Starting phenix.real_space_refine on Wed Jul 24 02:02:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz4_41733/07_2024/8tz4_41733_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz4_41733/07_2024/8tz4_41733.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz4_41733/07_2024/8tz4_41733.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz4_41733/07_2024/8tz4_41733.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz4_41733/07_2024/8tz4_41733_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz4_41733/07_2024/8tz4_41733_trim.cif" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.080 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 87 5.16 5 C 8130 2.51 5 N 1931 2.21 5 O 2095 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 TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 344": "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-5388/modules/chem_data/mon_lib" Total number of atoms: 24408 Number of models: 1 Model: "" Number of chains: 4 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: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'U08': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.79, per 1000 atoms: 0.48 Number of scatterers: 24408 At special positions: 0 Unit cell: (126.36, 128.52, 77.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 87 16.00 O 2095 8.00 N 1931 7.00 C 8130 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: 20.52 Conformation dependent library (CDL) restraints added in 3.0 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: 88 helices and 3 sheets defined 89.8% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.28 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 203 Proline residue: A 167 - end of helix removed outlier: 4.576A pdb=" N PHE A 177 " --> pdb=" O ASP A 173 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N TRP A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N TRP A 181 " --> pdb=" O PHE A 177 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL A 182 " --> pdb=" O TRP A 178 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ALA A 200 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N LYS A 201 " --> pdb=" O PHE A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 223 removed outlier: 3.923A pdb=" N LEU A 207 " --> pdb=" O GLY A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 230 removed outlier: 4.042A pdb=" N VAL A 230 " --> pdb=" O PRO A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 251 removed outlier: 4.536A pdb=" N VAL A 235 " --> pdb=" O TYR A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 271 removed outlier: 3.656A pdb=" N GLY A 271 " --> pdb=" O GLN A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 282 removed outlier: 4.341A pdb=" N GLY A 276 " --> pdb=" O TYR A 272 " (cutoff:3.500A) removed outlier: 3.525A 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 312 removed outlier: 4.338A pdb=" N LEU A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) Proline residue: A 296 - end of helix Processing helix chain 'A' and resid 312 through 330 Processing helix chain 'A' and resid 332 through 343 removed outlier: 3.659A pdb=" N ILE A 343 " --> pdb=" O ALA A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 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 382 through 389 removed outlier: 3.537A pdb=" N PHE A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY A 389 " --> pdb=" O TYR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 414 removed outlier: 4.168A 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: 4.099A pdb=" N ILE A 450 " --> pdb=" O ALA A 446 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N SER A 451 " --> pdb=" O SER A 447 " (cutoff:3.500A) removed outlier: 4.046A 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: 3.643A pdb=" N TYR A 494 " --> pdb=" O VAL A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 503 Processing helix chain 'A' and resid 506 through 523 removed outlier: 3.993A pdb=" N PHE A 511 " --> pdb=" O TRP A 507 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N MET A 512 " --> pdb=" O GLN A 508 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS A 515 " --> pdb=" O PHE A 511 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A 516 " --> pdb=" O MET A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 542 removed outlier: 3.700A pdb=" N ALA A 528 " --> pdb=" O ASN A 524 " (cutoff:3.500A) removed outlier: 3.670A 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 