Starting phenix.real_space_refine on Fri Aug 9 02:10:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz2_41731/08_2024/8tz2_41731_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz2_41731/08_2024/8tz2_41731.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz2_41731/08_2024/8tz2_41731.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz2_41731/08_2024/8tz2_41731.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz2_41731/08_2024/8tz2_41731_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz2_41731/08_2024/8tz2_41731_trim.cif" } resolution = 2.8 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= 0.002 sd= 0.089 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 6 5.49 5 S 87 5.16 5 Na 6 4.78 5 C 8256 2.51 5 N 1926 2.21 5 O 2145 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 131": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 131": "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: 24591 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: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 66 Unusual residues: {' NA': 2, 'LBN': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 40 Chain: "C" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 66 Unusual residues: {' NA': 2, 'LBN': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 40 Chain: "B" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 66 Unusual residues: {' NA': 2, 'LBN': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 40 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 11.07, per 1000 atoms: 0.45 Number of scatterers: 24591 At special positions: 0 Unit cell: (130.68, 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 6 15.00 Na 6 11.00 O 2145 8.00 N 1926 7.00 C 8256 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: 19.83 Conformation dependent library (CDL) restraints added in 2.9 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 89.6% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.06 Creating SS restraints... Processing helix chain 'A' and resid 90 through 103 Processing helix chain 'A' and resid 103 through 130 Processing helix chain 'A' and resid 134 through 157 Processing helix chain 'A' and resid 157 through 198 Proline residue: A 167 - end of helix removed outlier: 4.698A pdb=" N PHE A 177 " --> pdb=" O ASP A 173 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N TRP A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N TRP A 181 " --> pdb=" O PHE A 177 " (cutoff:3.500A) removed outlier: 4.037A 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 removed outlier: 3.716A pdb=" N LEU A 207 " --> pdb=" O GLY A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 230 removed outlier: 4.126A pdb=" N VAL A 230 " --> pdb=" O PRO A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 251 removed outlier: 4.610A pdb=" N VAL A 235 " --> pdb=" O TYR A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 270 Processing helix chain 'A' and resid 272 through 282 removed outlier: 4.392A pdb=" N GLY A 276 " --> pdb=" O TYR A 272 " (cutoff:3.500A) removed outlier: 3.547A 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 294 Processing helix chain 'A' and resid 294 through 312 Processing helix chain 'A' and resid 312 through 330 removed outlier: 3.527A pdb=" N TRP A 316 " --> pdb=" O GLY A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 342 Processing helix chain 'A' and resid 349 through 361 Proline residue: A 356 - end of helix Proline residue: A 359 - end of helix Processing helix chain 'A' and resid 362 through 375 Processing helix chain 'A' and resid 381 through 389 removed outlier: 3.502A pdb=" N TYR A 385 " --> pdb=" O VAL A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 414 removed outlier: 4.258A 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: 3.503A pdb=" N SER A 449 " --> pdb=" O GLY A 445 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE A 450 " --> pdb=" O ALA A 446 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N SER A 451 " --> pdb=" O SER A 447 " (cutoff:3.500A) removed outlier: 4.049A 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: 3.607A 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: 4.116A pdb=" N PHE A 511 " --> pdb=" O TRP A 507 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N MET A 512 " --> pdb=" O GLN A 508 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS A 515 " --> pdb=" O PHE A 511 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU A 516 " --> pdb=" O MET A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 542 removed outlier: 3.709A pdb=" N ALA A 528 " --> pdb=" O ASN A 524 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY A 542 " --> pdb=" O LEU A 538 " (cutoff:3.500A) 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: 3.558A pdb=" N ALA A 595 " --> pdb=" O ARG A 591 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N MET A 598 " --> pdb=" O THR A 594 " (cutoff:3.500A) removed outlier: 5.115A 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 Processing helix chain 'C' and resid 134 through 157 Processing helix chain 'C' and resid 157 through 198 Proline residue: C 167 - end of helix removed outlier: 4.698A pdb=" N PHE C 177 " --> pdb=" O ASP C 173 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N TRP C 178 " --> pdb=" O SER C 174 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N TRP C 181 " --> pdb=" O PHE C 177 " (cutoff:3.500A) removed outlier: 4.037A 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 removed outlier: 3.717A pdb=" N LEU C 207 " --> pdb=" O GLY C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 230 removed outlier: 4.126A pdb=" N VAL C 230 " --> pdb=" O PRO C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 251 removed outlier: 4.610A pdb=" N VAL C 235 " --> pdb=" O TYR C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 270 Processing helix chain 'C' and resid 272 through 282 removed outlier: 4.392A pdb=" N GLY C 276 " --> pdb=" O TYR C 272 " (cutoff:3.500A) removed outlier: 3.547A 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 294 Processing helix chain 'C' and resid 294 through 312 Processing helix chain 'C' and resid 312 through 330 removed outlier: 3.527A pdb=" N TRP C 316 " --> pdb=" O GLY C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 342 Processing helix chain 'C' and resid 349 through 361 Proline residue: C 356 - end of helix Proline residue: C 359 - end of helix Processing helix chain 'C' and resid 362 through 375 Processing helix chain 'C' and resid 381 through 389 removed outlier: 3.502A pdb=" N TYR C 385 " --> pdb=" O VAL C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 414 removed outlier: 4.259A 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: 3.504A pdb=" N SER C 449 " --> pdb=" O GLY C 445 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE C 450 " --> pdb=" O ALA C 446 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N SER C 451 " --> pdb=" O SER C 447 " (cutoff:3.500A) removed outlier: 4.049A 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: 3.607A 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: 4.116A pdb=" N PHE C 511 " --> pdb=" O TRP C 507 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N MET C 512 " --> pdb=" O GLN C 508 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS C 515 " --> pdb=" O PHE C 511 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU C 516 " --> pdb=" O MET C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 542 removed outlier: 3.708A pdb=" N ALA C 528 " --> pdb=" O ASN C 524 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY C 542 " --> pdb=" O LEU C 538 " (cutoff:3.500A) 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: 3.558A pdb=" N ALA C 595 " --> pdb=" O ARG C 591 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N MET C 598 " --> pdb=" O THR C 594 " (cutoff:3.500A) removed outlier: 5.115A 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 Processing helix chain 'B' and resid 134 through 157 Processing helix chain 'B' and resid 157 through 198 Proline residue: B 167 - end of helix removed outlier: 4.698A pdb=" N PHE B 177 " --> pdb=" O ASP B 173 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N TRP B 178 " --> pdb=" O SER B 174 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N TRP B 181 " --> pdb=" O PHE B 177 " (cutoff:3.500A) removed outlier: 4.037A 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 removed outlier: 3.717A pdb=" N LEU B 207 " --> pdb=" O GLY B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 230 removed outlier: 4.127A pdb=" N VAL B 230 " --> pdb=" O PRO B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 251 removed outlier: 4.610A pdb=" N VAL B 235 " --> pdb=" O TYR B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 270 Processing helix chain 'B' and resid 272 through 282 removed outlier: 4.391A pdb=" N GLY B 276 " --> pdb=" O TYR B 272 " (cutoff:3.500A) removed outlier: 3.547A 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 294 Processing helix chain 'B' and resid 294 through 312 Processing helix chain 'B' and resid 312 through 330 removed outlier: 3.526A pdb=" N TRP B 316 " --> pdb=" O GLY B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 342 Processing helix chain 'B' and resid 349 through 361 Proline residue: B 356 - end of helix Proline residue: B 359 - end of helix Processing helix chain 'B' and resid 362 through 375 Processing helix chain 'B' and resid 381 through 389 removed outlier: 3.502A pdb=" N TYR B 385 " --> pdb=" O VAL B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 414 removed outlier: 4.258A 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: 3.503A pdb=" N SER B 449 " --> pdb=" O GLY B 445 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE B 450 " --> pdb=" O ALA B 446 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N SER B 451 " --> pdb=" O SER B 447 " (cutoff:3.500A) removed outlier: 4.050A 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: 3.607A 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: 4.116A pdb=" N PHE B 511 " --> pdb=" O TRP B 507 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N MET B 512 " --> pdb=" O GLN B 508 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS B 515 " --> pdb=" O PHE B 511 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU B 516 " --> pdb=" O MET B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 542 removed outlier: 3.709A pdb=" N ALA B 528 " --> pdb=" O ASN B 524 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY B 542 " --> pdb=" O LEU B 538 " (cutoff:3.500A) 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: 3.558A pdb=" N ALA B 595 " --> pdb=" O ARG B 591 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N MET B 598 " --> pdb=" O THR B 594 " (cutoff:3.500A) removed outlier: 5.114A 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 547 979 hydrogen bonds defined for protein. 2874 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: 8.88 Time building geometry restraints manager: 20.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 12147 1.03 - 1.22: 30 1.22 - 1.42: 5373 1.42 - 1.61: 7191 1.61 - 1.81: 168 Bond restraints: 24909 Sorted by residual: bond pdb=" O4 LBN A 804 " pdb=" P1 LBN A 804 " ideal model delta sigma weight residual 1.497 1.646 -0.149 2.00e-02 2.50e+03 5.53e+01 bond pdb=" O4 LBN B 804 " pdb=" P1 LBN B 804 " ideal model delta sigma weight residual 1.497 1.646 -0.149 2.00e-02 2.50e+03 5.52e+01 bond pdb=" O4 LBN A 803 " pdb=" P1 LBN A 803 " ideal model delta sigma weight residual 1.497 1.645 -0.148 2.00e-02 2.50e+03 5.47e+01 bond pdb=" O4 LBN B 803 " pdb=" P1 LBN B 803 " ideal model delta sigma weight residual 1.497 1.645 -0.148 2.00e-02 2.50e+03 5.47e+01 bond pdb=" O4 LBN C 804 " pdb=" P1 LBN C 804 " ideal model delta sigma weight residual 1.497 1.645 -0.148 2.00e-02 2.50e+03 5.46e+01 ... (remaining 24904 not shown) Histogram of bond angle deviations from ideal: 99.37 - 106.32: 353 106.32 - 113.26: 28594 113.26 - 120.21: 8303 120.21 - 127.15: 7417 127.15 - 134.10: 168 Bond angle restraints: 44835 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 93.45 109.51 -16.06 3.00e+00 1.11e-01 2.87e+01 angle pdb=" O1 LBN A 803 " pdb=" P1 LBN A 803 " pdb=" O2 LBN A 803 " ideal model delta sigma weight residual 93.45 109.49 -16.04 3.00e+00 1.11e-01 2.86e+01 angle pdb=" O1 LBN A 804 " pdb=" P1 LBN A 804 " pdb=" O2 LBN A 804 " ideal model delta sigma weight residual 93.45 109.45 -16.00 3.00e+00 1.11e-01 2.85e+01 angle pdb=" O1 LBN B 803 " pdb=" P1 LBN B 803 " pdb=" O2 LBN B 803 " ideal model delta sigma weight residual 93.45 109.45 -16.00 3.00e+00 1.11e-01 2.84e+01 angle pdb=" O1 LBN B 804 " pdb=" P1 LBN B 804 " pdb=" O2 LBN B 804 " ideal model delta sigma weight residual 93.45 109.45 -16.00 3.00e+00 1.11e-01 2.84e+01 ... (remaining 44830 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.57: 11442 32.57 - 65.14: 411 65.14 - 97.71: 9 97.71 - 130.28: 6 130.28 - 162.85: 6 Dihedral angle restraints: 11874 sinusoidal: 6144 harmonic: 5730 Sorted by residual: dihedral pdb=" O5 LBN C 804 " pdb=" C2 LBN C 804 " pdb=" C3 LBN C 804 " pdb=" O7 LBN C 804 " ideal model delta sinusoidal sigma weight residual 62.67 -100.18 162.85 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" O5 LBN A 804 " pdb=" C2 LBN A 804 " pdb=" C3 LBN A 804 " pdb=" O7 LBN A 804 " ideal model delta sinusoidal sigma weight residual 62.67 -100.13 162.80 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" O5 LBN B 804 " pdb=" C2 LBN B 804 " pdb=" C3 LBN B 804 " pdb=" O7 LBN B 804 " ideal model delta sinusoidal sigma weight residual 62.67 -100.10 162.77 1 3.00e+01 1.11e-03 2.09e+01 ... (remaining 11871 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1390 0.038 - 0.075: 437 0.075 - 0.113: 153 0.113 - 0.150: 3 0.150 - 0.188: 6 Chirality restraints: 1989 Sorted by