Starting phenix.real_space_refine on Fri Apr 12 01:39:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz4_41733/04_2024/8tz4_41733_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz4_41733/04_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_41733/04_2024/8tz4_41733.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz4_41733/04_2024/8tz4_41733.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz4_41733/04_2024/8tz4_41733_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz4_41733/04_2024/8tz4_41733_trim_updated.pdb" } 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-5288/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: 12.46, per 1000 atoms: 0.51 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: 20.23 Conformation dependent library (CDL) restraints added in 2.8 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... running ksdssp... Secondary structure from input PDB file: 75 helices and 0 sheets defined 80.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.70 Creating SS restraints... Processing helix chain 'A' and resid 91 through 102 Processing helix chain 'A' and resid 104 through 129 Processing helix chain 'A' and resid 135 through 156 Processing helix chain 'A' and resid 158 through 202 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 204 through 222 Processing helix chain 'A' and resid 233 through 250 Processing helix chain 'A' and resid 253 through 281 removed outlier: 3.656A pdb=" N GLY A 271 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N TYR A 272 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N SER A 273 " --> pdb=" O PHE A 269 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ASP A 274 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ALA A 275 " --> pdb=" O GLY A 271 " (cutoff:3.500A) 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 285 through 287 No H-bonds generated for 'chain 'A' and resid 285 through 287' Processing helix chain 'A' and resid 289 through 311 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 313 through 329 Processing helix chain 'A' and resid 333 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 347 through 360 Proline residue: A 351 - end of helix removed outlier: 4.712A pdb=" N VAL A 354 " --> pdb=" O SER A 350 " (cutoff:3.500A) Proline residue: A 356 - end of helix Proline residue: A 359 - end of helix Processing helix chain 'A' and resid 363 through 374 Processing helix chain 'A' and resid 383 through 388 removed outlier: 3.537A pdb=" N PHE A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 413 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 424 through 428 Processing helix chain 'A' and resid 438 through 481 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) removed outlier: 4.112A pdb=" N MET A 480 " --> pdb=" O TRP A 476 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N PHE A 481 " --> pdb=" O LEU A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 495 removed outlier: 3.643A pdb=" N TYR A 494 " --> pdb=" O VAL A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 502 Processing helix chain 'A' and resid 507 through 522 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 525 through 541 Processing helix chain 'A' and resid 556 through 565 Processing helix chain 'A' and resid 575 through 585 Processing helix chain 'A' and resid 587 through 595 removed outlier: 4.883A pdb=" N ARG A 591 " --> pdb=" O SER A 588 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR A 594 " --> pdb=" O ARG A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 618 Processing helix chain 'C' and resid 91 through 102 Processing helix chain 'C' and resid 104 through 129 Processing helix chain 'C' and resid 135 through 156 Processing helix chain 'C' and resid 158 through 202 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 204 through 222 Processing helix chain 'C' and resid 233 through 250 Processing helix chain 'C' and resid 253 through 281 removed outlier: 3.707A pdb=" N GLY C 271 " --> pdb=" O GLN C 267 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N TYR C 272 " --> pdb=" O THR C 268 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N SER C 273 " --> pdb=" O PHE C 269 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ASP C 274 " --> pdb=" O LEU C 270 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ALA C 275 " --> pdb=" O GLY C 271 " (cutoff:3.500A) 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 285 through 287 No H-bonds generated for 'chain 'C' and resid 285 through 287' Processing helix chain 'C' and resid 289 through 311 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 313 through 329 Processing helix chain 'C' and resid 333 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 347 through 360 Proline residue: C 351 - end of helix removed outlier: 4.635A pdb=" N VAL C 354 " --> pdb=" O SER C 350 " (cutoff:3.500A) Proline residue: C 356 - end of helix Proline residue: C 359 - end of helix Processing helix chain 'C' and resid 363 through 375 Processing helix chain 'C' and resid 382 through 388 Processing helix chain 'C' and resid 392 through 413 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 424 through 428 Processing helix chain 'C' and resid 438 through 481 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) removed outlier: 4.155A pdb=" N MET C 480 " --> pdb=" O TRP C 476 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N PHE C 481 " --> pdb=" O LEU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 495 removed outlier: 3.634A pdb=" N TYR C 494 " --> pdb=" O VAL C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 502 Processing helix chain 'C' and resid 507 through 522 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 525 through 541 Processing helix chain 'C' and resid 556 through 565 Processing helix chain 'C' and resid 572 through 585 removed outlier: 3.604A pdb=" N LEU C 575 " --> pdb=" O PHE C 572 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLY C 576 " --> pdb=" O GLY C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 595 removed outlier: 4.833A pdb=" N ARG C 591 " --> pdb=" O SER C 588 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR C 594 " --> pdb=" O ARG C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 597 through 618 Processing helix chain 'B' and resid 91 through 102 Processing helix chain 'B' and resid 104 through 129 Processing helix chain 'B' and resid 135 through 156 Processing helix chain 'B' and resid 158 through 202 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 204 through 222 Processing helix chain 'B' and resid 233 through 250 Processing helix chain 'B' and resid 253 through 281 removed outlier: 3.695A pdb=" N GLY B 271 " --> pdb=" O GLN B 267 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N TYR B 272 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N SER B 273 " --> pdb=" O PHE B 269 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ASP B 274 " --> pdb=" O LEU B 270 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ALA B 275 " --> pdb=" O GLY B 271 " (cutoff:3.500A) 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 285 through 287 No H-bonds generated for 'chain 'B' and resid 285 through 287' Processing helix chain 'B' and resid 289 through 311 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 313 through 329 Processing helix chain 'B' and resid 333 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 347 through 360 Proline residue: B 351 - end of helix removed outlier: 4.634A pdb=" N VAL B 354 " --> pdb=" O SER B 350 " (cutoff:3.500A) Proline residue: B 356 - end of helix Proline residue: B 359 - end of helix Processing helix chain 'B' and resid 363 through 374 Processing helix chain 'B' and resid 379 through 388 removed outlier: 4.314A pdb=" N GLY B 383 " --> pdb=" O SER B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 413 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 424 through 428 Processing helix chain 'B' and resid 438 through 481 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) removed outlier: 4.112A pdb=" N MET B 480 " --> pdb=" O TRP B 476 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N PHE B 481 " --> pdb=" O LEU B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 495 removed outlier: 3.624A pdb=" N TYR B 494 " --> pdb=" O VAL B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 502 Processing helix chain 'B' and resid 507 through 522 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 525 through 541 Processing helix chain 'B' and resid 556 through 565 Processing helix chain 'B' and resid 572 through 585 removed outlier: 3.572A pdb=" N LEU B 575 " --> pdb=" O PHE B 572 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLY B 576 " --> pdb=" O GLY B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 595 removed outlier: 4.870A pdb=" N ARG B 591 " --> pdb=" O SER B 588 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR B 594 " --> pdb=" O ARG B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 618 858 hydrogen bonds defined for protein. 2466 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: 9.82 Time building geometry restraints manager: 20.95 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: 967 2.19 - 2.80: 48196 2.80 - 3.40: 69207 3.40 - 4.00: 87438 4.00 - 4.60: 138072 Nonbonded interactions: 343880 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 343875 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: 11.170 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: 0.000 Extract box with map and model: 10.520 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 82.200 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.450 ------------------------------------------------------------------------------- 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= 0.324 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 : 1.846 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: 0.4618 time to fit residues: 218.9857 Evaluate side-chains 194 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 1.788 ------------------------------------------------------------------------------- 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: 1.9990 chunk 66 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 144 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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: 0.8111 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12581 Z= 0.243 Angle : 0.462 5.810 17132 Z= 0.249 Chirality : 0.036 0.216 1987 Planarity : 0.004 0.034 2080 Dihedral : 6.940 92.318 1710 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.11 % Allowed : 8.63 % Favored : 90.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.56 (0.21), residues: 1593 helix: 2.94 (0.14), residues: 1287 sheet: None (None), residues: 0 loop : -0.39 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 316 HIS 0.002 0.001 HIS A 394 PHE 0.016 0.001 PHE A 164 TYR 0.010 0.001 TYR A 529 ARG 0.007 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 215 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 201 time to evaluate : 1.891 Fit side-chains revert: symmetry clash REVERT: A 131 PHE cc_start: 0.8149 (t80) cc_final: 0.7845 (t80) REVERT: A 307 MET cc_start: 0.8659 (mtm) cc_final: 0.8341 (mtm) REVERT: A 509 ASP cc_start: 0.8774 (m-30) cc_final: 0.8371 (m-30) REVERT: B 131 PHE cc_start: 0.7550 (t80) cc_final: 0.7155 (t80) REVERT: B 305 MET cc_start: 0.8443 (mmm) cc_final: 0.8091 (mmt) REVERT: B 426 ASN cc_start: 0.8315 (m-40) cc_final: 0.7507 (t0) REVERT: B 497 MET cc_start: 0.8273 (tmt) cc_final: 0.7922 (tmm) outliers start: 14 outliers final: 11 residues processed: 211 average time/residue: 0.4231 time to fit residues: 139.1299 Evaluate side-chains 200 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 189 time to evaluate : 1.910 ------------------------------------------------------------------------------- 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 340 SER 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 340 SER Chi-restraints excluded: chain C residue 617 MET Chi-restraints excluded: chain B residue 273 SER Chi-restraints excluded: chain B residue 340 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 98 optimal weight: 0.0670 chunk 39 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 49 optimal weight: 0.3980 chunk 116 optimal weight: 2.9990 overall best weight: 1.2924 ------------------------------------------------------------------------------- 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: 0.8113 moved from start: 0.2642 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= 0.189 Angle : 0.437 4.555 17132 Z= 0.231 Chirality : 0.035 0.117 1987 Planarity : 0.003 0.034 2080 Dihedral : 6.347 89.478 1710 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.27 % Allowed : 9.66 % Favored : 89.07 % 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: 3.61 (0.21), residues: 1593 helix: 3.03 (0.14), residues: 1281 sheet: None (None), residues: 0 loop : -0.53 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 316 HIS 0.001 0.000 HIS C 288 PHE 0.011 0.001 PHE A 259 TYR 0.012 0.001 TYR B 216 ARG 0.004 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 213 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 197 time to evaluate : 2.002 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 MET cc_start: 0.8693 (mtm) cc_final: 0.8451 (mtm) REVERT: A 509 ASP cc_start: 0.8846 (m-30) cc_final: 0.8579 (m-30) REVERT: B 131 PHE cc_start: 0.7489 (t80) cc_final: 0.7126 (t80) REVERT: B 154 MET cc_start: 0.8420 (mmp) cc_final: 0.8063 (mmt) REVERT: B 305 MET cc_start: 0.8447 (mmm) cc_final: 0.8018 (mmt) REVERT: B 426 ASN cc_start: 0.8343 (m-40) cc_final: 0.7585 (t0) REVERT: B 548 ASP cc_start: 0.7640 (t0) cc_final: 0.7434 (t0) outliers start: 16 outliers final: 14 residues processed: 204 average time/residue: 0.4438 time to fit residues: 141.6812 Evaluate side-chains 204 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 190 time to evaluate : 2.294 ------------------------------------------------------------------------------- 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 186 CYS Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 327 VAL 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 142 optimal weight: 0.8980 chunk 108 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 153 optimal weight: 0.5980 chunk 137 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 127 optimal weight: 1.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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: 0.8126 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12581 Z= 0.200 Angle : 0.432 4.469 17132 Z= 0.228 Chirality : 0.035 0.118 1987 Planarity : 0.003 0.036 2080 Dihedral : 6.200 89.042 1710 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.27 % Allowed : 10.13 % Favored : 88.60 % 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: 3.57 (0.21), residues: 1593 helix: 2.99 (0.14), residues: 1287 sheet: None (None), residues: 0 loop : -0.59 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 316 HIS 0.002 0.001 HIS B 152 PHE 0.013 0.001 PHE A 259 TYR 0.007 0.001 TYR A 519 ARG 0.002 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 209 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 193 time to evaluate : 2.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 172 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.7932 (mm) REVERT: A 307 MET cc_start: 0.8695 (mtm) cc_final: 0.8452 (mtm) REVERT: A 509 ASP cc_start: 0.8857 (m-30) cc_final: 0.8585 (m-30) REVERT: B 131 PHE cc_start: 0.7527 (t80) cc_final: 0.7132 (t80) REVERT: B 305 MET cc_start: 0.8471 (mmm) cc_final: 0.7975 (mmt) outliers start: 16 outliers final: 14 residues processed: 203 average time/residue: 0.4497 time to fit residues: 141.3430 Evaluate side-chains 204 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 189 time to evaluate : 2.046 ------------------------------------------------------------------------------- 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 350 SER 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 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 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: 10.0000 chunk 63 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 106 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 78 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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: 0.8126 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12581 Z= 0.200 Angle : 0.432 4.469 17132 Z= 0.228 Chirality : 0.035 0.118 1987 Planarity : 0.003 0.036 2080 Dihedral : 6.200 89.042 1710 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.19 % Allowed : 10.61 % 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: 3.57 (0.21), residues: 1593 helix: 2.99 (0.14), residues: 1287 sheet: None (None), residues: 0 loop : -0.59 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 316 HIS 0.002 0.001 HIS B 152 PHE 0.013 0.001 PHE A 259 TYR 0.007 0.001 TYR A 519 ARG 0.002 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 204 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 189 time to evaluate : 1.820 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 172 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.7933 (mm) REVERT: A 307 MET cc_start: 0.8695 (mtm) cc_final: 0.8452 (mtm) REVERT: A 509 ASP cc_start: 0.8854 (m-30) cc_final: 0.8585 (m-30) REVERT: B 131 PHE cc_start: 0.7520 (t80) cc_final: 0.7132 (t80) REVERT: B 305 MET cc_start: 0.8469 (mmm) cc_final: 0.7975 (mmt) outliers start: 15 outliers final: 14 residues processed: 198 average time/residue: 0.4459 time to fit residues: 136.7352 Evaluate side-chains 204 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 189 time to evaluate : 1.907 ------------------------------------------------------------------------------- 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 350 SER 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 138 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 148 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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: 0.8128 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 12581 Z= 0.216 Angle : 0.435 4.610 17132 Z= 0.231 Chirality : 0.035 0.119 1987 Planarity : 0.003 0.036 2080 Dihedral : 6.205 88.805 1710 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.27 % Allowed : 10.61 % Favored : 88.12 % 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: 3.55 (0.21), residues: 1593 helix: 2.98 (0.14), residues: 1287 sheet: None (None), residues: 0 loop : -0.61 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 316 HIS 0.001 0.000 HIS B 152 PHE 0.011 0.001 PHE A 259 TYR 0.007 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 206 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 190 time to evaluate : 1.854 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 172 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.7934 (mm) REVERT: A 307 MET cc_start: 0.8694 (mtm) cc_final: 0.8451 (mtm) REVERT: A 509 ASP cc_start: 0.8856 (m-30) cc_final: 0.8586 (m-30) REVERT: B 131 PHE cc_start: 0.7520 (t80) cc_final: 0.7130 (t80) REVERT: B 305 MET cc_start: 0.8472 (mmm) cc_final: 0.7980 (mmt) outliers start: 16 outliers final: 14 residues processed: 200 average time/residue: 0.4446 time to fit residues: 137.3267 Evaluate side-chains 204 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 189 time to evaluate : 1.878 ------------------------------------------------------------------------------- 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 350 SER 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 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: 0.9980 chunk 87 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 chunk 61 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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: 0.8127 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 12581 Z= 0.217 Angle : 0.435 4.564 17132 Z= 0.230 Chirality : 0.035 0.119 1987 Planarity : 0.003 0.036 2080 Dihedral : 6.223 88.823 1710 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.19 % Allowed : 10.61 % 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: 3.54 (0.21), residues: 1593 helix: 2.98 (0.14), residues: 1287 sheet: None (None), residues: 0 loop : -0.61 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 316 HIS 0.001 0.000 HIS B 152 PHE 0.011 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 204 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 189 time to evaluate : 2.309 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 172 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.7934 (mm) REVERT: A 307 MET cc_start: 0.8694 (mtm) cc_final: 0.8451 (mtm) REVERT: A 509 ASP cc_start: 0.8856 (m-30) cc_final: 0.8586 (m-30) REVERT: B 131 PHE cc_start: 0.7519 (t80) cc_final: 0.7130 (t80) REVERT: B 305 MET cc_start: 0.8474 (mmm) cc_final: 0.7980 (mmt) outliers start: 15 outliers final: 14 residues processed: 198 average time/residue: 0.4517 time to fit residues: 138.1471 Evaluate side-chains 204 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 189 time to evaluate : 1.954 ------------------------------------------------------------------------------- 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 350 SER 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 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: 4.9990 chunk 30 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 120 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 146 optimal weight: 0.6980 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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: 0.8119 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12581 Z= 0.163 Angle : 0.422 4.454 17132 Z= 0.221 Chirality : 0.035 0.116 1987 Planarity : 0.003 0.036 2080 Dihedral : 6.167 89.032 1710 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.19 % Allowed : 10.69 % Favored : 88.12 % 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: 3.60 (0.21), residues: 1593 helix: 3.03 (0.14), residues: 1284 sheet: None (None), residues: 0 loop : -0.63 (0.34), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 316 HIS 0.001 0.000 HIS B 152 PHE 0.013 0.001 PHE C 177 TYR 0.014 0.001 TYR B 216 ARG 0.001 0.000 ARG A 108 *********************** 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 205 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 190 time to evaluate : 1.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 TYR cc_start: 0.7546 (m-10) cc_final: 0.7329 (m-10) REVERT: A 172 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.7929 (mm) REVERT: A 307 MET cc_start: 0.8689 (mtm) cc_final: 0.8448 (mtm) REVERT: A 509 ASP cc_start: 0.8842 (m-30) cc_final: 0.8572 (m-30) REVERT: C 154 MET cc_start: 0.8007 (mmp) cc_final: 0.7579 (mmp) REVERT: B 131 PHE cc_start: 0.7537 (t80) cc_final: 0.7142 (t80) REVERT: B 176 TRP cc_start: 0.7102 (t-100) cc_final: 0.6865 (t-100) REVERT: B 305 MET cc_start: 0.8470 (mmm) cc_final: 0.7976 (mmt) outliers start: 15 outliers final: 14 residues processed: 198 average time/residue: 0.4489 time to fit residues: 139.0010 Evaluate side-chains 200 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 185 time to evaluate : 1.779 ------------------------------------------------------------------------------- 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 350 SER 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 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 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: 1.9990 chunk 146 optimal weight: 0.5980 chunk 85 optimal weight: 3.9990 chunk 62 optimal weight: 0.0570 chunk 112 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 135 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- 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: 0.8119 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12581 Z= 0.163 Angle : 0.422 4.454 17132 Z= 0.221 Chirality : 0.035 0.116 1987 Planarity : 0.003 0.036 2080 Dihedral : 6.167 89.032 1710 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.19 % Allowed : 10.69 % Favored : 88.12 % 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: 3.60 (0.21), residues: 1593 helix: 3.03 (0.14), residues: 1284 sheet: None (None), residues: 0 loop : -0.63 (0.34), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 316 HIS 0.001 0.000 HIS B 152 PHE 0.013 0.001 PHE C 177 TYR 0.014 0.001 TYR B 216 ARG 0.001 0.000 ARG A 108 *********************** 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 200 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 185 time to evaluate : 1.