Starting phenix.real_space_refine on Fri Apr 12 08:51:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz1_41730/04_2024/8tz1_41730_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz1_41730/04_2024/8tz1_41730.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz1_41730/04_2024/8tz1_41730.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz1_41730/04_2024/8tz1_41730.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz1_41730/04_2024/8tz1_41730_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz1_41730/04_2024/8tz1_41730_trim_updated.pdb" } resolution = 2.54 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= 0.006 sd= 0.063 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 12 5.49 5 S 87 5.16 5 Na 6 4.78 5 C 8436 2.51 5 N 1938 2.21 5 O 2208 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 "C TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 24852 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 8129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8129 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 18, 'TRANS': 514} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 69 Chain: "C" Number of atoms: 8129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8129 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 18, 'TRANS': 514} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 69 Chain: "B" Number of atoms: 8129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8129 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 18, 'TRANS': 514} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 69 Chain: "A" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 153 Unusual residues: {' NA': 2, 'LBN': 4, 'RBV%rna3p': 1} Classifications: {'undetermined': 7} Modifications used: {'rna3p': 1} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 74 Chain: "C" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 153 Unusual residues: {' NA': 2, 'LBN': 4, 'RBV%rna3p': 1} Classifications: {'undetermined': 7} Modifications used: {'rna3p': 1} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 74 Chain: "B" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 153 Unusual residues: {' NA': 2, 'LBN': 4, 'RBV%rna3p': 1} Classifications: {'undetermined': 7} Modifications used: {'rna3p': 1} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 74 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 11.55, per 1000 atoms: 0.46 Number of scatterers: 24852 At special positions: 0 Unit cell: (128.52, 126.36, 75.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 87 16.00 P 12 15.00 Na 6 11.00 O 2208 8.00 N 1938 7.00 C 8436 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: 22.22 Conformation dependent library (CDL) restraints added in 2.9 seconds 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2946 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 78 helices and 0 sheets defined 79.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.86 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 197 Proline residue: A 167 - end of helix removed outlier: 4.562A pdb=" N PHE A 177 " --> pdb=" O ASP A 173 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N TRP A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N TRP A 181 " --> pdb=" O PHE A 177 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL A 182 " --> pdb=" O TRP A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 202 No H-bonds generated for 'chain 'A' and resid 199 through 202' 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: 3.891A pdb=" N GLY A 271 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N TYR A 272 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N SER A 273 " --> pdb=" O PHE A 269 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ASP A 274 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ALA A 275 " --> pdb=" O GLY A 271 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLY A 276 " --> pdb=" O TYR A 272 " (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: 4.148A 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 removed outlier: 3.612A pdb=" N VAL A 324 " --> pdb=" O LYS A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 341 Processing helix chain 'A' and resid 347 through 354 Proline residue: A 351 - end of helix removed outlier: 4.437A pdb=" N VAL A 354 " --> pdb=" O SER A 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 347 through 354' Processing helix chain 'A' and resid 358 through 360 No H-bonds generated for 'chain 'A' and resid 358 through 360' Processing helix chain 'A' and resid 363 through 374 Processing helix chain 'A' and resid 382 through 388 Processing helix chain 'A' and resid 392 through 413 removed outlier: 4.184A 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: 3.880A pdb=" N ILE A 450 " --> pdb=" O ALA A 446 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N SER A 451 " --> pdb=" O SER A 447 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU A 452 " --> pdb=" O SER A 448 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N MET A 480 " --> pdb=" O TRP A 476 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N PHE A 481 " --> pdb=" O LEU A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 495 Processing helix chain 'A' and resid 497 through 502 Processing helix chain 'A' and resid 507 through 522 removed outlier: 4.073A pdb=" N PHE A 511 " --> pdb=" O TRP A 507 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N MET A 512 " --> pdb=" O GLN A 508 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS A 515 " --> pdb=" O PHE A 511 " (cutoff:3.500A) removed outlier: 3.718A 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 572 through 585 removed outlier: 3.531A pdb=" N VAL A 578 " --> pdb=" O LEU A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 618 removed outlier: 4.879A pdb=" N ARG A 591 " --> pdb=" O SER A 588 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR A 594 " --> pdb=" O ARG A 591 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY A 596 " --> pdb=" O ILE A 593 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA A 597 " --> pdb=" O THR A 594 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N MET A 598 " --> pdb=" O ALA A 595 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY A 604 " --> pdb=" O LEU A 601 " (cutoff:3.500A) 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 197 Proline residue: C 167 - end of helix removed outlier: 4.563A pdb=" N PHE C 177 " --> pdb=" O ASP C 173 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N TRP C 178 " --> pdb=" O SER C 174 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N TRP C 181 " --> pdb=" O PHE C 177 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL C 182 " --> pdb=" O TRP C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 202 No H-bonds generated for 'chain 'C' and resid 199 through 202' 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: 3.891A pdb=" N GLY C 271 " --> pdb=" O GLN C 267 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N TYR C 272 " --> pdb=" O THR C 268 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N SER C 273 " --> pdb=" O PHE C 269 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ASP C 274 " --> pdb=" O LEU C 270 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ALA C 275 " --> pdb=" O GLY C 271 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLY C 276 " --> pdb=" O TYR C 272 " (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: 4.148A 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 removed outlier: 3.612A pdb=" N VAL C 324 " --> pdb=" O LYS C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 341 Processing helix chain 'C' and resid 347 through 354 Proline residue: C 351 - end of helix removed outlier: 4.438A pdb=" N VAL C 354 " --> pdb=" O SER C 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 347 through 354' Processing helix chain 'C' and resid 358 through 360 No H-bonds generated for 'chain 'C' and resid 358 through 360' Processing helix chain 'C' and resid 363 through 374 Processing helix chain 'C' and resid 382 through 388 Processing helix chain 'C' and resid 392 through 413 removed outlier: 4.185A 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: 3.880A pdb=" N ILE C 450 " --> pdb=" O ALA C 446 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N SER C 451 " --> pdb=" O SER C 447 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU C 452 " --> pdb=" O SER C 448 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N MET C 480 " --> pdb=" O TRP C 476 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N PHE C 481 " --> pdb=" O LEU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 495 Processing helix chain 'C' and resid 497 through 502 Processing helix chain 'C' and resid 507 through 522 removed outlier: 4.073A pdb=" N PHE C 511 " --> pdb=" O TRP C 507 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N MET C 512 " --> pdb=" O GLN C 508 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS C 515 " --> pdb=" O PHE C 511 " (cutoff:3.500A) removed outlier: 3.718A 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: 3.531A pdb=" N VAL C 578 " --> pdb=" O LEU C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 618 removed outlier: 4.879A pdb=" N ARG C 591 " --> pdb=" O SER C 588 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR C 594 " --> pdb=" O ARG C 591 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY C 596 " --> pdb=" O ILE C 593 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA C 597 " --> pdb=" O THR C 594 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N MET C 598 " --> pdb=" O ALA C 595 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY C 604 " --> pdb=" O LEU C 601 " (cutoff:3.500A) 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 197 Proline residue: B 167 - end of helix removed outlier: 4.562A pdb=" N PHE B 177 " --> pdb=" O ASP B 173 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N TRP B 178 " --> pdb=" O SER B 174 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N TRP B 181 " --> pdb=" O PHE B 177 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL B 182 " --> pdb=" O TRP B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 202 No H-bonds generated for 'chain 'B' and resid 199 through 202' 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: 3.892A pdb=" N GLY B 271 " --> pdb=" O GLN B 267 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N TYR B 272 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N SER B 273 " --> pdb=" O PHE B 269 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ASP B 274 " --> pdb=" O LEU B 270 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ALA B 275 " --> pdb=" O GLY B 271 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLY B 276 " --> pdb=" O TYR B 272 " (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: 4.149A 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 removed outlier: 3.611A pdb=" N VAL B 324 " --> pdb=" O LYS B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 341 Processing helix chain 'B' and resid 347 through 354 Proline residue: B 351 - end of helix removed outlier: 4.437A pdb=" N VAL B 354 " --> pdb=" O SER B 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 347 through 354' Processing helix chain 'B' and resid 358 through 360 No H-bonds generated for 'chain 'B' and resid 358 through 360' Processing helix chain 'B' and resid 363 through 374 Processing helix chain 'B' and resid 382 through 388 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: 3.880A pdb=" N ILE B 450 " --> pdb=" O ALA B 446 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N SER B 451 " --> pdb=" O SER B 447 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU B 452 " --> pdb=" O SER B 448 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N MET B 480 " --> pdb=" O TRP B 476 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N PHE B 481 " --> pdb=" O LEU B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 495 Processing helix chain 'B' and resid 497 through 502 Processing helix chain 'B' and resid 507 through 522 removed outlier: 4.073A pdb=" N PHE B 511 " --> pdb=" O TRP B 507 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N MET B 512 " --> pdb=" O GLN B 508 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS B 515 " --> pdb=" O PHE B 511 " (cutoff:3.500A) removed outlier: 3.719A 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: 3.531A pdb=" N VAL B 578 " --> pdb=" O LEU B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 618 removed outlier: 4.879A pdb=" N ARG B 591 " --> pdb=" O SER B 588 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR B 594 " --> pdb=" O ARG B 591 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY B 596 " --> pdb=" O ILE B 593 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA B 597 " --> pdb=" O THR B 594 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N MET B 598 " --> pdb=" O ALA B 595 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY B 604 " --> pdb=" O LEU B 601 " (cutoff:3.500A) 852 hydrogen bonds defined for protein. 2259 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: 9.71 Time building geometry restraints manager: 22.99 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 - 1.23: 48 1.23 - 1.42: 5424 1.42 - 1.61: 7365 1.61 - 1.81: 183 Bond restraints: 25167 Sorted by residual: bond pdb=" C2' RBV B 801 " pdb=" C3' RBV B 801 " ideal model delta sigma weight residual 1.523 1.207 0.316 1.50e-02 4.44e+03 4.44e+02 bond pdb=" C2' RBV C 801 " pdb=" C3' RBV C 801 " ideal model delta sigma weight residual 1.523 1.207 0.316 1.50e-02 4.44e+03 4.44e+02 bond pdb=" C2' RBV A 801 " pdb=" C3' RBV A 801 " ideal model delta sigma weight residual 1.523 1.208 0.315 1.50e-02 4.44e+03 4.42e+02 bond pdb=" C4' RBV C 801 " pdb=" O4' RBV C 801 " ideal model delta sigma weight residual 1.451 1.270 0.181 1.50e-02 4.44e+03 1.45e+02 bond pdb=" C4' RBV A 801 " pdb=" O4' RBV A 801 " ideal model delta sigma weight residual 1.451 1.270 0.181 1.50e-02 4.44e+03 1.45e+02 ... (remaining 25162 not shown) Histogram of bond angle deviations from ideal: 99.77 - 106.61: 402 106.61 - 113.45: 28855 113.45 - 120.30: 8368 120.30 - 127.14: 7360 127.14 - 133.98: 162 Bond angle restraints: 45147 Sorted by residual: angle pdb=" O1 LBN B 805 " pdb=" P1 LBN B 805 " pdb=" O2 LBN B 805 " ideal model delta sigma weight residual 93.45 109.67 -16.22 3.00e+00 1.11e-01 2.92e+01 angle pdb=" O1 LBN A 805 " pdb=" P1 LBN A 805 " pdb=" O2 LBN A 805 " ideal model delta sigma weight residual 93.45 109.65 -16.20 3.00e+00 1.11e-01 2.92e+01 angle pdb=" O1 LBN C 805 " pdb=" P1 LBN C 805 " pdb=" O2 LBN C 805 " ideal model delta sigma weight residual 93.45 109.63 -16.18 3.00e+00 1.11e-01 2.91e+01 angle pdb=" O1 LBN B 807 " pdb=" P1 LBN B 807 " pdb=" O2 LBN B 807 " ideal model delta