal weight: 5.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 ASN C 204 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12948 Z= 0.173 Angle : 0.495 6.102 17547 Z= 0.267 Chirality : 0.036 0.125 1995 Planarity : 0.004 0.043 2115 Dihedral : 13.097 149.238 1998 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.11 % Allowed : 8.31 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.99 (0.21), residues: 1593 helix: 2.42 (0.14), residues: 1317 sheet: None (None), residues: 0 loop : -0.25 (0.36), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 323 HIS 0.004 0.001 HIS C 288 PHE 0.022 0.001 PHE C 279 TYR 0.008 0.001 TYR C 310 ARG 0.002 0.000 ARG A 557 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 181 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 167 time to evaluate : 2.411 Fit side-chains revert: symmetry clash REVERT: A 193 LEU cc_start: 0.8170 (mt) cc_final: 0.7893 (mm) REVERT: A 231 TYR cc_start: 0.7883 (t80) cc_final: 0.7513 (t80) REVERT: A 248 LEU cc_start: 0.8110 (tp) cc_final: 0.7684 (mm) REVERT: A 483 TYR cc_start: 0.8280 (t80) cc_final: 0.7836 (t80) REVERT: A 554 MET cc_start: 0.8554 (ptt) cc_final: 0.8072 (ptt) REVERT: C 355 ARG cc_start: 0.7706 (ttt180) cc_final: 0.7369 (ttp80) REVERT: C 472 SER cc_start: 0.8545 (OUTLIER) cc_final: 0.8290 (t) REVERT: B 142 VAL cc_start: 0.7567 (t) cc_final: 0.7220 (p) REVERT: B 231 TYR cc_start: 0.7789 (t80) cc_final: 0.7334 (t80) REVERT: B 248 LEU cc_start: 0.8004 (tp) cc_final: 0.7634 (mm) REVERT: B 325 MET cc_start: 0.8612 (mtm) cc_final: 0.7734 (mtm) REVERT: B 421 LYS cc_start: 0.7840 (mttt) cc_final: 0.7406 (mmtt) outliers start: 14 outliers final: 6 residues processed: 174 average time/residue: 1.8200 time to fit residues: 358.9430 Evaluate side-chains 170 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 163 time to evaluate : 1.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 444 GLN Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain B residue 199 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 91 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 120 optimal weight: 0.6980 chunk 139 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 ASN C 204 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12948 Z= 0.262 Angle : 0.581 6.814 17547 Z= 0.313 Chirality : 0.039 0.134 1995 Planarity : 0.004 0.046 2115 Dihedral : 13.979 150.589 1998 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.11 % Allowed : 8.63 % Favored : 90.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.21), residues: 1593 helix: 2.14 (0.14), residues: 1320 sheet: None (None), residues: 0 loop : -0.25 (0.35), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 323 HIS 0.005 0.001 HIS C 288 PHE 0.028 0.002 PHE A 279 TYR 0.011 0.002 TYR C 310 ARG 0.005 0.001 ARG B 589 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 181 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 167 time to evaluate : 1.838 Fit side-chains revert: symmetry clash REVERT: A 193 LEU cc_start: 0.8128 (mt) cc_final: 0.7868 (mm) REVERT: A 231 TYR cc_start: 0.7964 (t80) cc_final: 0.7515 (t80) REVERT: A 248 LEU cc_start: 0.8242 (tp) cc_final: 0.7805 (mm) REVERT: A 483 TYR cc_start: 0.8350 (t80) cc_final: 0.7867 (t80) REVERT: A 554 MET cc_start: 0.8563 (ptt) cc_final: 0.8076 (ptt) REVERT: C 222 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7984 (tt) REVERT: C 355 ARG cc_start: 0.7792 (ttt180) cc_final: 0.7456 (ttp80) REVERT: B 142 VAL cc_start: 0.7531 (t) cc_final: 0.7181 (p) REVERT: B 231 TYR cc_start: 0.7893 (t80) cc_final: 0.7488 (t80) REVERT: B 248 LEU cc_start: 0.8182 (tp) cc_final: 0.7807 (mm) REVERT: B 325 MET cc_start: 0.8632 (mtm) cc_final: 0.7885 (mtm) REVERT: B 421 LYS cc_start: 0.7902 (mttt) cc_final: 0.7404 (mmtt) outliers start: 14 outliers final: 13 residues processed: 178 average time/residue: 1.7330 time to fit residues: 350.3740 Evaluate side-chains 178 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 164 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 444 GLN Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 413 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 133 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 129 optimal weight: 0.0980 chunk 135 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 151 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 ASN C 204 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12948 Z= 0.180 Angle : 0.504 6.192 17547 Z= 0.272 Chirality : 0.037 0.127 1995 Planarity : 0.004 0.044 2115 Dihedral : 13.329 150.874 1998 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.95 % Allowed : 9.03 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.98 (0.21), residues: 1593 helix: 2.42 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -0.27 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 323 HIS 0.004 0.001 HIS C 288 PHE 0.022 0.001 PHE C 279 TYR 0.008 0.001 TYR C 310 ARG 0.002 0.000 ARG C 599 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 174 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 162 time to evaluate : 1.919 Fit side-chains revert: symmetry clash REVERT: A 193 LEU cc_start: 0.8118 (mt) cc_final: 0.7854 (mm) REVERT: A 231 TYR cc_start: 0.7887 (t80) cc_final: 0.7535 (t80) REVERT: A 248 LEU cc_start: 0.8134 (tp) cc_final: 0.7702 (mm) REVERT: A 483 TYR cc_start: 0.8342 (t80) cc_final: 0.7881 (t80) REVERT: A 554 MET cc_start: 0.8557 (ptt) cc_final: 0.8093 (ptt) REVERT: C 317 ILE cc_start: 0.8466 (mt) cc_final: 0.8059 (tp) REVERT: C 355 ARG cc_start: 0.7699 (ttt180) cc_final: 0.7359 (ttp80) REVERT: C 472 SER cc_start: 0.8559 (OUTLIER) cc_final: 0.8295 (t) REVERT: B 142 VAL cc_start: 0.7565 (t) cc_final: 0.7225 (p) REVERT: B 231 TYR cc_start: 0.7795 (t80) cc_final: 0.7373 (t80) REVERT: B 248 LEU cc_start: 0.8028 (tp) cc_final: 0.7664 (mm) REVERT: B 325 MET cc_start: 0.8632 (mtm) cc_final: 0.7750 (mtm) REVERT: B 421 LYS cc_start: 0.7842 (mttt) cc_final: 0.7412 (mmtt) outliers start: 12 outliers final: 9 residues processed: 171 average time/residue: 1.8120 time to fit residues: 350.9279 Evaluate side-chains 172 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 162 time to evaluate : 1.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 444 GLN Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 458 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 92 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 104 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 126 optimal weight: 0.7980 chunk 13 optimal weight: 0.4980 chunk 97 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: