Starting phenix.real_space_refine on Fri Apr 12 08:54:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz5_41734/04_2024/8tz5_41734_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz5_41734/04_2024/8tz5_41734.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz5_41734/04_2024/8tz5_41734_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz5_41734/04_2024/8tz5_41734_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz5_41734/04_2024/8tz5_41734_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz5_41734/04_2024/8tz5_41734.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz5_41734/04_2024/8tz5_41734.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz5_41734/04_2024/8tz5_41734_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz5_41734/04_2024/8tz5_41734_trim_updated.pdb" } resolution = 2.74 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= 0.010 sd= 0.235 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 3 4.78 5 C 8439 2.51 5 N 1935 2.21 5 O 2205 1.98 5 H 12165 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 344": "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 "C PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 344": "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: 24846 Number of models: 1 Model: "" Number of chains: 6 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: "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: "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: "A" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 153 Unusual residues: {' NA': 1, 'LBN': 4, 'U56': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 74 Chain: "B" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 153 Unusual residues: {' NA': 1, 'LBN': 4, 'U56': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 74 Chain: "C" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 153 Unusual residues: {' NA': 1, 'LBN': 4, 'U56': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 74 Time building chain proxies: 11.33, per 1000 atoms: 0.46 Number of scatterers: 24846 At special positions: 0 Unit cell: (127.65, 129.87, 75.48, 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 3 11.00 O 2205 8.00 N 1935 7.00 C 8439 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: 20.71 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: 78 helices and 0 sheets defined 80.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.10 Creating SS restraints... Processing helix chain 'A' and resid 91 through 102 Processing helix chain 'A' and resid 104 through 129 removed outlier: 3.577A pdb=" N ILE A 110 " --> pdb=" O THR A 106 " (cutoff:3.500A) 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: 4.797A pdb=" N PHE A 177 " --> pdb=" O ASP A 173 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N TRP A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N TRP A 181 " --> pdb=" O PHE A 177 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL A 182 " --> pdb=" O TRP A 178 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ALA A 200 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 5.128A 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 280 removed outlier: 3.729A pdb=" N GLY A 271 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N TYR A 272 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N SER A 273 " --> pdb=" O PHE A 269 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ASP A 274 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ALA A 275 " --> pdb=" O GLY A 271 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLY A 276 " --> pdb=" O TYR A 272 " (cutoff:3.500A) removed outlier: 3.665A 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 293 Processing helix chain 'A' and resid 295 through 311 Processing helix chain 'A' and resid 313 through 329 removed outlier: 3.549A pdb=" N ILE A 317 " --> pdb=" O LEU A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 341 Processing helix chain 'A' and resid 347 through 360 Proline residue: A 351 - end of helix removed outlier: 4.623A 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 382 through 388 Processing helix chain 'A' and resid 392 through 413 removed outlier: 4.278A 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: 3.610A pdb=" N SER A 449 " --> pdb=" O GLY A 445 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE A 450 " --> pdb=" O ALA A 446 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N SER A 451 " --> pdb=" O SER A 447 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU A 452 " --> pdb=" O SER A 448 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N MET A 480 " --> pdb=" O TRP A 476 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N PHE A 481 " --> pdb=" O LEU A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 495 removed outlier: 3.621A 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: 4.101A pdb=" N PHE A 511 " --> pdb=" O TRP A 507 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N MET A 512 " --> pdb=" O GLN A 508 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS A 515 " --> pdb=" O PHE A 511 " (cutoff:3.500A) removed outlier: 3.638A 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: 4.018A pdb=" N GLY A 576 " --> pdb=" O PHE A 572 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE A 577 " --> pdb=" O GLY A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 595 removed outlier: 5.077A pdb=" N ARG A 591 " --> pdb=" O SER A 588 " (cutoff:3.500A) removed outlier: 3.768A 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 'B' and resid 91 through 102 Processing helix chain 'B' and resid 104 through 129 removed outlier: 3.577A pdb=" N ILE B 110 " --> pdb=" O THR B 106 " (cutoff:3.500A) 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: 4.796A pdb=" N PHE B 177 " --> pdb=" O ASP B 173 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N TRP B 178 " --> pdb=" O SER B 174 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N TRP B 181 " --> pdb=" O PHE B 177 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL B 182 " --> pdb=" O TRP B 178 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ALA B 200 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 5.127A 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 280 removed outlier: 3.729A pdb=" N GLY B 271 " --> pdb=" O GLN B 267 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N TYR B 272 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N SER B 273 " --> pdb=" O PHE B 269 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ASP B 274 " --> pdb=" O LEU B 270 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ALA B 275 " --> pdb=" O GLY B 271 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLY B 276 " --> pdb=" O TYR B 272 " (cutoff:3.500A) removed outlier: 3.664A 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 293 Processing helix chain 'B' and resid 295 through 311 Processing helix chain 'B' and resid 313 through 329 removed outlier: 3.548A pdb=" N ILE B 317 " --> pdb=" O LEU B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 341 Processing helix chain 'B' and resid 347 through 360 Proline residue: B 351 - end of helix removed outlier: 4.623A 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 382 through 388 Processing helix chain 'B' and resid 392 through 413 removed outlier: 4.278A 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: 3.610A pdb=" N SER B 449 " --> pdb=" O GLY B 445 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE B 450 " --> pdb=" O ALA B 446 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N SER B 451 " --> pdb=" O SER B 447 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU B 452 " --> pdb=" O SER B 448 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N MET B 480 " --> pdb=" O TRP B 476 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N PHE B 481 " --> pdb=" O LEU B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 495 removed outlier: 3.622A 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: 4.101A pdb=" N PHE B 511 " --> pdb=" O TRP B 507 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N MET B 512 " --> pdb=" O GLN B 508 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS B 515 " --> pdb=" O PHE B 511 " (cutoff:3.500A) removed outlier: 3.638A 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: 4.017A pdb=" N GLY B 576 " --> pdb=" O PHE B 572 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE B 577 " --> pdb=" O GLY B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 595 removed outlier: 5.077A pdb=" N ARG B 591 " --> pdb=" O SER B 588 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR B 594 " --> pdb=" O ARG B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 618 Processing helix chain 'C' and resid 91 through 102 Processing helix chain 'C' and resid 104 through 129 removed outlier: 3.577A pdb=" N ILE C 110 " --> pdb=" O THR C 106 " (cutoff:3.500A) 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: 4.796A pdb=" N PHE C 177 " --> pdb=" O ASP C 173 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N TRP C 178 " --> pdb=" O SER C 174 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N TRP C 181 " --> pdb=" O PHE C 177 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL C 182 " --> pdb=" O TRP C 178 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ALA C 200 " --> pdb=" O VAL C 196 " (cutoff:3.500A) removed outlier: 5.128A 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 280 removed outlier: 3.729A pdb=" N GLY C 271 " --> pdb=" O GLN C 267 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N TYR C 272 " --> pdb=" O THR C 268 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N SER C 273 " --> pdb=" O PHE C 269 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ASP C 274 " --> pdb=" O LEU C 270 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ALA C 275 " --> pdb=" O GLY C 271 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLY C 276 " --> pdb=" O TYR C 272 " (cutoff:3.500A) removed outlier: 3.665A 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 293 Processing helix chain 'C' and resid 295 through 311 