sigma weight residual 93.45 109.59 -16.14 3.00e+00 1.11e-01 2.89e+01 angle pdb=" O1 LBN B 804 " pdb=" P1 LBN B 804 " pdb=" O2 LBN B 804 " ideal model delta sigma weight residual 93.45 109.58 -16.13 3.00e+00 1.11e-01 2.89e+01 ... (remaining 45142 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.59: 11629 35.59 - 71.19: 458 71.19 - 106.78: 12 106.78 - 142.38: 3 142.38 - 177.97: 9 Dihedral angle restraints: 12111 sinusoidal: 6381 harmonic: 5730 Sorted by residual: dihedral pdb=" O5 LBN B 804 " pdb=" C2 LBN B 804 " pdb=" C3 LBN B 804 " pdb=" O7 LBN B 804 " ideal model delta sinusoidal sigma weight residual 62.67 -115.30 177.97 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O5 LBN C 804 " pdb=" C2 LBN C 804 " pdb=" C3 LBN C 804 " pdb=" O7 LBN C 804 " ideal model delta sinusoidal sigma weight residual 62.67 -115.29 177.96 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O5 LBN A 804 " pdb=" C2 LBN A 804 " pdb=" C3 LBN A 804 " pdb=" O7 LBN A 804 " ideal model delta sinusoidal sigma weight residual 62.67 -115.27 177.94 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 12108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1879 0.072 - 0.144: 116 0.144 - 0.215: 9 0.215 - 0.287: 0 0.287 - 0.359: 3 Chirality restraints: 2007 Sorted by residual: chirality pdb=" C2' RBV C 801 " pdb=" C1' RBV C 801 " pdb=" C3' RBV C 801 " pdb=" O2' RBV C 801 " both_signs ideal model delta sigma weight residual False -2.75 -2.39 -0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" C2' RBV B 801 " pdb=" C1' RBV B 801 " pdb=" C3' RBV B 801 " pdb=" O2' RBV B 801 " both_signs ideal model delta sigma weight residual False -2.75 -2.40 -0.36 2.00e-01 2.50e+01 3.18e+00 chirality pdb=" C2' RBV A 801 " pdb=" C1' RBV A 801 " pdb=" C3' RBV A 801 " pdb=" O2' RBV A 801 " both_signs ideal model delta sigma weight residual False -2.75 -2.40 -0.36 2.00e-01 2.50e+01 3.16e+00 ... (remaining 2004 not shown) Planarity restraints: 3663 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 524 " 0.037 2.00e-02 2.50e+03 3.98e-02 2.37e+01 pdb=" CG ASN A 524 " -0.001 2.00e-02 2.50e+03 pdb=" OD1 ASN A 524 " -0.037 2.00e-02 2.50e+03 pdb=" ND2 ASN A 524 " -0.000 2.00e-02 2.50e+03 pdb="HD21 ASN A 524 " 0.059 2.00e-02 2.50e+03 pdb="HD22 ASN A 524 " -0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 524 " -0.037 2.00e-02 2.50e+03 3.95e-02 2.34e+01 pdb=" CG ASN C 524 " 0.002 2.00e-02 2.50e+03 pdb=" OD1 ASN C 524 " 0.036 2.00e-02 2.50e+03 pdb=" ND2 ASN C 524 " 0.000 2.00e-02 2.50e+03 pdb="HD21 ASN C 524 " -0.058 2.00e-02 2.50e+03 pdb="HD22 ASN C 524 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 524 " 0.037 2.00e-02 2.50e+03 3.94e-02 2.33e+01 pdb=" CG ASN B 524 " -0.002 2.00e-02 2.50e+03 pdb=" OD1 ASN B 524 " -0.036 2.00e-02 2.50e+03 pdb=" ND2 ASN B 524 " -0.000 2.00e-02 2.50e+03 pdb="HD21 ASN B 524 " 0.058 2.00e-02 2.50e+03 pdb="HD22 ASN B 524 " -0.057 2.00e-02 2.50e+03 ... (remaining 3660 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 1995 2.24 - 2.83: 53741 2.83 - 3.42: 63406 3.42 - 4.01: 87779 4.01 - 4.60: 138500 Nonbonded interactions: 345421 Sorted by model distance: nonbonded pdb=" O ALA C 446 " pdb=" HG SER C 449 " model vdw 1.648 1.850 nonbonded pdb=" O ALA A 446 " pdb=" HG SER A 449 " model vdw 1.648 1.850 nonbonded pdb=" O ALA B 446 " pdb=" HG SER B 449 " model vdw 1.649 1.850 nonbonded pdb=" OE1 GLN B 315 " pdb=" H GLN B 315 " model vdw 1.659 1.850 nonbonded pdb=" OE1 GLN A 315 " pdb=" H GLN A 315 " model vdw 1.659 1.850 ... (remaining 345416 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain '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: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.380 Extract box with map and model: 5.030 Check model and map are aligned: 0.390 Set scattering table: 0.270 Process input model: 85.660 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.316 13002 Z= 0.708 Angle : 0.876 16.218 17625 Z= 0.374 Chirality : 0.040 0.359 2007 Planarity : 0.002 0.033 2121 Dihedral : 16.716 177.972 4617 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 1.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 0.48 % Allowed : 3.56 % Favored : 95.96 % 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: 2.87 (0.14), residues: 1338 sheet: None (None), residues: 0 loop : -0.75 (0.37), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 261 HIS 0.001 0.000 HIS B 288 PHE 0.011 0.001 PHE C 488 TYR 0.009 0.001 TYR C 231 ARG 0.002 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 202 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 196 time to evaluate : 1.929 Fit side-chains REVERT: A 305 MET cc_start: 0.7963 (mmm) cc_final: 0.7629 (mmt) REVERT: A 421 LYS cc_start: 0.8396 (mttt) cc_final: 0.8189 (mmtt) REVERT: C 421 LYS cc_start: 0.8359 (mttt) cc_final: 0.8134 (mmtt) REVERT: C 555 SER cc_start: 0.7935 (m) cc_final: 0.7709 (p) REVERT: B 305 MET cc_start: 0.7888 (mmm) cc_final: 0.7471 (mmt) REVERT: B 421 LYS cc_start: 0.8374 (mttt) cc_final: 0.8130 (mmtt) REVERT: B 508 GLN cc_start: 0.7876 (mt0) cc_final: 0.7445 (mm-40) outliers start: 6 outliers final: 3 residues processed: 202 average time/residue: 1.9739 time to fit residues: 447.4463 Evaluate side-chains 143 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 140 time to evaluate : 1.