574 through 586 Processing helix chain 'A' and resid 589 through 596 removed outlier: 3.650A pdb=" N GLY A 596 " --> pdb=" O ASP A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 619 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 203 Proline residue: C 167 - end of helix removed outlier: 4.564A pdb=" N PHE C 177 " --> pdb=" O ASP C 173 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N TRP C 178 " --> pdb=" O SER C 174 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N TRP C 181 " --> pdb=" O PHE C 177 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL C 182 " --> pdb=" O TRP C 178 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALA C 200 " --> pdb=" O VAL C 196 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N LYS C 201 " --> pdb=" O PHE C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 223 removed outlier: 3.916A pdb=" N LEU C 207 " --> pdb=" O GLY C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 230 removed outlier: 4.043A pdb=" N VAL C 230 " --> pdb=" O PRO C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 251 removed outlier: 4.555A 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: 4.302A pdb=" N GLY C 276 " --> pdb=" O TYR C 272 " (cutoff:3.500A) removed outlier: 3.546A 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 312 removed outlier: 4.345A pdb=" N LEU C 295 " --> pdb=" O ALA C 291 " (cutoff:3.500A) Proline residue: C 296 - end of helix Processing helix chain 'C' and resid 312 through 330 Processing helix chain 'C' and resid 332 through 343 removed outlier: 3.644A pdb=" N ILE C 343 " --> pdb=" O ALA C 339 " (cutoff:3.500A) 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 376 removed outlier: 3.559A pdb=" N THR C 376 " --> pdb=" O ALA C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 380 No H-bonds generated for 'chain 'C' and resid 378 through 380' Processing helix chain 'C' and resid 381 through 389 Processing helix chain 'C' and resid 391 through 414 removed outlier: 4.235A 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: 4.114A pdb=" N ILE C 450 " --> pdb=" O ALA C 446 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N SER C 451 " --> pdb=" O SER C 447 " (cutoff:3.500A) removed outlier: 4.050A 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: 3.634A pdb=" N TYR C 494 " --> pdb=" O VAL C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 503 Processing helix chain 'C' and resid 506 through 523 removed outlier: 3.982A pdb=" N PHE C 511 " --> pdb=" O TRP C 507 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N MET C 512 " --> pdb=" O GLN C 508 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS C 515 " --> pdb=" O PHE C 511 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU C 516 " --> pdb=" O MET C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 542 removed outlier: 3.806A pdb=" N ALA C 528 " --> pdb=" O ASN C 524 " (cutoff:3.500A) removed outlier: 3.693A 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 596 removed outlier: 3.546A pdb=" N ALA C 595 " --> pdb=" O ARG C 591 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY C 596 " --> pdb=" O ASP C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 619 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 203 Proline residue: B 167 - end of helix removed outlier: 4.561A pdb=" N PHE B 177 " --> pdb=" O ASP B 173 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N TRP B 178 " --> pdb=" O SER B 174 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N TRP B 181 " --> pdb=" O PHE B 177 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL B 182 " --> pdb=" O TRP B 178 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ALA B 200 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N LYS B 201 " --> pdb=" O PHE B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 223 removed outlier: 3.936A pdb=" N LEU B 207 " --> pdb=" O GLY B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 230 removed outlier: 4.047A pdb=" N VAL B 230 " --> pdb=" O PRO B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 251 removed outlier: 4.560A 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: 4.377A pdb=" N GLY B 276 " --> pdb=" O TYR B 272 " (cutoff:3.500A) removed outlier: 3.501A 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 312 removed outlier: 4.378A pdb=" N LEU B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) Proline residue: B 296 - end of helix Processing helix chain 'B' and resid 312 through 330 