Processing helix chain 'C' and resid 313 through 329 removed outlier: 3.549A pdb=" N ILE C 317 " --> pdb=" O LEU C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 341 Processing helix chain 'C' and resid 347 through 360 Proline residue: C 351 - end of helix removed outlier: 4.622A 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 374 Processing helix chain 'C' and resid 382 through 388 Processing helix chain 'C' and resid 392 through 413 removed outlier: 4.279A 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: 3.610A pdb=" N SER C 449 " --> pdb=" O GLY C 445 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ILE C 450 " --> pdb=" O ALA C 446 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N SER C 451 " --> pdb=" O SER C 447 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU C 452 " --> pdb=" O SER C 448 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N MET C 480 " --> pdb=" O TRP C 476 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N PHE C 481 " --> pdb=" O LEU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 495 removed outlier: 3.621A 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: 4.101A pdb=" N PHE C 511 " --> pdb=" O TRP C 507 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N MET C 512 " --> pdb=" O GLN C 508 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS C 515 " --> pdb=" O PHE C 511 " (cutoff:3.500A) removed outlier: 3.638A 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: 4.017A pdb=" N GLY C 576 " --> pdb=" O PHE C 572 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE C 577 " --> pdb=" O GLY C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 595 removed outlier: 5.077A pdb=" N ARG C 591 " --> pdb=" O SER C 588 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR C 594 " --> pdb=" O ARG C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 597 through 618 837 hydrogen bonds defined for protein. 2475 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: 9.36 Time building geometry restraints manager: 21.55 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: 45 1.22 - 1.42: 5418 1.42 - 1.61: 7377 1.61 - 1.81: 183 Bond restraints: 25170 Sorted by residual: bond pdb=" C15 U56 C 801 " pdb=" C17 U56 C 801 " ideal model delta sigma weight residual 1.542 1.249 0.293 2.00e-02 2.50e+03 2.15e+02 bond pdb=" C15 U56 B 801 " pdb=" C17 U56 B 801 " ideal model delta sigma weight residual 1.542 1.249 0.293 2.00e-02 2.50e+03 2.14e+02 bond pdb=" C15 U56 A 801 " pdb=" C17 U56 A 801 " ideal model delta sigma weight residual 1.542 1.250 0.292 2.00e-02 2.50e+03 2.14e+02 bond pdb=" C12 U56 A 801 " pdb=" C15 U56 A 801 " ideal model delta sigma weight residual 1.352 1.566 -0.214 2.00e-02 2.50e+03 1.14e+02 bond pdb=" C12 U56 C 801 " pdb=" C15 U56 C 801 " ideal model delta sigma weight residual 1.352 1.566 -0.214 2.00e-02 2.50e+03 1.14e+02 ... (remaining 25165 not shown) Histogram of bond angle deviations from ideal: 100.04 - 106.84: 414 106.84 - 113.63: 28951 113.63 - 120.43: 8862 120.43 - 127.22: 6758 127.22 - 134.02: 165 Bond angle restraints: 45150 Sorted by residual: angle pdb=" O1 LBN B 803 " pdb=" P1 LBN B 803 " pdb=" O2 LBN B 803 " ideal model delta sigma weight residual 93.45 110.01 -16.56 3.00e+00 1.11e-01 3.05e+01 angle pdb=" O1 LBN C 803 " pdb=" P1 LBN C 803 " pdb=" O2 LBN C 803 " ideal model delta sigma weight residual 93.45 110.00 -16.55 3.00e+00 1.11e-01 3.04e+01 angle pdb=" O1 LBN A 803 " pdb=" P1 LBN A 803 " pdb=" O2 LBN A 803 " ideal model delta sigma weight residual 93.45 109.98 -16.53 3.00e+00 1.11e-01 3.04e+01 angle pdb=" O1 LBN B 806 " pdb=" P1 LBN B 806 " pdb=" O2 LBN B 806 " ideal model delta sigma weight residual 93.45 109.57 -16.12 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 93.45 109.55 -16.10 3.00e+00 1.11e-01 2.88e+01 ... (remaining 45145 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.45: 11617 34.45 - 68.89: 416 68.89 - 103.34: 15 103.34 - 137.78: 3 137.78 - 172.23: 9 Dihedral angle restraints: 12060 sinusoidal: 6330 harmonic: 5730 Sorted by residual: dihedral pdb=" O5 LBN C 804 " pdb=" C2 LBN C 804 " pdb=" C3 LBN C 804 " pdb=" O7 LBN C 804 " ideal model delta sinusoidal sigma weight residual 62.67 -125.10 -172.23 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" O5 LBN B 804 " pdb=" C2 LBN B 804 " pdb=" C3 LBN B 804 " pdb=" O7 LBN B 804 " ideal model delta sinusoidal sigma weight residual 62.67 -125.11 -172.22 1 3.00e+01 1.11e-03 2.12e+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 -125.17 -172.16 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 12057 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1595 0.043 - 0.086: 318 0.086 - 0.130: 79 0.130 - 0.173: 7 0.173 - 0.216: 8 Chirality restraints: 2007 Sorted by residual: chirality pdb=" C17 U56 B 801 " pdb=" C10 U56 B 801 " pdb=" C15 U56 B 801 " pdb=" O18 U56 B 801 " both_signs ideal model delta sigma weight residual False -2.58 -2.37 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" C17 U56 C 801 " pdb=" C10 U56 C 801 " pdb=" C15 U56 C 801 " pdb=" O18 U56 C 801 " both_signs ideal model delta sigma weight residual False -2.58 -2.37 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" C17 U56 A 801 " pdb=" C10 U56 A 801 " pdb=" C15 U56 A 801 " pdb=" O18 U56 A 801 " both_signs ideal model delta sigma weight residual False -2.58 -2.37 -0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 2004 not shown) Planarity restraints: 3660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 195 " -0.008 2.00e-02 2.50e+03 1.60e-02 2.55e+00 pdb=" C LEU A 195 " 0.028 2.00e-02 2.50e+03 pdb=" O LEU A 195 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL A 196 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 195 " 0.008 2.00e-02 2.50e+03 1.59e-02 2.54e+00 pdb=" C LEU C 195 " -0.028 2.00e-02 2.50e+03 pdb=" O LEU C 195 " 0.010 2.00e-02 2.50e+03 pdb=" N VAL C 196 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 195 " -0.008 2.00e-02 2.50e+03 1.59e-02 2.52e+00 pdb=" C LEU B 195 " 0.027 2.00e-02 2.50e+03 pdb=" O LEU B 195 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL B 196 " -0.009 2.00e-02 2.50e+03 ... (remaining 3657 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 1251 2.21 - 2.81: 50009 2.81 - 3.41: 67215 3.41 - 4.00: 88158 4.00 - 4.60: 139810 Nonbonded interactions: 346443 Sorted by model distance: nonbonded pdb="HH21 ARG A 436 " pdb=" OE2 GLU A 440 " model vdw 1.615 1.850 nonbonded pdb="HH21 ARG C 436 " pdb=" OE2 GLU C 440 " model vdw 1.615 1.850 nonbonded pdb="HH21 ARG B 436 " pdb=" OE2 GLU B 440 " model vdw 1.616 1.850 nonbonded pdb=" O LEU B 248 " pdb=" HG1 THR B 252 " model vdw 1.647 1.850 nonbonded pdb=" O LEU A 248 " pdb=" HG1 THR A 252 " model vdw 1.647 1.850 ... (remaining 346438 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: 1.200 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: 0.300 Extract box with map and model: 4.770 Check model and map are aligned: 0.380 Set scattering table: 0.250 Process input model: 81.630 Find NCS groups from input model: 1.280 Set up NCS constraints: 0.120 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:12.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 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 0.293 13005 Z= 0.613 Angle : 0.836 16.562 17628 Z= 0.335 Chirality : 0.038 0.216 2007 Planarity : 0.003 0.036 2118 Dihedral : 16.172 172.227 4566 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.24 % Allowed : 2.38 % Favored : 97.39 % 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: 2.53 (0.21), residues: 1593 helix: 2.18 (0.14), residues: 1311 sheet: None (None), residues: 0 loop : -0.78 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 414 HIS 0.001 0.000 HIS B 394 PHE 0.011 0.001 PHE B 413 TYR 0.006 0.001 TYR B 285 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 235 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 232 time to evaluate : 1.510 Fit side-chains revert: symmetry clash REVERT: A 429 LYS cc_start: 0.7730 (ptpt) cc_final: 0.7135 (ptmm) REVERT: A 502 MET cc_start: 0.7747 (mtm) cc_final: 0.7396 (mmp) REVERT: B 229 LYS cc_start: 0.7870 (mmtt) cc_final: 0.7436 (mmmt) REVERT: B 313 LEU cc_start: 0.8498 (mt) cc_final: 0.8187 (mp) REVERT: B 429 LYS cc_start: 0.7483 (ptpt) cc_final: 0.6874 (ptmm) REVERT: B 444 GLN cc_start: 0.7612 (mt0) cc_final: 0.7262 (tm-30) REVERT: B 502 MET cc_start: 0.7579 (mtm) cc_final: 0.7201 (mmp) REVERT: B 508 GLN cc_start: 0.7724 (mt0) cc_final: 0.7271 (mm110) REVERT: C 229 LYS cc_start: 0.7381 (mmtt) cc_final: 0.7019 (mmtt) REVERT: C 313 LEU cc_start: 0.8663 (mt) cc_final: 0.8375 (mt) REVERT: C 429 LYS cc_start: 0.7596 (ptpt) cc_final: 0.7140 (ptmm) REVERT: C 444 GLN cc_start: 0.7269 (mt0) cc_final: 0.7022 (tm-30) REVERT: C 502 MET cc_start: 0.7615 (mtm) cc_final: 0.7331 (mmp) outliers start: 3 outliers final: 0 residues processed: 235 average time/residue: 1.9577 time to fit residues: 516.7828 Evaluate side-chains 172 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 1.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 144 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN A 571 ASN B 265 GLN B 471 ASN B 479 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13005 Z= 0.181 Angle : 0.473 4.911 17628 Z= 0.244 Chirality : 0.037 0.121 2007 Planarity : 0.004 0.054 2118 Dihedral : 16.579 178.844 2016 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 0.95 % Allowed : 7.84 % Favored : 91.21 % 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: 2.77 (0.21), residues: 1593 helix: 2.34 (0.15), residues: 1293 sheet: None (None), residues: 0 loop : -0.48 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 316 HIS 0.003 0.001 HIS A 288 PHE 0.018 0.001 PHE B 413 TYR 0.007 0.001 TYR B 357 ARG 0.003 0.000 ARG C 108 *********************** 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 190 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 178 time to evaluate : 1.821 Fit side-chains REVERT: A 129 MET cc_start: 0.7410 (mtp) cc_final: 0.7179 (mtt) REVERT: A 229 LYS cc_start: 0.7994 (mmtt) cc_final: 0.7436 (mmtt) REVERT: A 429 LYS cc_start: 0.7621 (ptpt) cc_final: 0.6959 (ptmm) REVERT: A 502 MET cc_start: 0.7653 (mtm) cc_final: 0.7334 (mmp) REVERT: B 229 LYS cc_start: 0.7946 (mmtt) cc_final: 0.7581 (mmtp) REVERT: B 283 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7533 (mm-30) REVERT: B 305 MET cc_start: 0.8774 (mmp) cc_final: 0.8156 (mmt) REVERT: B 313 LEU cc_start: 0.8831 (mt) cc_final: 0.8513 (mp) REVERT: B 429 LYS cc_start: 0.7476 (ptpt) cc_final: 0.7100 (ptmm) REVERT: B 485 GLN cc_start: 0.8552 (mp10) cc_final: 0.8117 (mp10) REVERT: B 502 MET cc_start: 0.7636 (mtm) cc_final: 0.7318 (mmp) REVERT: B 508 GLN cc_start: 0.7878 (mt0) cc_final: 0.7471 (mm110) REVERT: C 229 LYS cc_start: 0.7692 (mmtt) cc_final: 0.7325 (mmtt) REVERT: C 313 LEU cc_start: 0.8873 (mt) cc_final: 0.8490 (mt) REVERT: C 502 MET cc_start: 0.7885 (mtm) cc_final: 0.7538 (mmp) REVERT: C 585 MET cc_start: 0.7748 (mtm) cc_final: 0.7524 (mtm) REVERT: C 601 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.7061 (tt) outliers start: 12 outliers final: 5 residues processed: 186 average time/residue: 1.9595 time to fit residues: 410.3990 Evaluate side-chains 172 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 166 time to evaluate : 1.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 340 SER Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 601 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 156 optimal weight: 0.5980 chunk 128 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 571 ASN C 571 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13005 Z= 0.216 Angle : 0.463 5.083 17628 Z= 0.244 Chirality : 0.037 0.126 2007 Planarity : 0.004 0.053 2118 Dihedral : 15.917 179.886 2016 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.27 % Allowed : 8.16 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.64 (0.21), residues: 1593 helix: 2.25 (0.15), residues: 1302 sheet: None (None), residues: 0 loop : -0.59 (0.36), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 316 HIS 0.004 0.001 HIS B 288 PHE 0.017 0.001 PHE A 413 TYR 0.008 0.001 TYR C 285 ARG 0.002 0.000 ARG A 251 *********************** 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 193 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 177 time to evaluate : 1.575 Fit side-chains REVERT: A 229 LYS cc_start: 0.8062 (mmtt) cc_final: 0.7451 (mmtt) REVERT: A 365 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7649 (mt-10) REVERT: A 416 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.6867 (tp30) REVERT: A 429 LYS cc_start: 0.7628 (ptpt) cc_final: 0.7011 (ptmm) REVERT: A 502 MET cc_start: 0.7584 (mtm) cc_final: 0.7259 (mmp) REVERT: B 229 LYS cc_start: 0.8021 (mmtt) cc_final: 0.7628 (mmtt) REVERT: B 305 MET cc_start: 0.8799 (mmp) cc_final: 0.8106 (mmt) REVERT: B 313 LEU cc_start: 0.8994 (mt) cc_final: 0.8659 (mp) REVERT: B 485 GLN cc_start: 0.8550 (mp10) cc_final: 0.8135 (mp10) REVERT: B 502 MET cc_start: 0.7718 (mtm) cc_final: 0.7359 (mmp) REVERT: B 508 GLN cc_start: 0.7981 (mt0) cc_final: 0.7573 (mm110) REVERT: C 229 LYS cc_start: 0.7973 (mmtt) cc_final: 0.7497 (mmtt) REVERT: C 313 LEU cc_start: 0.8941 (mt) cc_final: 0.8639 (mt) REVERT: C 477 LEU cc_start: 0.7978 (tp) cc_final: 0.7716 (tp) outliers start: 16 outliers final: 6 residues processed: 189 average time/residue: 2.0512 time to fit residues: 434.5249 Evaluate side-chains 173 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 166 time to evaluate : 2.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain B residue 584 SER Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 340 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 142 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 620 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13005 Z= 0.238 Angle : 0.479 5.674 17628 Z= 0.252 Chirality : 0.037 0.125 2007 Planarity : 0.004 0.056 2118 Dihedral : 15.772 179.664 2016 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.50 % Allowed : 8.95 % Favored : 89.55 % 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: 2.53 (0.21), residues: 1593 helix: 2.19 (0.15), residues: 1302 sheet: None (None), residues: 0 loop : -0.68 (0.35), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 316 HIS 0.005 0.001 HIS B 288 PHE 0.016 0.001 PHE A 488 TYR 0.007 0.001 TYR C 285 ARG 0.002 0.000 ARG A 251 *********************** 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 192 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 173 time to evaluate : 1.993 Fit side-chains REVERT: A 229 LYS cc_start: 0.8194 (mmtt) cc_final: 0.7719 (mmtt) REVERT: A 365 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7632 (mt-10) REVERT: A 429 LYS cc_start: 0.7634 (ptpt) cc_final: 0.7004 (ptmm) REVERT: A 502 MET cc_start: 0.7637 (mtm) cc_final: 0.7304 (mmp) REVERT: B 229 LYS cc_start: 0.8045 (mmtt) cc_final: 0.7615 (mmmt) REVERT: B 283 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7629 (mm-30) REVERT: B 305 MET cc_start: 0.8806 (mmp) cc_final: 0.8082 (mmt) REVERT: B 313 LEU cc_start: 0.9008 (mt) cc_final: 0.8749 (mt) REVERT: B 485 GLN cc_start: 0.8577 (mp10) cc_final: 0.8157 (mp10) REVERT: B 502 MET cc_start: 0.7701 (mtm) cc_final: 0.7365 (mmp) REVERT: B 508 GLN cc_start: 0.8143 (mt0) cc_final: 0.7652 (mm110) REVERT: C 229 LYS cc_start: 0.8020 (mmtt) cc_final: 0.7544 (mmtt) REVERT: C 313 LEU cc_start: 0.8956 (mt) cc_final: 0.8642 (mt) outliers start: 19 outliers final: 10 residues processed: 185 average time/residue: 2.0824 time to fit residues: 431.6855 Evaluate side-chains 182 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 172 time to evaluate : 2.