residual: chirality pdb=" C2 LBN C 804 " pdb=" C1 LBN C 804 " pdb=" C3 LBN C 804 " pdb=" O7 LBN C 804 " both_signs ideal model delta sigma weight residual False -2.36 -2.55 0.19 2.00e-01 2.50e+01 8.82e-01 chirality pdb=" C2 LBN A 804 " pdb=" C1 LBN A 804 " pdb=" C3 LBN A 804 " pdb=" O7 LBN A 804 " both_signs ideal model delta sigma weight residual False -2.36 -2.55 0.19 2.00e-01 2.50e+01 8.73e-01 chirality pdb=" C2 LBN B 804 " pdb=" C1 LBN B 804 " pdb=" C3 LBN B 804 " pdb=" O7 LBN B 804 " both_signs ideal model delta sigma weight residual False -2.36 -2.55 0.18 2.00e-01 2.50e+01 8.53e-01 ... (remaining 1986 not shown) Planarity restraints: 3639 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 195 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.95e+00 pdb=" C LEU B 195 " -0.042 2.00e-02 2.50e+03 pdb=" O LEU B 195 " 0.016 2.00e-02 2.50e+03 pdb=" N VAL B 196 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 195 " -0.012 2.00e-02 2.50e+03 2.43e-02 5.91e+00 pdb=" C LEU A 195 " 0.042 2.00e-02 2.50e+03 pdb=" O LEU A 195 " -0.016 2.00e-02 2.50e+03 pdb=" N VAL A 196 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 195 " -0.012 2.00e-02 2.50e+03 2.42e-02 5.86e+00 pdb=" C LEU C 195 " 0.042 2.00e-02 2.50e+03 pdb=" O LEU C 195 " -0.016 2.00e-02 2.50e+03 pdb=" N VAL C 196 " -0.014 2.00e-02 2.50e+03 ... (remaining 3636 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 956 2.18 - 2.79: 47350 2.79 - 3.39: 68133 3.39 - 4.00: 88119 4.00 - 4.60: 139696 Nonbonded interactions: 344254 Sorted by model distance: nonbonded pdb=" OE1 GLN C 206 " pdb=" H GLN C 206 " model vdw 1.581 2.450 nonbonded pdb=" OE1 GLN A 206 " pdb=" H GLN A 206 " model vdw 1.582 2.450 nonbonded pdb=" OE1 GLN B 206 " pdb=" H GLN B 206 " model vdw 1.582 2.450 nonbonded pdb=" OE1 GLU B 525 " pdb=" H GLU B 525 " model vdw 1.642 2.450 nonbonded pdb=" OE1 GLU C 525 " pdb=" H GLU C 525 " model vdw 1.642 2.450 ... (remaining 344249 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: 2.000 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: 0.380 Extract box with map and model: 0.920 Check model and map are aligned: 0.190 Set scattering table: 0.210 Process input model: 77.360 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.080 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:10.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.149 12744 Z= 0.480 Angle : 0.753 16.062 17313 Z= 0.343 Chirality : 0.041 0.188 1989 Planarity : 0.004 0.036 2097 Dihedral : 15.024 162.847 4380 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % 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 (0.21), residues: 1593 helix: 2.46 (0.14), residues: 1326 sheet: None (None), residues: 0 loop : -0.12 (0.39), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 316 HIS 0.003 0.001 HIS A 367 PHE 0.015 0.001 PHE B 413 TYR 0.009 0.001 TYR B 231 ARG 0.002 0.000 ARG C 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 242 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 1.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 436 ARG cc_start: 0.7876 (mtm-85) cc_final: 0.7618 (mmt180) REVERT: C 222 LEU cc_start: 0.7957 (tp) cc_final: 0.7687 (mt) REVERT: B 222 LEU cc_start: 0.8096 (tp) cc_final: 0.7841 (mt) REVERT: B 430 MET cc_start: 0.7923 (mtt) cc_final: 0.7649 (mtt) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 1.9693 time to fit residues: 531.6165 Evaluate side-chains 156 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 1.930 ------------------------------------------------------------------------------- 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: 2.9990 chunk 120 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 81 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 144 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12744 Z= 0.160 Angle : 0.473 5.947 17313 Z= 0.252 Chirality : 0.036 0.118 1989 Planarity : 0.004 0.041 2097 Dihedral : 12.530 127.101 1830 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 0.87 % Allowed : 9.26 % Favored : 89.87 % 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: 3.70 (0.21), residues: 1593 helix: 2.89 (0.14), residues: 1305 sheet: None (None), residues: 0 loop : 0.25 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 316 HIS 0.003 0.001 HIS B 367 PHE 0.010 0.001 PHE C 279 TYR 0.009 0.001 TYR B 231 ARG 0.002 0.000 ARG C 589 *********************** 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 166 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 155 time to evaluate : 1.799 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 436 ARG cc_start: 0.8080 (mtm-85) cc_final: 0.7525 (mmt180) REVERT: C 201 LYS cc_start: 0.7187 (mptt) cc_final: 0.6476 (tttt) REVERT: C 222 LEU cc_start: 0.8065 (tp) cc_final: 0.7529 (mt) REVERT: C 305 MET cc_start: 0.7849 (mmm) cc_final: 0.7597 (mmp) REVERT: C 370 MET cc_start: 0.8407 (mtm) cc_final: 0.8031 (mtp) REVERT: C 430 MET cc_start: 0.7897 (mtt) cc_final: 0.7441 (mtt) REVERT: B 222 LEU cc_start: 0.7818 (tp) cc_final: 0.7602 (mt) REVERT: B 440 GLU cc_start: 0.7778 (tt0) cc_final: 0.7573 (tt0) outliers start: 11 outliers final: 4 residues processed: 162 average time/residue: 1.7926 time to fit residues: 327.9749 Evaluate side-chains 151 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 147 time to evaluate : 1.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain B residue 350 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 39 optimal weight: 0.3980 chunk 144 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12744 Z= 0.243 Angle : 0.500 6.060 17313 Z= 0.266 Chirality : 0.037 0.124 1989 Planarity : 0.004 0.046 2097 Dihedral : 11.843 133.142 1830 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.43 % Allowed : 9.66 % Favored : 88.92 % 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: 3.51 (0.21), residues: 1593 helix: 2.79 (0.14), residues: 1311 sheet: None (None), residues: 0 loop : -0.05 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 316 HIS 0.004 0.001 HIS B 367 PHE 0.014 0.001 PHE A 279 TYR 0.007 0.001 TYR B 231 ARG 0.002 0.000 ARG A 436 *********************** 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 179 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 161 time to evaluate : 2.112 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 LYS cc_start: 0.7112 (mptt) cc_final: 0.6574 (tttt) REVERT: C 201 LYS cc_start: 0.7370 (mptt) cc_final: 0.6717 (tttt) REVERT: C 222 LEU cc_start: 0.8117 (tp) cc_final: 0.7586 (mt) REVERT: C 305 MET cc_start: 0.7907 (mmm) cc_final: 0.7628 (mmp) REVERT: C 355 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7766 (ttt-90) REVERT: C 430 MET cc_start: 0.8151 (mtt) cc_final: 0.7586 (mtt) REVERT: C 592 ASP cc_start: 0.7402 (m-30) cc_final: 0.7160 (m-30) REVERT: B 222 LEU cc_start: 0.7914 (tp) cc_final: 0.7612 (mt) outliers start: 18 outliers final: 11 residues processed: 172 average time/residue: 1.9117 time to fit residues: 369.9929 Evaluate side-chains 163 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 151 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 550 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 142 optimal weight: 1.9990 chunk 108 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 204 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12744 Z= 0.264 Angle : 0.512 6.164 17313 Z= 0.271 Chirality : 0.038 0.160 1989 Planarity : 0.004 0.047 2097 Dihedral : 11.054 131.755 1830 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.58 % Allowed : 11.24 % Favored : 87.17 % 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: 3.24 (0.21), residues: 1593 helix: 2.64 (0.14), residues: 1305 sheet: None (None), residues: 0 loop : -0.29 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 316 HIS 0.003 0.001 HIS B 367 PHE 0.014 0.001 PHE A 279 TYR 0.007 0.001 TYR A 483 ARG 0.002 0.000 ARG B 133 *********************** 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 178 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 158 time to evaluate : 2.005 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 LYS cc_start: 0.7314 (mptt) cc_final: 0.6724 (tttt) REVERT: C 201 LYS cc_start: 0.7352 (mptt) cc_final: 0.6688 (tttt) REVERT: C 222 LEU cc_start: 0.8067 (tp) cc_final: 0.7506 (mt) REVERT: C 305 MET cc_start: 0.7894 (mmm) cc_final: 0.7659 (mmp) REVERT: C 355 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7803 (ttt-90) REVERT: C 430 MET cc_start: 0.8178 (mtt) cc_final: 0.7588 (mtt) REVERT: C 592 ASP cc_start: 0.7476 (m-30) cc_final: 0.7172 (m-30) REVERT: B 222 LEU cc_start: 0.7931 (tp) cc_final: 0.7565 (mt) REVERT: B 267 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7683 (tt0) outliers start: 20 outliers final: 12 residues processed: 174 average time/residue: 1.9723 time to fit residues: 384.8618 Evaluate side-chains 161 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 147 time to evaluate : 1.