Processing helix chain 'B' and resid 332 through 343 removed outlier: 3.625A pdb=" N ILE B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) 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 376 removed outlier: 3.577A pdb=" N THR B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 380 No H-bonds generated for 'chain 'B' and resid 378 through 380' Processing helix chain 'B' and resid 381 through 389 Processing helix chain 'B' and resid 391 through 414 removed outlier: 4.184A 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: 3.516A pdb=" N SER B 449 " --> pdb=" O GLY B 445 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE B 450 " --> pdb=" O ALA B 446 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N SER B 451 " --> pdb=" O SER B 447 " (cutoff:3.500A) removed outlier: 4.007A 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: 3.624A 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: 4.010A pdb=" N PHE B 511 " --> pdb=" O TRP B 507 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N MET B 512 " --> pdb=" O GLN B 508 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B 516 " --> pdb=" O MET B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 542 removed outlier: 3.829A pdb=" N ALA B 528 " --> pdb=" O ASN B 524 " (cutoff:3.500A) removed outlier: 3.712A 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 596 removed outlier: 3.506A pdb=" N ALA B 595 " --> pdb=" O ARG B 591 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY B 596 " --> pdb=" O ASP B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 619 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. 2877 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: 10.23 Time building geometry restraints manager: 21.16 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: 19 1.22 - 1.42: 5353 1.42 - 1.61: 7070 1.61 - 1.81: 157 Bond restraints: 24746 Sorted by residual: bond pdb=" C3 U08 A 801 " pdb=" C4 U08 A 801 " ideal model delta sigma weight residual 1.520 1.252 0.268 2.00e-02 2.50e+03 1.79e+02 bond pdb=" C1 U08 A 801 " pdb=" C2 U08 A 801 " ideal model delta sigma weight residual 1.552 1.297 0.255 2.00e-02 2.50e+03 1.62e+02 bond pdb=" C11 U08 A 801 " pdb=" N5 U08 A 801 " ideal model delta sigma weight residual 1.328 1.509 -0.181 2.00e-02 2.50e+03 8.21e+01 bond pdb=" C4 U08 A 801 " pdb=" O1 U08 A 801 " ideal model delta sigma weight residual 1.435 1.607 -0.172 2.00e-02 2.50e+03 7.41e+01 bond pdb=" C2 U08 A 801 " pdb=" C3 U08 A 801 " ideal model delta sigma weight residual 1.527 1.699 -0.172 2.00e-02 2.50e+03 7.35e+01 ... (remaining 24741 not shown) Histogram of bond angle deviations from ideal: 100.31 - 116.23: 31286 116.23 - 132.15: 13321 132.15 - 148.07: 46 148.07 - 163.98: 0 163.98 - 179.90: 1 Bond angle restraints: 44654 Sorted by residual: angle pdb=" N2 U08 A 801 " pdb=" C12 U08 A 801 " pdb=" N4 U08 A 801 " ideal model delta sigma weight residual 128.80 120.15 8.65 3.00e+00 1.11e-01 8.30e+00 angle pdb=" CA GLY B 568 " pdb=" C GLY B 568 " pdb=" N PHE B 569 " ideal model delta sigma weight residual 114.58 116.66 -2.08 8.60e-01 1.35e+00 5.83e+00 angle pdb=" CA GLY C 568 " pdb=" C GLY C 568 " pdb=" N PHE C 569 " ideal model delta sigma weight residual 114.58 116.64 -2.06 8.60e-01 1.35e+00 5.75e+00 angle pdb=" N GLY C 568 " pdb=" CA GLY C 568 " pdb=" C GLY C 568 " ideal model delta sigma weight residual 110.38 113.56 -3.18 1.48e+00 4.57e-01 4.63e+00 angle pdb=" C12 U08 A 801 " pdb=" N2 U08 A 801 " pdb=" N1 U08 A 801 " ideal model delta sigma weight residual 113.47 119.81 -6.34 3.00e+00 1.11e-01 4.46e+00 ... (remaining 44649 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.24: 11359 28.24 - 56.48: 341 56.48 - 84.72: 47 84.72 - 112.96: 5 112.96 - 141.20: 2 Dihedral angle restraints: 11754 sinusoidal: 6024 harmonic: 5730 Sorted by residual: dihedral pdb=" O1 U08 A 801 " pdb=" C4 U08 A 801 " pdb=" C6 U08 A 801 " pdb=" O4 U08 A 801 " ideal model delta sinusoidal sigma weight residual 172.60 -46.20 -141.20 1 3.00e+01 1.11e-03 1.90e+01 dihedral pdb=" C3 U08 A 801 " pdb=" C4 U08 A 801 " pdb=" C6 U08 A 801 " pdb=" O4 U08 A 801 " ideal model delta sinusoidal sigma weight residual -69.46 69.06 -138.52 1 3.00e+01 1.11e-03 1.87e+01 dihedral pdb=" N3 U08 A 801 " pdb=" C1 U08 A 801 " pdb=" C8 U08 A 801 " pdb=" O1 U08 A 801 " ideal model delta sinusoidal sigma weight residual -124.25 -23.10 -101.15 1 3.00e+01 1.11e-03 1.27e+01 ... (remaining 11751 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1656 