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 584 SER Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 340 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 87 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 114 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 106 optimal weight: 30.0000 chunk 0 optimal weight: 40.0000 chunk 78 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 620 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 13005 Z= 0.413 Angle : 0.603 6.967 17628 Z= 0.320 Chirality : 0.042 0.142 2007 Planarity : 0.006 0.062 2118 Dihedral : 16.276 175.074 2016 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.90 % Allowed : 9.03 % 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: 1.63 (0.21), residues: 1593 helix: 1.58 (0.14), residues: 1305 sheet: None (None), residues: 0 loop : -1.12 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 194 HIS 0.005 0.002 HIS B 175 PHE 0.023 0.002 PHE A 413 TYR 0.011 0.002 TYR B 494 ARG 0.004 0.001 ARG A 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 197 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 173 time to evaluate : 2.069 Fit side-chains REVERT: A 229 LYS cc_start: 0.8139 (mmtt) cc_final: 0.7722 (mmtt) REVERT: A 365 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7633 (mt-10) REVERT: A 440 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6956 (tt0) REVERT: A 444 GLN cc_start: 0.7933 (mt0) cc_final: 0.7498 (mt0) REVERT: A 502 MET cc_start: 0.7617 (mtm) cc_final: 0.7267 (mmp) REVERT: A 592 ASP cc_start: 0.7537 (m-30) cc_final: 0.7328 (m-30) REVERT: B 229 LYS cc_start: 0.8196 (mmtt) cc_final: 0.7785 (mmmt) REVERT: B 283 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7641 (mm-30) REVERT: B 305 MET cc_start: 0.8855 (mmp) cc_final: 0.8162 (mmt) REVERT: B 313 LEU cc_start: 0.9017 (mt) cc_final: 0.8734 (mt) REVERT: B 485 GLN cc_start: 0.8639 (mp10) cc_final: 0.8218 (mp10) REVERT: B 502 MET cc_start: 0.7645 (mtm) cc_final: 0.7337 (mmp) REVERT: B 508 GLN cc_start: 0.8187 (mt0) cc_final: 0.7695 (mm110) REVERT: C 229 LYS cc_start: 0.8187 (mmtt) cc_final: 0.7761 (mmtt) REVERT: C 313 LEU cc_start: 0.8962 (mt) cc_final: 0.8618 (mt) outliers start: 24 outliers final: 12 residues processed: 190 average time/residue: 2.0048 time to fit residues: 428.3155 Evaluate side-chains 176 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 163 time to evaluate : 2.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 440 GLU Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 584 SER Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 340 SER Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 447 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 138 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 620 ASN B 204 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13005 Z= 0.193 Angle : 0.454 5.121 17628 Z= 0.238 Chirality : 0.036 0.123 2007 Planarity : 0.004 0.053 2118 Dihedral : 15.038 178.472 2016 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.35 % Allowed : 10.21 % Favored : 88.44 % 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: 2.31 (0.21), residues: 1593 helix: 2.08 (0.15), residues: 1296 sheet: None (None), residues: 0 loop : -0.99 (0.34), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 194 HIS 0.003 0.001 HIS C 288 PHE 0.014 0.001 PHE C 279 TYR 0.006 0.001 TYR C 553 ARG 0.002 0.000 ARG A 557 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 186 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 169 time to evaluate : 2.000 Fit side-chains REVERT: A 229 LYS cc_start: 0.8172 (mmtt) cc_final: 0.7735 (mmtt) REVERT: A 365 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7584 (mt-10) REVERT: A 502 MET cc_start: 0.7623 (mtm) cc_final: 0.7293 (mmp) REVERT: A 592 ASP cc_start: 0.7481 (m-30) cc_final: 0.7260 (m-30) REVERT: B 229 LYS cc_start: 0.8096 (mmtt) cc_final: 0.7657 (mmmt) REVERT: B 283 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7628 (mm-30) REVERT: B 305 MET cc_start: 0.8838 (mmp) cc_final: 0.8092 (mmt) REVERT: B 313 LEU cc_start: 0.8987 (mt) cc_final: 0.8722 (mt) REVERT: B 365 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7943 (mt-10) REVERT: B 502 MET cc_start: 0.7596 (mtm) cc_final: 0.7289 (mmp) REVERT: B 508 GLN cc_start: 0.8132 (mt0) cc_final: 0.7636 (mm110) REVERT: C 229 LYS cc_start: 0.8150 (mmtt) cc_final: 0.7703 (mmtt) REVERT: C 313 LEU cc_start: 0.8949 (mt) cc_final: 0.8576 (mt) REVERT: C 428 MET cc_start: 0.7775 (mmp) cc_final: 0.7544 (mmp) outliers start: 17 outliers final: 10 residues processed: 183 average time/residue: 1.9731 time to fit residues: 406.9989 Evaluate side-chains 176 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 166 time to evaluate : 1.