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain B residue 171 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 1.9990 chunk 120 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 144 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13002 Z= 0.151 Angle : 0.459 4.778 17625 Z= 0.241 Chirality : 0.036 0.136 2007 Planarity : 0.004 0.038 2121 Dihedral : 16.459 156.826 2071 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 0.95 % Allowed : 8.23 % Favored : 90.82 % 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: 3.23 (0.21), residues: 1593 helix: 2.69 (0.14), residues: 1335 sheet: None (None), residues: 0 loop : -1.06 (0.33), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 112 HIS 0.002 0.000 HIS C 288 PHE 0.017 0.001 PHE A 164 TYR 0.007 0.001 TYR C 231 ARG 0.002 0.000 ARG A 557 *********************** 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 178 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 166 time to evaluate : 1.922 Fit side-chains REVERT: A 283 GLU cc_start: 0.7234 (mm-30) cc_final: 0.6936 (mm-30) REVERT: A 305 MET cc_start: 0.8020 (mmm) cc_final: 0.7721 (mmt) REVERT: A 421 LYS cc_start: 0.8433 (mttt) cc_final: 0.8199 (mmtt) REVERT: C 421 LYS cc_start: 0.8382 (mttt) cc_final: 0.8067 (mmtt) REVERT: C 555 SER cc_start: 0.7719 (m) cc_final: 0.7428 (p) REVERT: B 169 GLN cc_start: 0.7964 (tm-30) cc_final: 0.7750 (tm-30) REVERT: B 264 LYS cc_start: 0.7514 (mttt) cc_final: 0.7266 (mtmt) REVERT: B 305 MET cc_start: 0.8082 (mmm) cc_final: 0.7712 (mmt) REVERT: B 421 LYS cc_start: 0.8442 (mttt) cc_final: 0.8087 (mmtt) REVERT: B 470 MET cc_start: 0.7476 (ttm) cc_final: 0.7101 (ttm) REVERT: B 508 GLN cc_start: 0.7915 (mt0) cc_final: 0.7538 (mm-40) REVERT: B 556 MET cc_start: 0.7550 (ttt) cc_final: 0.7258 (ttp) outliers start: 12 outliers final: 2 residues processed: 173 average time/residue: 1.9288 time to fit residues: 376.9042 Evaluate side-chains 154 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 152 time to evaluate : 1.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 189 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 120 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13002 Z= 0.255 Angle : 0.483 5.149 17625 Z= 0.257 Chirality : 0.038 0.131 2007 Planarity : 0.004 0.046 2121 Dihedral : 15.665 160.976 2067 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.87 % Allowed : 8.95 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.74 (0.21), residues: 1593 helix: 2.35 (0.15), residues: 1335 sheet: None (None), residues: 0 loop : -1.16 (0.31), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 112 HIS 0.002 0.001 HIS B 367 PHE 0.015 0.001 PHE C 413 TYR 0.009 0.001 TYR A 231 ARG 0.002 0.000 ARG A 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 166 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 155 time to evaluate : 2.226 Fit side-chains REVERT: A 283 GLU cc_start: 0.7568 (mm-30) cc_final: 0.7230 (mm-30) REVERT: A 305 MET cc_start: 0.8147 (mmm) cc_final: 0.7825 (mmt) REVERT: A 421 LYS cc_start: 0.8408 (mttt) cc_final: 0.8041 (mmtt) REVERT: C 421 LYS cc_start: 0.8476 (mttt) cc_final: 0.8051 (mmtt) REVERT: B 169 GLN cc_start: 0.7955 (tm-30) cc_final: 0.7718 (tm-30) REVERT: B 264 LYS cc_start: 0.7738 (mttt) cc_final: 0.7513 (mttp) REVERT: B 305 MET cc_start: 0.7976 (mmm) cc_final: 0.7553 (mmt) REVERT: B 421 LYS cc_start: 0.8420 (mttt) cc_final: 0.8029 (mmtt) REVERT: B 470 MET cc_start: 0.7605 (ttm) cc_final: 0.7204 (ttm) REVERT: B 506 ASP cc_start: 0.7761 (p0) cc_final: 0.7536 (p0) REVERT: B 508 GLN cc_start: 0.7953 (mt0) cc_final: 0.7536 (mm-40) REVERT: B 524 ASN cc_start: 0.8490 (p0) cc_final: 0.8074 (p0) outliers start: 11 outliers final: 4 residues processed: 160 average time/residue: 2.0509 time to fit residues: 367.5120 Evaluate side-chains 157 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 153 time to evaluate : 2.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 506 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 142 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 41 optimal weight: 0.0970 chunk 127 optimal weight: 1.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13002 Z= 0.272 Angle : 0.474 5.532 17625 Z= 0.252 Chirality : 0.037 0.134 2007 Planarity : 0.004 0.048 2121 Dihedral : 15.228 160.064 2067 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.95 % Allowed : 10.29 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.54 (0.22), residues: 1593 helix: 2.20 (0.15), residues: 1335 sheet: None (None), residues: 0 loop : -1.16 (0.32), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 112 HIS 0.003 0.001 HIS C 288 PHE 0.021 0.001 PHE C 164 TYR 0.009 0.001 TYR A 310 ARG 0.002 0.000 ARG A 557 *********************** 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 170 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 158 time to evaluate : 1.890 Fit side-chains REVERT: A 283 GLU cc_start: 0.7619 (mm-30) cc_final: 0.7313 (mm-30) REVERT: A 305 MET cc_start: 0.8150 (mmm) cc_final: 0.7774 (mmt) REVERT: A 421 LYS cc_start: 0.8361 (mttt) cc_final: 0.8005 (mmtt) REVERT: C 421 LYS cc_start: 0.8442 (mttt) cc_final: 0.8025 (mmtt) REVERT: B 169 GLN cc_start: 0.7965 (tm-30) cc_final: 0.7706 (tm-30) REVERT: B 264 LYS cc_start: 0.7724 (mttt) cc_final: 0.7396 (mtmt) REVERT: B 267 GLN cc_start: 0.7904 (tt0) cc_final: 0.7667 (mt0) REVERT: B 305 MET cc_start: 0.8026 (mmm) cc_final: 0.7575 (mmt) REVERT: B 421 LYS cc_start: 0.8386 (mttt) cc_final: 0.7958 (mmtt) REVERT: B 470 MET cc_start: 0.7619 (ttm) cc_final: 0.7212 (ttm) REVERT: B 508 GLN cc_start: 0.7945 (mt0) cc_final: 0.7455 (tp40) outliers start: 12 outliers final: 2 residues processed: 161 average time/residue: 2.0673 time to fit residues: 373.7821 Evaluate side-chains 156 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 154 time to evaluate : 2.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 556 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: 7.9990 chunk 114 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 106 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 78 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13002 Z= 0.291 Angle : 0.476 5.579 17625 Z= 0.254 Chirality : 0.038 0.131 2007 Planarity : 0.004 0.048 2121 Dihedral : 15.225 160.079 2067 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.87 % Allowed : 10.61 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.22), residues: 1593 helix: 2.12 (0.15), residues: 1335 sheet: None (None), residues: 0 loop : -1.20 (0.33), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 112 HIS 0.003 0.001 HIS A 288 PHE 0.014 0.001 PHE C 279 TYR 0.008 0.001 TYR A 310 ARG 0.002 0.000 ARG B 251 *********************** 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 166 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 155 time to evaluate : 2.104 Fit side-chains REVERT: A 283 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7346 (mm-30) REVERT: A 305 MET cc_start: 0.8179 (mmm) cc_final: 0.7808 (mmt) REVERT: A 421 LYS cc_start: 0.8358 (mttt) cc_final: 0.8021 (mmtt) REVERT: C 421 LYS cc_start: 0.8413 (mttt) cc_final: 0.8037 (mmtt) REVERT: B 169 GLN cc_start: 0.7914 (tm-30) cc_final: 0.7643 (tm-30) REVERT: B 264 LYS cc_start: 0.7717 (mttt) cc_final: 0.7396 (mtmt) REVERT: B 267 GLN cc_start: 0.7899 (tt0) cc_final: 0.7648 (mt0) REVERT: B 305 MET cc_start: 0.8034 (mmm) cc_final: 0.7560 (mmt) REVERT: B 421 LYS cc_start: 0.8304 (mttt) cc_final: 0.7880 (mmtt) REVERT: B 470 MET cc_start: 0.7648 (ttm) cc_final: 0.7258 (ttm) REVERT: B 508 GLN cc_start: 0.7896 (mt0) cc_final: 0.7472 (tp40) REVERT: B 524 ASN cc_start: 0.8517 (p0) cc_final: 0.8093 (p0) outliers start: 11 outliers final: 7 residues processed: 161 average time/residue: 2.0771 time to fit residues: 375.6913 Evaluate side-chains 161 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 154 time to evaluate : 1.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 506 ASP Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 260 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 138 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 127 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13002 Z= 0.214 Angle : 0.446 5.305 17625 Z= 0.237 Chirality : 0.036 0.131 2007 Planarity : 0.004 0.045 2121 Dihedral : 14.829 158.906 2067 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.11 % Allowed : 10.85 % 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: 2.58 (0.22), residues: 1593 helix: 2.23 (0.15), residues: 1335 sheet: None (None), residues: 0 loop : -1.19 (0.33), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 112 HIS 0.002 0.001 HIS B 288 PHE 0.020 0.001 PHE C 164 TYR 0.007 0.001 TYR A 310 ARG 0.002 0.000 ARG B 108 *********************** 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 168 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 154 time to evaluate : 1.789 Fit side-chains REVERT: A 283 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7346 (mm-30) REVERT: A 305 MET cc_start: 0.8206 (mmm) cc_final: 0.7839 (mmt) REVERT: A 421 LYS cc_start: 0.8305 (mttt) cc_final: 0.7961 (mmtt) REVERT: C 421 LYS cc_start: 0.8411 (mttt) cc_final: 0.8008 (mmtt) REVERT: B 169 GLN cc_start: 0.7950 (tm-30) cc_final: 0.7662 (tm-30) REVERT: B 264 LYS cc_start: 0.7710 (mttt) cc_final: 0.7385 (mtmt) REVERT: B 267 GLN cc_start: 0.7860 (tt0) cc_final: 0.7609 (mt0) REVERT: B 305 MET cc_start: 0.8019 (mmm) cc_final: 0.7558 (mmt) REVERT: B 421 LYS cc_start: 0.8322 (mttt) cc_final: 0.7908 (mmtt) REVERT: B 470 MET cc_start: 0.7625 (ttm) cc_final: 0.7238 (ttm) REVERT: B 508 GLN cc_start: 0.7825 (mt0) cc_final: 0.7417 (tp40) outliers start: 14 outliers final: 8 residues processed: 163 average time/residue: 2.0434 time to fit residues: 373.8931 Evaluate side-chains 162 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 154 time to evaluate : 1.