0.047 - 0.094: 296 0.094 - 0.141: 34 0.141 - 0.188: 0 0.188 - 0.235: 1 Chirality restraints: 1987 Sorted by residual: chirality pdb=" C3 U08 A 801 " pdb=" C2 U08 A 801 " pdb=" C4 U08 A 801 " pdb=" O3 U08 A 801 " both_signs ideal model delta sigma weight residual False -2.67 -2.44 -0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA PRO A 234 " pdb=" N PRO A 234 " pdb=" C PRO A 234 " pdb=" CB PRO A 234 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.45e-01 chirality pdb=" CA PRO B 234 " pdb=" N PRO B 234 " pdb=" C PRO B 234 " pdb=" CB PRO B 234 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.32e-01 ... (remaining 1984 not shown) Planarity restraints: 3622 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 195 " 0.011 2.00e-02 2.50e+03 2.18e-02 4.77e+00 pdb=" C LEU B 195 " -0.038 2.00e-02 2.50e+03 pdb=" O LEU B 195 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL B 196 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 195 " 0.011 2.00e-02 2.50e+03 2.16e-02 4.68e+00 pdb=" C LEU C 195 " -0.037 2.00e-02 2.50e+03 pdb=" O LEU C 195 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL C 196 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 195 " -0.011 2.00e-02 2.50e+03 2.14e-02 4.56e+00 pdb=" C LEU A 195 " 0.037 2.00e-02 2.50e+03 pdb=" O LEU A 195 " -0.014 2.00e-02 2.50e+03 pdb=" N VAL A 196 " -0.012 2.00e-02 2.50e+03 ... (remaining 3619 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 907 2.19 - 2.80: 48106 2.80 - 3.40: 69112 3.40 - 4.00: 87284 4.00 - 4.60: 137866 Nonbonded interactions: 343275 Sorted by model distance: nonbonded pdb=" OE1 GLU C 525 " pdb=" H GLU C 525 " model vdw 1.592 1.850 nonbonded pdb=" OE1 GLU B 525 " pdb=" H GLU B 525 " model vdw 1.616 1.850 nonbonded pdb=" O VAL B 490 " pdb=" HG SER B 493 " model vdw 1.680 1.850 nonbonded pdb=" O SER A 451 " pdb="HD22 ASN A 455 " model vdw 1.682 1.850 nonbonded pdb=" O VAL C 490 " pdb=" HG SER C 493 " model vdw 1.682 1.850 ... (remaining 343270 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 90 through 622) selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.770 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: 0.350 Extract box with map and model: 0.860 Check model and map are aligned: 0.190 Set scattering table: 0.210 Process input model: 82.560 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 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 : 0.005 0.268 12581 Z= 0.289 Angle : 0.434 8.645 17132 Z= 0.235 Chirality : 0.035 0.235 1987 Planarity : 0.003 0.025 2080 Dihedral : 12.312 141.200 4260 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % 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: 3.71 (0.21), residues: 1593 helix: 3.00 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -0.42 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 316 HIS 0.001 0.000 HIS A 394 PHE 0.009 0.001 PHE B 413 TYR 0.010 0.001 TYR A 519 ARG 0.001 0.000 ARG C 539 *********************** 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 316 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 316 time to evaluate : 2.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 PHE cc_start: 0.8078 (t80) cc_final: 0.7680 (t80) REVERT: A 509 ASP cc_start: 0.8800 (m-30) cc_final: 0.8479 (m-30) REVERT: C 145 ILE cc_start: 0.9110 (mt) cc_final: 0.8904 (mm) REVERT: C 305 MET cc_start: 0.8074 (mmm) cc_final: 0.7813 (mmt) REVERT: C 489 GLU cc_start: 0.8207 (mp0) cc_final: 0.7925 (mp0) REVERT: C 592 ASP cc_start: 0.7869 (m-30) cc_final: 0.7650 (m-30) REVERT: B 124 ILE cc_start: 0.9309 (tt) cc_final: 0.8820 (tp) REVERT: B 131 PHE cc_start: 0.7450 (t80) cc_final: 0.7166 (t80) REVERT: B 138 PHE cc_start: 0.8410 (t80) cc_final: 0.8164 (t80) REVERT: B 248 LEU cc_start: 0.8207 (tp) cc_final: 0.7926 (mm) REVERT: B 305 MET cc_start: 0.8423 (mmm) cc_final: 0.8047 (mmt) REVERT: B 497 MET cc_start: 0.8191 (tmt) cc_final: 0.7963 (tmm) REVERT: B 575 LEU cc_start: 0.8554 (tp) cc_final: 0.8339 (mt) outliers start: 0 outliers final: 0 residues processed: 316 average time/residue: 0.4599 time to fit residues: 220.5018 Evaluate side-chains 194 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 1.797 ------------------------------------------------------------------------------- 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: 3.9990 chunk 120 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 92 optimal weight: 0.3980 chunk 144 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 