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 584 SER Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 340 SER Chi-restraints excluded: chain C residue 447 SER 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: 5.9990 chunk 129 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 153 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 620 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13005 Z= 0.196 Angle : 0.452 5.299 17628 Z= 0.237 Chirality : 0.036 0.122 2007 Planarity : 0.004 0.055 2118 Dihedral : 14.615 178.578 2016 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.35 % Allowed : 10.61 % 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: 2.51 (0.22), residues: 1593 helix: 2.23 (0.15), residues: 1296 sheet: None (None), residues: 0 loop : -0.94 (0.34), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 323 HIS 0.004 0.001 HIS B 288 PHE 0.014 0.001 PHE C 279 TYR 0.006 0.001 TYR C 553 ARG 0.001 0.000 ARG A 557 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 187 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 170 time to evaluate : 1.815 Fit side-chains REVERT: A 229 LYS cc_start: 0.8236 (mmtt) cc_final: 0.7776 (mmtt) REVERT: A 365 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7580 (mt-10) REVERT: A 502 MET cc_start: 0.7577 (mtm) cc_final: 0.7240 (mmp) REVERT: A 592 ASP cc_start: 0.7494 (m-30) cc_final: 0.7271 (m-30) REVERT: B 229 LYS cc_start: 0.8171 (mmtt) cc_final: 0.7821 (mmtp) REVERT: B 305 MET cc_start: 0.8863 (mmp) cc_final: 0.8094 (mmt) REVERT: B 313 LEU cc_start: 0.9003 (mt) cc_final: 0.8764 (mt) REVERT: B 365 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7946 (mt-10) REVERT: B 502 MET cc_start: 0.7589 (mtm) cc_final: 0.7285 (mmp) REVERT: B 508 GLN cc_start: 0.8082 (mt0) cc_final: 0.7574 (mm-40) REVERT: C 229 LYS cc_start: 0.8197 (mmtt) cc_final: 0.7766 (mmtt) REVERT: C 313 LEU cc_start: 0.8971 (mt) cc_final: 0.8596 (mt) outliers start: 17 outliers final: 9 residues processed: 183 average time/residue: 2.1058 time to fit residues: 433.2177 Evaluate side-chains 176 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 167 time to evaluate : 2.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 584 SER Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 340 SER Chi-restraints excluded: chain C residue 447 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 91 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 139 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 620 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13005 Z= 0.265 Angle : 0.496 5.926 17628 Z= 0.261 Chirality : 0.038 0.126 2007 Planarity : 0.005 0.057 2118 Dihedral : 14.744 176.041 2016 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.35 % Allowed : 10.69 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.21), residues: 1593 helix: 2.05 (0.15), residues: 1305 sheet: None (None), residues: 0 loop : -1.04 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 261 HIS 0.004 0.001 HIS C 288 PHE 0.016 0.002 PHE A 488 TYR 0.008 0.001 TYR B 494 ARG 0.002 0.000 ARG C 233 *********************** 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 184 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 167 time to evaluate : 1.768 Fit side-chains REVERT: A 229 LYS cc_start: 0.8268 (mmtt) cc_final: 0.7850 (mmtt) REVERT: A 365 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7539 (mt-10) REVERT: A 502 MET cc_start: 0.7610 (mtm) cc_final: 0.7287 (mmp) REVERT: A 592 ASP cc_start: 0.7491 (m-30) cc_final: 0.7277 (m-30) REVERT: B 229 LYS cc_start: 0.8200 (mmtt) cc_final: 0.7853 (mmtp) REVERT: B 283 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7699 (mm-30) REVERT: B 305 MET cc_start: 0.8872 (mmp) cc_final: 0.8172 (mmt) REVERT: B 313 LEU cc_start: 0.9016 (mt) cc_final: 0.8755 (mt) REVERT: B 314 MET cc_start: 0.8352 (OUTLIER) cc_final: 0.8112 (mtp) REVERT: B 365 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7960 (mt-10) REVERT: B 502 MET cc_start: 0.7705 (mtm) cc_final: 0.7361 (mmp) REVERT: B 508 GLN cc_start: 0.8158 (mt0) cc_final: 0.7626 (mm-40) REVERT: C 229 LYS cc_start: 0.8193 (mmtt) cc_final: 0.7752 (mmtt) REVERT: C 313 LEU cc_start: 0.8969 (mt) cc_final: 0.8578 (mt) outliers start: 17 outliers final: 9 residues processed: 180 average time/residue: 2.1094 time to fit residues: 429.1335 Evaluate side-chains 177 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 167 time to evaluate : 2.