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 TYR cc_start: 0.7546 (m-10) cc_final: 0.7329 (m-10) REVERT: A 172 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.7929 (mm) REVERT: A 307 MET cc_start: 0.8690 (mtm) cc_final: 0.8447 (mtm) REVERT: A 509 ASP cc_start: 0.8842 (m-30) cc_final: 0.8571 (m-30) REVERT: C 154 MET cc_start: 0.8008 (mmp) cc_final: 0.7577 (mmp) REVERT: B 131 PHE cc_start: 0.7534 (t80) cc_final: 0.7142 (t80) REVERT: B 176 TRP cc_start: 0.7099 (t-100) cc_final: 0.6867 (t-100) REVERT: B 305 MET cc_start: 0.8470 (mmm) cc_final: 0.7976 (mmt) outliers start: 15 outliers final: 14 residues processed: 193 average time/residue: 0.4621 time to fit residues: 140.4514 Evaluate side-chains 203 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 188 time to evaluate : 2.035 ------------------------------------------------------------------------------- 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 350 SER 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 92 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 126 optimal weight: 0.3980 chunk 13 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- 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: 0.8119 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12581 Z= 0.163 Angle : 0.422 4.454 17132 Z= 0.221 Chirality : 0.035 0.116 1987 Planarity : 0.003 0.036 2080 Dihedral : 6.167 89.032 1710 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.19 % Allowed : 10.69 % Favored : 88.12 % 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: 3.60 (0.21), residues: 1593 helix: 3.03 (0.14), residues: 1284 sheet: None (None), residues: 0 loop : -0.63 (0.34), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 316 HIS 0.001 0.000 HIS B 152 PHE 0.013 0.001 PHE C 177 TYR 0.014 0.001 TYR B 216 ARG 0.001 0.000 ARG A 108 ********************** 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 203 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 188 time to evaluate : 1.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 TYR cc_start: 0.7546 (m-10) cc_final: 0.7329 (m-10) REVERT: A 172 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.7929 (mm) REVERT: A 307 MET cc_start: 0.8689 (mtm) cc_final: 0.8447 (mtm) REVERT: A 509 ASP cc_start: 0.8842 (m-30) cc_final: 0.8571 (m-30) REVERT: C 154 MET cc_start: 0.8006 (mmp) cc_final: 0.7577 (mmp) REVERT: B 131 PHE cc_start: 0.7534 (t80) cc_final: 0.7142 (t80) REVERT: B 176 TRP cc_start: 0.7101 (t-100) cc_final: 0.6867 (t-100) REVERT: B 305 MET cc_start: 0.8470 (mmm) cc_final: 0.7976 (mmt) outliers start: 15 outliers final: 14 residues processed: 196 average time/residue: 0.4550 time to fit residues: 139.6229 Evaluate side-chains 203 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 188 time to evaluate : 1.611 ------------------------------------------------------------------------------- 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 350 SER 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 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 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: 0.9980 chunk 18 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 126 optimal weight: 0.3980 chunk 52 optimal weight: 2.9990 chunk 129 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3469 r_free = 0.3469 target = 0.127020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.099636 restraints weight = 47792.981| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.76 r_work: 0.2844 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12581 Z= 0.163 Angle : 0.422 4.454 17132 Z= 0.221 Chirality : 0.035 0.116 1987 Planarity : 0.003 0.036 2080 Dihedral : 6.167 89.032 1710 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.19 % Allowed : 10.69 % Favored : 88.12 % 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: 3.60 (0.21), residues: 1593 helix: 3.03 (0.14), residues: 1284 sheet: None (None), residues: 0 loop : -0.63 (0.34), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 316 HIS 0.001 0.000 HIS B 152 PHE 0.013 0.001 PHE C 177 TYR 0.014 0.001 TYR B 216 ARG 0.001 0.000 ARG A 108 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4843.25 seconds wall clock time: 94 minutes 42.04 seconds (5682.04 seconds total)