551 GLN C 479 ASN B 204 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 12581 Z= 0.165 Angle : 0.448 5.340 17132 Z= 0.238 Chirality : 0.035 0.156 1987 Planarity : 0.003 0.039 2080 Dihedral : 7.383 91.954 1710 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.11 % Allowed : 8.23 % Favored : 90.66 % 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: 3.95 (0.21), residues: 1593 helix: 3.12 (0.14), residues: 1311 sheet: None (None), residues: 0 loop : -0.08 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 316 HIS 0.001 0.000 HIS C 132 PHE 0.013 0.001 PHE A 164 TYR 0.008 0.001 TYR A 519 ARG 0.004 0.000 ARG C 355 *********************** 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 216 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 202 time to evaluate : 1.874 Fit side-chains revert: symmetry clash REVERT: A 131 PHE cc_start: 0.7925 (t80) cc_final: 0.7481 (t80) REVERT: A 509 ASP cc_start: 0.8824 (m-30) cc_final: 0.8523 (m-30) REVERT: B 131 PHE cc_start: 0.7136 (t80) cc_final: 0.6799 (t80) REVERT: B 248 LEU cc_start: 0.8226 (tp) cc_final: 0.7930 (mm) REVERT: B 305 MET cc_start: 0.8434 (mmm) cc_final: 0.8080 (mmt) REVERT: B 497 MET cc_start: 0.8152 (tmt) cc_final: 0.7736 (tmm) REVERT: B 575 LEU cc_start: 0.8644 (tp) cc_final: 0.8417 (mt) outliers start: 14 outliers final: 9 residues processed: 210 average time/residue: 0.4173 time to fit residues: 136.3597 Evaluate side-chains 193 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 184 time to evaluate : 1.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 617 MET Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 273 SER Chi-restraints excluded: chain B residue 328 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 39 optimal weight: 0.7980 chunk 144 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 12581 Z= 0.254 Angle : 0.471 5.481 17132 Z= 0.253 Chirality : 0.036 0.113 1987 Planarity : 0.003 0.036 2080 Dihedral : 6.474 91.010 1710 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.27 % Allowed : 9.74 % Favored : 88.99 % 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: 3.72 (0.21), residues: 1593 helix: 2.99 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -0.32 (0.36), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 150 HIS 0.002 0.001 HIS A 394 PHE 0.015 0.001 PHE A 259 TYR 0.014 0.001 TYR B 216 ARG 0.007 0.000 ARG C 355 *********************** 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 221 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 205 time to evaluate : 1.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 PHE cc_start: 0.7981 (t80) cc_final: 0.7650 (t80) REVERT: A 307 MET cc_start: 0.8661 (mtm) cc_final: 0.8385 (mtm) REVERT: B 131 PHE cc_start: 0.7149 (t80) cc_final: 0.6836 (t80) REVERT: B 248 LEU cc_start: 0.8186 (tp) cc_final: 0.7964 (mm) REVERT: B 305 MET cc_start: 0.8423 (mmm) cc_final: 0.7974 (mmt) REVERT: B 497 MET cc_start: 0.8310 (tmt) cc_final: 0.8109 (tmm) outliers start: 16 outliers final: 13 residues processed: 212 average time/residue: 0.4110 time to fit residues: 134.9759 Evaluate side-chains 202 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 189 time to evaluate : 1.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 617 MET Chi-restraints excluded: chain B residue 273 SER Chi-restraints excluded: chain B residue 328 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 142 optimal weight: 0.9990 chunk 108 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 145 optimal weight: 4.9990 chunk 153 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 12581 Z= 0.342 Angle : 0.503 5.300 17132 Z= 0.274 Chirality : 0.037 0.151 1987 Planarity : 0.003 0.038 2080 Dihedral : 6.661 93.742 1710 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.43 % Allowed : 9.74 % Favored : 88.84 % 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: 3.34 (0.21), residues: 1593 helix: 2.76 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -0.68 (0.34), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 150 HIS 0.002 0.001 HIS C 288 PHE 0.015 0.001 PHE A 259 TYR 0.010 0.001 TYR A 529 ARG 0.004 0.000 ARG C 355 *********************** 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 204 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 186 time to evaluate : 1.856 Fit side-chains revert: symmetry clash REVERT: A 131 PHE cc_start: 0.8053 (t80) cc_final: 0.7792 (t80) REVERT: A 307 MET cc_start: 0.8648 (mtm) cc_final: 0.8358 (mtm) REVERT: B 131 PHE cc_start: 0.7412 (t80) cc_final: 0.7074 (t80) REVERT: B 248 LEU cc_start: 0.8255 (tp) cc_final: 0.8012 (mm) REVERT: B 305 MET cc_start: 0.8454 (mmm) cc_final: 0.7961 (mmt) REVERT: B 497 MET cc_start: 0.8365 (tmt) cc_final: 0.7949 (tmm) outliers start: 18 outliers final: 14 residues processed: 194 average time/residue: 0.4421 time to fit residues: 135.1025 Evaluate side-chains 199 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 185 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 186 CYS Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain B residue 273 SER Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 585 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 87 optimal weight: 4.9990 chunk 2 optimal weight: 8.9990 chunk 114 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 131 optimal weight: 0.5980 chunk 106 optimal weight: 0.0010 chunk 0 optimal weight: 20.0000 chunk 78 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 12581 Z= 0.342 Angle : 0.503 5.300 17132 Z= 0.274 Chirality : 0.037 0.151 1987 Planarity : 0.003 0.038 2080 Dihedral : 6.661 93.742 1710 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.11 % Allowed : 10.69 % Favored : 88.20 % 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: 3.34 (0.21), residues: 1593 helix: 2.76 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -0.68 (0.34), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 150 HIS 0.002 0.001 HIS C 288 PHE 0.015 0.001 PHE A 259 TYR 0.010 0.001 TYR A 529 ARG 0.004 0.000 ARG C 355 *********************** 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 199 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 185 time to evaluate : 1.794 Fit side-chains revert: symmetry clash REVERT: A 131 PHE cc_start: 0.8048 (t80) cc_final: 0.7792 (t80) REVERT: A 307 MET cc_start: 0.8650 (mtm) cc_final: 0.8358 (mtm) REVERT: B 131 PHE cc_start: 0.7406 (t80) cc_final: 0.7074 (t80) REVERT: B 248 LEU cc_start: 0.8252 (tp) cc_final: 0.8012 (mm) REVERT: B 305 MET cc_start: 0.8450 (mmm) cc_final: 0.7960 (mmt) REVERT: B 497 MET cc_start: 0.8367 (tmt) cc_final: 0.7948 (tmm) outliers start: 14 outliers final: 14 residues processed: 191 average time/residue: 0.4430 time to fit residues: 133.0862 Evaluate side-chains 199 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 185 time to evaluate : 1.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 186 CYS Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain B residue 273 SER Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 585 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 138 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 153 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 148 optimal weight: 0.7980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12581 Z= 0.266 Angle : 0.470 4.887 17132 Z= 0.254 Chirality : 0.036 0.132 1987 Planarity : 0.003 0.039 2080 Dihedral : 6.523 92.775 1710 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.50 % Allowed : 10.45 % Favored : 88.04 % 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: 3.41 (0.21), residues: 1593 helix: 2.81 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -0.66 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 150 HIS 0.002 0.001 HIS B 152 PHE 0.012 0.001 PHE A 259 TYR 0.009 0.001 TYR A 519 ARG 0.002 0.000 ARG C 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 209 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 190 time to evaluate : 1.847 Fit side-chains revert: symmetry clash REVERT: A 131 PHE cc_start: 0.8054 (t80) cc_final: 0.7744 (t80) REVERT: A 307 MET cc_start: 0.8689 (mtm) cc_final: 0.8422 (mtm) REVERT: C 497 MET cc_start: 0.8507 (tmm) cc_final: 0.7474 (tmm) REVERT: B 131 PHE cc_start: 0.7215 (t80) cc_final: 0.6879 (t80) REVERT: B 176 TRP cc_start: 0.7048 (t-100) cc_final: 0.6804 (t-100) REVERT: B 248 LEU cc_start: 0.8203 (tp) cc_final: 0.7950 (mm) REVERT: B 305 MET cc_start: 0.8441 (mmm) cc_final: 0.7969 (mmt) REVERT: B 497 MET cc_start: 0.8366 (tmt) cc_final: 0.7969 (tmm) outliers start: 19 outliers final: 18 residues processed: 198 average time/residue: 0.4197 time to fit residues: 130.1288 Evaluate side-chains 204 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 186 time to evaluate : 1.