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain B residue 267 GLN Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 550 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 87 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 114 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 106 optimal weight: 0.3980 chunk 0 optimal weight: 40.0000 chunk 78 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 12744 Z= 0.302 Angle : 0.529 6.522 17313 Z= 0.281 Chirality : 0.038 0.125 1989 Planarity : 0.004 0.049 2097 Dihedral : 10.678 127.574 1830 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.22 % Allowed : 11.16 % Favored : 86.62 % 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: 3.06 (0.21), residues: 1593 helix: 2.53 (0.14), residues: 1305 sheet: None (None), residues: 0 loop : -0.41 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 316 HIS 0.003 0.001 HIS C 288 PHE 0.015 0.001 PHE A 279 TYR 0.009 0.002 TYR C 231 ARG 0.002 0.000 ARG B 133 *********************** 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 187 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 159 time to evaluate : 1.881 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 LYS cc_start: 0.7325 (mptt) cc_final: 0.6701 (tttt) REVERT: C 201 LYS cc_start: 0.7377 (mptt) cc_final: 0.6743 (tmmt) REVERT: C 222 LEU cc_start: 0.8058 (tp) cc_final: 0.7489 (mt) REVERT: C 355 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7888 (ttt-90) REVERT: C 430 MET cc_start: 0.8258 (mtt) cc_final: 0.7637 (mtt) REVERT: C 489 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.6406 (mp0) REVERT: C 592 ASP cc_start: 0.7440 (m-30) cc_final: 0.7218 (m-30) REVERT: B 222 LEU cc_start: 0.7942 (tp) cc_final: 0.7518 (mt) REVERT: B 267 GLN cc_start: 0.8065 (OUTLIER) cc_final: 0.7661 (tt0) REVERT: B 313 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8045 (mt) outliers start: 28 outliers final: 17 residues processed: 180 average time/residue: 1.8944 time to fit residues: 383.2508 Evaluate side-chains 175 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 154 time to evaluate : 1.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 489 GLU Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 267 GLN Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 550 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 138 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 chunk 148 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 204 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12744 Z= 0.235 Angle : 0.487 5.920 17313 Z= 0.258 Chirality : 0.037 0.124 1989 Planarity : 0.004 0.045 2097 Dihedral : 10.435 127.421 1830 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.22 % Allowed : 11.56 % Favored : 86.22 % 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: 3.26 (0.21), residues: 1593 helix: 2.68 (0.14), residues: 1305 sheet: None (None), residues: 0 loop : -0.41 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 316 HIS 0.003 0.001 HIS C 288 PHE 0.013 0.001 PHE A 279 TYR 0.008 0.001 TYR C 231 ARG 0.001 0.000 ARG A 355 *********************** 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 186 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 158 time to evaluate : 1.918 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 LYS cc_start: 0.7337 (mptt) cc_final: 0.6707 (tttt) REVERT: C 201 LYS cc_start: 0.7307 (mptt) cc_final: 0.6661 (tmmt) REVERT: C 222 LEU cc_start: 0.8064 (tp) cc_final: 0.7486 (mt) REVERT: C 355 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7811 (ttt-90) REVERT: C 370 MET cc_start: 0.8706 (mtm) cc_final: 0.8351 (mtp) REVERT: C 430 MET cc_start: 0.8265 (mtt) cc_final: 0.7662 (mtt) REVERT: C 489 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.6317 (mp0) REVERT: C 592 ASP cc_start: 0.7511 (m-30) cc_final: 0.7182 (m-30) REVERT: B 267 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.7652 (tt0) outliers start: 28 outliers final: 16 residues processed: 180 average time/residue: 1.8895 time to fit residues: 383.4197 Evaluate side-chains 171 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 152 time to evaluate : 1.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 489 GLU Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 267 GLN Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 550 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 17 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 204 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12744 Z= 0.165 Angle : 0.452 5.499 17313 Z= 0.237 Chirality : 0.035 0.120 1989 Planarity : 0.003 0.041 2097 Dihedral : 10.028 123.565 1830 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.98 % Allowed : 11.72 % Favored : 86.30 % 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: 3.59 (0.21), residues: 1593 helix: 2.91 (0.14), residues: 1305 sheet: None (None), residues: 0 loop : -0.32 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 