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 PHE Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 506 ASP Chi-restraints excluded: chain B residue 413 PHE 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: 4.9990 chunk 112 optimal weight: 3.9990 chunk 129 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 chunk 153 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13002 Z= 0.173 Angle : 0.429 5.629 17625 Z= 0.226 Chirality : 0.035 0.127 2007 Planarity : 0.004 0.043 2121 Dihedral : 14.488 158.349 2067 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.79 % Allowed : 11.08 % 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: 2.73 (0.22), residues: 1593 helix: 2.35 (0.15), residues: 1335 sheet: None (None), residues: 0 loop : -1.18 (0.33), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 112 HIS 0.002 0.000 HIS B 288 PHE 0.016 0.001 PHE A 164 TYR 0.006 0.001 TYR A 310 ARG 0.002 0.000 ARG B 599 *********************** 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 168 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 158 time to evaluate : 1.930 Fit side-chains REVERT: A 283 GLU cc_start: 0.7592 (mm-30) cc_final: 0.7331 (mm-30) REVERT: A 305 MET cc_start: 0.8149 (mmm) cc_final: 0.7783 (mmt) REVERT: A 421 LYS cc_start: 0.8312 (mttt) cc_final: 0.7947 (mmtt) REVERT: C 108 ARG cc_start: 0.6607 (ttm-80) cc_final: 0.6349 (ttt-90) REVERT: C 421 LYS cc_start: 0.8403 (mttt) cc_final: 0.7994 (mmtt) REVERT: B 169 GLN cc_start: 0.7869 (tm-30) cc_final: 0.7583 (tm-30) REVERT: B 264 LYS cc_start: 0.7705 (mttt) cc_final: 0.7430 (mtmt) REVERT: B 267 GLN cc_start: 0.7868 (tt0) cc_final: 0.7624 (mt0) REVERT: B 305 MET cc_start: 0.8000 (mmm) cc_final: 0.7540 (mmt) REVERT: B 421 LYS cc_start: 0.8317 (mttt) cc_final: 0.7907 (mmtt) REVERT: B 470 MET cc_start: 0.7623 (ttm) cc_final: 0.7236 (ttm) REVERT: B 508 GLN cc_start: 0.7809 (mt0) cc_final: 0.7402 (tp40) REVERT: B 524 ASN cc_start: 0.8453 (p0) cc_final: 0.8052 (p0) outliers start: 10 outliers final: 5 residues processed: 163 average time/residue: 2.0737 time to fit residues: 377.9955 Evaluate side-chains 161 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 156 time to evaluate : 1.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain C residue 260 ASP 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: 1.9990 chunk 97 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 120 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13002 Z= 0.249 Angle : 0.460 5.276 17625 Z= 0.244 Chirality : 0.037 0.130 2007 Planarity : 0.004 0.044 2121 Dihedral : 14.731 160.072 2067 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.63 % Allowed : 11.32 % 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: 2.57 (0.22), residues: 1593 helix: 2.23 (0.15), residues: 1335 sheet: None (None), residues: 0 loop : -1.23 (0.33), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 112 HIS 0.003 0.001 HIS C 288 PHE 0.019 0.001 PHE C 164 TYR 0.008 0.001 TYR A 310 ARG 0.001 0.000 ARG A 599 *********************** 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 163 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 155 time to evaluate : 1.998 Fit side-chains REVERT: A 283 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7342 (mm-30) REVERT: A 305 MET cc_start: 0.8213 (mmm) cc_final: 0.7850 (mmt) REVERT: A 421 LYS cc_start: 0.8297 (mttt) cc_final: 0.7928 (mmtt) REVERT: C 108 ARG cc_start: 0.6632 (ttm-80) cc_final: 0.6389 (ttt-90) REVERT: C 421 LYS cc_start: 0.8392 (mttt) cc_final: 0.7955 (mmtt) REVERT: B 169 GLN cc_start: 0.7875 (tm-30) cc_final: 0.7584 (tm-30) REVERT: B 264 LYS cc_start: 0.7718 (mttt) cc_final: 0.7381 (mtmt) REVERT: B 267 GLN cc_start: 0.7891 (tt0) cc_final: 0.7646 (mt0) REVERT: B 305 MET cc_start: 0.8010 (mmm) cc_final: 0.7550 (mmt) REVERT: B 421 LYS cc_start: 0.8304 (mttt) cc_final: 0.7905 (mmtt) REVERT: B 470 MET cc_start: 0.7640 (ttm) cc_final: 0.7254 (ttm) REVERT: B 508 GLN cc_start: 0.7853 (mt0) cc_final: 0.7445 (tp40) outliers start: 8 outliers final: 5 residues processed: 159 average time/residue: 2.1767 time to fit residues: 389.4589 Evaluate side-chains 158 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 153 time to evaluate : 2.