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 186 CYS Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 617 MET Chi-restraints excluded: chain B residue 273 SER Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 417 THR 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: 0.9990 chunk 112 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12581 Z= 0.225 Angle : 0.463 4.845 17132 Z= 0.250 Chirality : 0.035 0.116 1987 Planarity : 0.003 0.039 2080 Dihedral : 6.521 92.814 1710 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.43 % Allowed : 10.61 % Favored : 87.97 % 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: 3.42 (0.21), residues: 1593 helix: 2.82 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -0.68 (0.34), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 150 HIS 0.001 0.000 HIS B 152 PHE 0.012 0.001 PHE A 259 TYR 0.007 0.001 TYR A 519 ARG 0.001 0.000 ARG C 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 203 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 185 time to evaluate : 1.968 Fit side-chains revert: symmetry clash REVERT: A 131 PHE cc_start: 0.8055 (t80) cc_final: 0.7787 (t80) REVERT: A 307 MET cc_start: 0.8685 (mtm) cc_final: 0.8416 (mtm) REVERT: C 497 MET cc_start: 0.8516 (tmm) cc_final: 0.7511 (tmm) REVERT: B 131 PHE cc_start: 0.7208 (t80) cc_final: 0.6877 (t80) REVERT: B 176 TRP cc_start: 0.7044 (t-100) cc_final: 0.6807 (t-100) REVERT: B 248 LEU cc_start: 0.8201 (tp) cc_final: 0.7948 (mm) REVERT: B 305 MET cc_start: 0.8444 (mmm) cc_final: 0.7975 (mmt) REVERT: B 497 MET cc_start: 0.8358 (tmt) cc_final: 0.7976 (tmm) outliers start: 18 outliers final: 18 residues processed: 193 average time/residue: 0.4331 time to fit residues: 131.9492 Evaluate side-chains 207 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 189 time to evaluate : 1.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 186 CYS Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 617 MET Chi-restraints excluded: chain B residue 273 SER Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 417 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 91 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 139 optimal weight: 5.9990 chunk 146 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12581 Z= 0.224 Angle : 0.463 4.846 17132 Z= 0.250 Chirality : 0.035 0.116 1987 Planarity : 0.003 0.039 2080 Dihedral : 6.540 92.809 1710 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.43 % Allowed : 10.61 % Favored : 87.97 % 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: 3.42 (0.21), residues: 1593 helix: 2.82 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -0.68 (0.34), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 150 HIS 0.001 0.000 HIS A 226 PHE 0.012 0.001 PHE A 259 TYR 0.007 0.001 TYR A 519 ARG 0.001 0.000 ARG C 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 207 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 189 time to evaluate : 2.315 Fit side-chains revert: symmetry clash REVERT: A 131 PHE cc_start: 0.8054 (t80) cc_final: 0.7787 (t80) REVERT: A 307 MET cc_start: 0.8684 (mtm) cc_final: 0.8416 (mtm) REVERT: C 497 MET cc_start: 0.8516 (tmm) cc_final: 0.7511 (tmm) REVERT: B 131 PHE cc_start: 0.7208 (t80) cc_final: 0.6877 (t80) REVERT: B 176 TRP cc_start: 0.7044 (t-100) cc_final: 0.6808 (t-100) REVERT: B 248 LEU cc_start: 0.8201 (tp) cc_final: 0.7947 (mm) REVERT: B 305 MET cc_start: 0.8443 (mmm) cc_final: 0.7975 (mmt) REVERT: B 497 MET cc_start: 0.8359 (tmt) cc_final: 0.7976 (tmm) outliers start: 18 outliers final: 18 residues processed: 197 average time/residue: 0.4122 time to fit residues: 127.5796 Evaluate side-chains 207 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 189 time to evaluate : 1.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 186 CYS Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 617 MET Chi-restraints excluded: chain B residue 273 SER Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 417 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 133 optimal weight: 0.9990 chunk 142 optimal weight: 0.7980 chunk 146 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 62 optimal weight: 0.0020 chunk 112 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 129 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12581 Z= 0.194 Angle : 0.460 4.825 17132 Z= 0.247 Chirality : 0.035 0.114 1987 Planarity : 0.003 0.039 2080 Dihedral : 6.520 92.730 1710 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.43 % Allowed : 10.53 % Favored : 88.04 % 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: 3.43 (0.21), residues: 1593 helix: 2.83 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -0.67 (0.34), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 150 HIS 0.001 0.000 HIS B 288 PHE 0.012 0.001 PHE A 259 TYR 0.007 0.001 TYR A 519 ARG 0.001 0.000 ARG C 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 208 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 190 time to evaluate : 2.603 Fit side-chains revert: symmetry clash REVERT: A 131 PHE cc_start: 0.8052 (t80) cc_final: 0.7785 (t80) REVERT: A 307 MET cc_start: 0.8680 (mtm) cc_final: 0.8411 (mtm) REVERT: C 497 MET cc_start: 0.8511 (tmm) cc_final: 0.7506 (tmm) REVERT: B 131 PHE cc_start: 0.7206 (t80) cc_final: 0.6876 (t80) REVERT: B 176 TRP cc_start: 0.7043 (t-100) cc_final: 0.6808 (t-100) REVERT: B 248 LEU cc_start: 0.8196 (tp) cc_final: 0.7944 (mm) REVERT: B 305 MET cc_start: 0.8439 (mmm) cc_final: 0.7971 (mmt) REVERT: B 497 MET cc_start: 0.8352 (tmt) cc_final: 0.7972 (tmm) outliers start: 18 outliers final: 18 residues processed: 198 average time/residue: 0.4215 time to fit residues: 131.1381 Evaluate side-chains 207 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 189 time to evaluate : 1.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 186 CYS Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 617 MET Chi-restraints excluded: chain B residue 273 SER Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 417 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 92 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 chunk 145 optimal weight: 0.8980 chunk 126 optimal weight: 1.9990 chunk 13 optimal weight: 0.0980 chunk 97 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12581 Z= 0.194 Angle : 0.460 4.825 17132 Z= 0.247 Chirality : 0.035 0.114 1987 Planarity : 0.003 0.039 2080 Dihedral : 6.520 92.730 1710 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.43 % Allowed : 10.53 % Favored : 88.04 % 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: 3.43 (0.21), residues: 1593 helix: 2.83 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -0.67 (0.34), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 150 HIS 0.001 0.000 HIS B 288 PHE 0.012 0.001 PHE A 259 TYR 0.007 0.001 TYR A 519 ARG 0.001 0.000 ARG C 355 ********************** 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 207 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 189 time to evaluate : 1.780 Fit side-chains revert: symmetry clash REVERT: A 131 PHE cc_start: 0.8054 (t80) cc_final: 0.7785 (t80) REVERT: A 307 MET cc_start: 0.8680 (mtm) cc_final: 0.8411 (mtm) REVERT: C 497 MET cc_start: 0.8511 (tmm) cc_final: 0.7506 (tmm) REVERT: B 131 PHE cc_start: 0.7206 (t80) cc_final: 0.6876 (t80) REVERT: B 176 TRP cc_start: 0.7043 (t-100) cc_final: 0.6808 (t-100) REVERT: B 248 LEU cc_start: 0.8198 (tp) cc_final: 0.7944 (mm) REVERT: B 305 MET cc_start: 0.8439 (mmm) cc_final: 0.7971 (mmt) REVERT: B 497 MET cc_start: 0.8352 (tmt) cc_final: 0.7972 (tmm) outliers start: 18 outliers final: 18 residues processed: 197 average time/residue: 0.4374 time to fit residues: 135.4574 Evaluate side-chains 207 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 189 time to evaluate : 1.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 186 CYS Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 617 MET Chi-restraints excluded: chain B residue 273 SER Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 417 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 38 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 129 optimal weight: 0.4980 chunk 15 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 110 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.125600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.098000 restraints weight = 48089.215| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.59 r_work: 0.2817 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12581 Z= 0.194 Angle : 0.460 4.825 17132 Z= 0.247 Chirality : 0.035 0.114 1987 Planarity : 0.003 0.039 2080 Dihedral : 6.520 92.730 1710 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.43 % Allowed : 10.53 % Favored : 88.04 % 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: 3.43 (0.21), residues: 1593 helix: 2.83 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -0.67 (0.34), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 150 HIS 0.001 0.000 HIS B 288 PHE 0.012 0.001 PHE A 259 TYR 0.007 0.001 TYR A 519 ARG 0.001 0.000 ARG C 355 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4938.12 seconds wall clock time: 86 minutes 56.23 seconds (5216.23 seconds total)