316 HIS 0.002 0.001 HIS C 288 PHE 0.012 0.001 PHE C 279 TYR 0.008 0.001 TYR C 231 ARG 0.001 0.000 ARG A 355 *********************** 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 178 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 153 time to evaluate : 1.999 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 LYS cc_start: 0.7331 (mptt) cc_final: 0.6704 (tttt) REVERT: A 242 GLN cc_start: 0.8528 (mt0) cc_final: 0.8284 (mt0) REVERT: A 537 SER cc_start: 0.8143 (OUTLIER) cc_final: 0.7745 (m) REVERT: C 201 LYS cc_start: 0.7311 (mptt) cc_final: 0.6699 (tmmt) REVERT: C 222 LEU cc_start: 0.8017 (tp) cc_final: 0.7423 (mt) REVERT: C 242 GLN cc_start: 0.8636 (mt0) cc_final: 0.8314 (mt0) REVERT: C 355 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7764 (ttt-90) REVERT: C 430 MET cc_start: 0.8255 (mtt) cc_final: 0.7683 (mtt) REVERT: C 489 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.6264 (mp0) REVERT: C 592 ASP cc_start: 0.7386 (m-30) cc_final: 0.7144 (m-30) REVERT: B 222 LEU cc_start: 0.8118 (tt) cc_final: 0.7759 (mt) REVERT: B 305 MET cc_start: 0.7828 (mmp) cc_final: 0.7444 (mmt) outliers start: 25 outliers final: 14 residues processed: 173 average time/residue: 1.8972 time to fit residues: 370.3538 Evaluate side-chains 167 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 150 time to evaluate : 1.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 489 GLU Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 550 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 91 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 120 optimal weight: 0.6980 chunk 139 optimal weight: 0.8980 chunk 146 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12744 Z= 0.165 Angle : 0.450 5.568 17313 Z= 0.236 Chirality : 0.035 0.119 1989 Planarity : 0.003 0.041 2097 Dihedral : 9.854 118.794 1830 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.90 % Allowed : 12.11 % Favored : 85.99 % 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: 3.67 (0.21), residues: 1593 helix: 2.96 (0.14), residues: 1305 sheet: None (None), residues: 0 loop : -0.29 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 316 HIS 0.002 0.001 HIS C 288 PHE 0.015 0.001 PHE C 146 TYR 0.007 0.001 TYR C 231 ARG 0.001 0.000 ARG A 355 *********************** 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 177 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 153 time to evaluate : 1.766 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.6702 (mmt) cc_final: 0.6375 (mmm) REVERT: A 201 LYS cc_start: 0.7336 (mptt) cc_final: 0.6721 (tttt) REVERT: A 242 GLN cc_start: 0.8538 (mt0) cc_final: 0.8296 (mt0) REVERT: A 537 SER cc_start: 0.8136 (OUTLIER) cc_final: 0.7750 (m) REVERT: C 201 LYS cc_start: 0.7317 (mptt) cc_final: 0.6710 (tttt) REVERT: C 222 LEU cc_start: 0.8027 (tp) cc_final: 0.7387 (mt) REVERT: C 242 GLN cc_start: 0.8643 (mt0) cc_final: 0.8231 (mt0) REVERT: C 355 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7778 (ttt-90) REVERT: C 430 MET cc_start: 0.8257 (mtt) cc_final: 0.7677 (mtt) REVERT: C 489 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.6311 (mp0) REVERT: C 585 MET cc_start: 0.7093 (OUTLIER) cc_final: 0.6516 (mtt) REVERT: B 222 LEU cc_start: 0.8112 (tt) cc_final: 0.7717 (mt) REVERT: B 305 MET cc_start: 0.7832 (mmp) cc_final: 0.7437 (mmt) outliers start: 24 outliers final: 15 residues processed: 169 average time/residue: 1.8853 time to fit residues: 358.0025 Evaluate side-chains 167 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 148 time to evaluate : 2.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 489 GLU Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 550 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 133 optimal weight: 3.9990 chunk 142 optimal weight: 0.0980 chunk 146 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 135 optimal weight: 0.5980 chunk 93 optimal weight: 0.9990 chunk 151 optimal weight: 0.8980 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 12744 Z= 0.132 Angle : 0.428 5.384 17313 Z= 0.224 Chirality : 0.035 0.119 1989 Planarity : 0.003 0.038 2097 Dihedral : 9.344 106.066 1830 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.43 % Allowed : 12.83 % Favored : 85.75 % 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: 3.92 (0.21), residues: 1593 helix: 3.20 (0.14), residues: 1290 sheet: None (None), residues: 0 loop : -0.35 (0.35), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 316 HIS 0.001 0.000 HIS B 288 PHE 0.009 0.001 PHE C 243 TYR 0.006 0.001 TYR C 231 ARG 0.001 0.000 ARG A 355 *********************** 