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain C residue 260 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 133 optimal weight: 0.5980 chunk 142 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 135 optimal weight: 0.0970 chunk 93 optimal weight: 0.8980 chunk 151 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13002 Z= 0.156 Angle : 0.423 6.476 17625 Z= 0.223 Chirality : 0.035 0.125 2007 Planarity : 0.004 0.042 2121 Dihedral : 14.216 157.809 2067 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.40 % Allowed : 11.80 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.83 (0.22), residues: 1593 helix: 2.41 (0.15), residues: 1335 sheet: None (None), residues: 0 loop : -1.16 (0.33), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 323 HIS 0.002 0.000 HIS B 288 PHE 0.011 0.001 PHE B 279 TYR 0.005 0.001 TYR A 310 ARG 0.001 0.000 ARG B 557 *********************** 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 163 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 158 time to evaluate : 2.125 Fit side-chains REVERT: A 283 GLU cc_start: 0.7589 (mm-30) cc_final: 0.7333 (mm-30) REVERT: A 305 MET cc_start: 0.8145 (mmm) cc_final: 0.7780 (mmt) REVERT: A 421 LYS cc_start: 0.8308 (mttt) cc_final: 0.7943 (mmtt) REVERT: C 108 ARG cc_start: 0.6609 (ttm-80) cc_final: 0.6378 (ttt-90) REVERT: C 421 LYS cc_start: 0.8391 (mttt) cc_final: 0.7977 (mmtt) REVERT: B 169 GLN cc_start: 0.7831 (tm-30) cc_final: 0.7555 (tm-30) REVERT: B 264 LYS cc_start: 0.7732 (mttt) cc_final: 0.7448 (mtmt) REVERT: B 267 GLN cc_start: 0.7861 (tt0) cc_final: 0.7620 (mt0) REVERT: B 305 MET cc_start: 0.8016 (mmm) cc_final: 0.7570 (mmt) REVERT: B 421 LYS cc_start: 0.8300 (mttt) cc_final: 0.7898 (mmtt) REVERT: B 470 MET cc_start: 0.7614 (ttm) cc_final: 0.7247 (ttm) REVERT: B 508 GLN cc_start: 0.7803 (mt0) cc_final: 0.7423 (tp40) REVERT: B 524 ASN cc_start: 0.8467 (p0) cc_final: 0.8041 (p0) outliers start: 5 outliers final: 5 residues processed: 161 average time/residue: 2.1230 time to fit residues: 383.3556 Evaluate side-chains 159 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 154 time to evaluate : 2.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain C residue 260 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 92 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 158 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13002 Z= 0.252 Angle : 0.468 9.151 17625 Z= 0.247 Chirality : 0.037 0.126 2007 Planarity : 0.004 0.044 2121 Dihedral : 14.578 159.379 2067 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.40 % Allowed : 12.11 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.64 (0.22), residues: 1593 helix: 2.30 (0.15), residues: 1329 sheet: None (None), residues: 0 loop : -1.24 (0.33), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 112 HIS 0.003 0.001 HIS C 288 PHE 0.020 0.001 PHE C 164 TYR 0.008 0.001 TYR A 310 ARG 0.001 0.000 ARG A 599 ********************** 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 159 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 154 time to evaluate : 1.772 Fit side-chains REVERT: A 283 GLU cc_start: 0.7602 (mm-30) cc_final: 0.7344 (mm-30) REVERT: A 305 MET cc_start: 0.8213 (mmm) cc_final: 0.7850 (mmt) REVERT: A 421 LYS cc_start: 0.8292 (mttt) cc_final: 0.7915 (mmtt) REVERT: C 108 ARG cc_start: 0.6732 (ttm-80) cc_final: 0.6436 (ttt-90) REVERT: C 421 LYS cc_start: 0.8379 (mttt) cc_final: 0.7957 (mmtt) REVERT: B 169 GLN cc_start: 0.7909 (tm-30) cc_final: 0.7603 (tm-30) REVERT: B 264 LYS cc_start: 0.7746 (mttt) cc_final: 0.7458 (mtmt) REVERT: B 267 GLN cc_start: 0.7892 (tt0) cc_final: 0.7648 (mt0) REVERT: B 305 MET cc_start: 0.8024 (mmm) cc_final: 0.7570 (mmt) REVERT: B 421 LYS cc_start: 0.8296 (mttt) cc_final: 0.7899 (mmtt) REVERT: B 470 MET cc_start: 0.7643 (ttm) cc_final: 0.7257 (ttm) REVERT: B 508 GLN cc_start: 0.7852 (mt0) cc_final: 0.7445 (tp40) outliers start: 5 outliers final: 5 residues processed: 157 average time/residue: 2.1244 time to fit residues: 374.2724 Evaluate side-chains 158 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 153 time to evaluate : 2.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain C residue 260 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 38 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 129 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.102416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.069459 restraints weight = 46049.583| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 1.85 r_work: 0.2677 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2569 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13002 Z= 0.298 Angle : 0.487 9.953 17625 Z= 0.258 Chirality : 0.038 0.130 2007 Planarity : 0.004 0.046 2121 Dihedral : 14.763 161.037 2067 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.48 % Allowed : 12.19 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.22), residues: 1593 helix: 2.18 (0.15), residues: 1329 sheet: None (None), residues: 0 loop : -1.24 (0.33), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 112 HIS 0.003 0.001 HIS C 288 PHE 0.018 0.001 PHE B 164 TYR 0.009 0.001 TYR A 310 ARG 0.002 0.000 ARG B 557 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7700.36 seconds wall clock time: 137 minutes 18.91 seconds (8238.91 seconds total)