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 584 SER Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 541 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 133 optimal weight: 0.6980 chunk 142 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 620 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13005 Z= 0.195 Angle : 0.447 5.109 17628 Z= 0.234 Chirality : 0.036 0.123 2007 Planarity : 0.004 0.054 2118 Dihedral : 14.411 179.509 2016 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.79 % Allowed : 11.40 % 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: 2.60 (0.22), residues: 1593 helix: 2.27 (0.15), residues: 1302 sheet: None (None), residues: 0 loop : -0.86 (0.35), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 261 HIS 0.003 0.001 HIS B 288 PHE 0.014 0.001 PHE C 279 TYR 0.006 0.001 TYR C 553 ARG 0.002 0.000 ARG A 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 177 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 167 time to evaluate : 1.830 Fit side-chains REVERT: A 229 LYS cc_start: 0.8269 (mmtt) cc_final: 0.7839 (mmtt) REVERT: A 365 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7587 (mt-10) REVERT: A 592 ASP cc_start: 0.7497 (m-30) cc_final: 0.7279 (m-30) REVERT: B 229 LYS cc_start: 0.8154 (mmtt) cc_final: 0.7817 (mmtp) REVERT: B 283 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7676 (mm-30) REVERT: B 305 MET cc_start: 0.8858 (mmp) cc_final: 0.8127 (mmt) REVERT: B 313 LEU cc_start: 0.9028 (mt) cc_final: 0.8786 (mt) REVERT: B 314 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.8095 (mtp) REVERT: B 502 MET cc_start: 0.7604 (mtm) cc_final: 0.7303 (mmp) REVERT: B 508 GLN cc_start: 0.8077 (mt0) cc_final: 0.7564 (mm-40) REVERT: C 229 LYS cc_start: 0.8182 (mmtt) cc_final: 0.7756 (mmtt) REVERT: C 313 LEU cc_start: 0.8958 (mt) cc_final: 0.8574 (mt) outliers start: 10 outliers final: 7 residues processed: 175 average time/residue: 2.0486 time to fit residues: 401.9912 Evaluate side-chains 173 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 165 time to evaluate : 1.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 584 SER Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 447 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 92 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 158 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 620 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13005 Z= 0.184 Angle : 0.444 5.159 17628 Z= 0.232 Chirality : 0.036 0.120 2007 Planarity : 0.004 0.054 2118 Dihedral : 14.266 179.857 2016 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.87 % Allowed : 11.56 % Favored : 87.57 % 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: 2.71 (0.22), residues: 1593 helix: 2.34 (0.15), residues: 1302 sheet: None (None), residues: 0 loop : -0.82 (0.35), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 323 HIS 0.003 0.001 HIS B 288 PHE 0.014 0.001 PHE C 279 TYR 0.006 0.001 TYR C 553 ARG 0.002 0.000 ARG C 436 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 176 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 165 time to evaluate : 1.771 Fit side-chains REVERT: A 229 LYS cc_start: 0.8262 (mmtt) cc_final: 0.7815 (mmtp) REVERT: A 365 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7572 (mt-10) REVERT: A 592 ASP cc_start: 0.7492 (m-30) cc_final: 0.7259 (m-30) REVERT: B 229 LYS cc_start: 0.8033 (mmtt) cc_final: 0.7669 (mmtp) REVERT: B 283 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7673 (mm-30) REVERT: B 305 MET cc_start: 0.8857 (mmp) cc_final: 0.8112 (mmt) REVERT: B 313 LEU cc_start: 0.9036 (mt) cc_final: 0.8793 (mt) REVERT: B 314 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.8103 (mtp) REVERT: B 502 MET cc_start: 0.7592 (mtm) cc_final: 0.7297 (mmp) REVERT: B 508 GLN cc_start: 0.8067 (mt0) cc_final: 0.7552 (mm-40) REVERT: C 229 LYS cc_start: 0.8150 (mmtt) cc_final: 0.7739 (mmtt) REVERT: C 313 LEU cc_start: 0.8963 (mt) cc_final: 0.8586 (mt) outliers start: 11 outliers final: 8 residues processed: 173 average time/residue: 2.0356 time to fit residues: 394.5353 Evaluate side-chains 173 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 164 time to evaluate : 2.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 584 SER Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 447 SER 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: 4.9990 chunk 18 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 126 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 620 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.147529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.105259 restraints weight = 35030.383| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 1.18 r_work: 0.2972 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13005 Z= 0.248 Angle : 0.485 5.624 17628 Z= 0.254 Chirality : 0.037 0.125 2007 Planarity : 0.004 0.057 2118 Dihedral : 14.476 177.533 2016 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.71 % Allowed : 11.80 % 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: 2.44 (0.21), residues: 1593 helix: 2.17 (0.15), residues: 1302 sheet: None (None), residues: 0 loop : -0.96 (0.34), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 261 HIS 0.004 0.001 HIS B 288 PHE 0.015 0.001 PHE A 488 TYR 0.007 0.001 TYR B 494 ARG 0.002 0.000 ARG A 599 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7941.62 seconds wall clock time: 141 minutes 29.97 seconds (8489.97 seconds total)