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 164 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 146 time to evaluate : 1.772 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 LYS cc_start: 0.7324 (mptt) cc_final: 0.6765 (tttt) REVERT: A 242 GLN cc_start: 0.8451 (mt0) cc_final: 0.8243 (mt0) REVERT: A 537 SER cc_start: 0.8095 (OUTLIER) cc_final: 0.7753 (m) REVERT: C 201 LYS cc_start: 0.7311 (mptt) cc_final: 0.6711 (tttt) REVERT: C 222 LEU cc_start: 0.8098 (tp) cc_final: 0.7464 (mt) REVERT: C 242 GLN cc_start: 0.8561 (mt0) cc_final: 0.8284 (mt0) REVERT: C 342 ASN cc_start: 0.8957 (OUTLIER) cc_final: 0.8702 (m-40) REVERT: C 355 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7725 (ttt-90) REVERT: C 430 MET cc_start: 0.8246 (mtt) cc_final: 0.7685 (mtt) REVERT: C 489 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.6333 (mp0) REVERT: B 201 LYS cc_start: 0.7302 (mptt) cc_final: 0.6707 (tttt) REVERT: B 222 LEU cc_start: 0.8091 (tt) cc_final: 0.7689 (mt) REVERT: B 482 ASP cc_start: 0.7742 (m-30) cc_final: 0.7521 (m-30) outliers start: 18 outliers final: 9 residues processed: 159 average time/residue: 1.8800 time to fit residues: 336.5822 Evaluate side-chains 157 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 144 time to evaluate : 1.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 342 ASN Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 489 GLU Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 550 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: 2.9990 chunk 104 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12744 Z= 0.303 Angle : 0.528 7.037 17313 Z= 0.279 Chirality : 0.038 0.126 1989 Planarity : 0.004 0.045 2097 Dihedral : 10.085 107.117 1830 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.43 % Allowed : 13.22 % Favored : 85.35 % 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: 3.36 (0.21), residues: 1593 helix: 2.74 (0.14), residues: 1305 sheet: None (None), residues: 0 loop : -0.34 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 507 HIS 0.004 0.001 HIS B 288 PHE 0.016 0.001 PHE A 279 TYR 0.008 0.001 TYR B 553 ARG 0.003 0.000 ARG C 436 ********************** REFINEMENT MACRO_CYCLE 10 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 175 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 157 time to evaluate : 1.891 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.6763 (mmt) cc_final: 0.6383 (mmm) REVERT: A 201 LYS cc_start: 0.7421 (mptt) cc_final: 0.6784 (tttt) REVERT: C 201 LYS cc_start: 0.7374 (mptt) cc_final: 0.6706 (tttt) REVERT: C 222 LEU cc_start: 0.8087 (tp) cc_final: 0.7501 (mt) REVERT: C 355 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.7817 (ttt-90) REVERT: C 430 MET cc_start: 0.8321 (mtt) cc_final: 0.7717 (mtt) REVERT: C 489 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.6327 (mp0) REVERT: C 592 ASP cc_start: 0.7491 (m-30) cc_final: 0.7201 (m-30) REVERT: B 222 LEU cc_start: 0.8141 (tt) cc_final: 0.7762 (mt) outliers start: 18 outliers final: 12 residues processed: 171 average time/residue: 2.0398 time to fit residues: 393.9469 Evaluate side-chains 168 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 154 time to evaluate : 1.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 489 GLU Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 342 ASN Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 550 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 38 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 15 optimal weight: 0.0980 chunk 23 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 204 GLN ** B 242 GLN ** 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 = 0.3590 r_free = 0.3590 target = 0.142475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.098280 restraints weight = 36129.394| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 1.34 r_work: 0.2918 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12744 Z= 0.204 Angle : 0.473 6.194 17313 Z= 0.248 Chirality : 0.036 0.121 1989 Planarity : 0.003 0.043 2097 Dihedral : 9.668 105.178 1830 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.35 % Allowed : 13.54 % Favored : 85.11 % 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: 3.52 (0.21), residues: 1593 helix: 2.86 (0.14), residues: 1305 sheet: None (None), residues: 0 loop : -0.32 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 316 HIS 0.003 0.001 HIS C 288 PHE 0.013 0.001 PHE C 146 TYR 0.007 0.001 TYR C 231 ARG 0.001 0.000 ARG C 436 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7430.81 seconds wall clock time: 129 minutes 23.69 seconds (7763.69 seconds total)