Starting phenix.real_space_refine on Fri Apr 12 00:46:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tza_41739/04_2024/8tza_41739_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tza_41739/04_2024/8tza_41739.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tza_41739/04_2024/8tza_41739_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tza_41739/04_2024/8tza_41739_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tza_41739/04_2024/8tza_41739_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tza_41739/04_2024/8tza_41739.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tza_41739/04_2024/8tza_41739.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tza_41739/04_2024/8tza_41739_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tza_41739/04_2024/8tza_41739_trim_updated.pdb" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.061 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 87 5.16 5 C 8103 2.51 5 N 1923 2.21 5 O 2115 1.98 5 H 12069 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 564": "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: 24297 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 8076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8076 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 18, 'TRANS': 514} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 77 Chain: "A" Number of atoms: 8076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8076 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 18, 'TRANS': 514} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 77 Chain: "C" Number of atoms: 8076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8076 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 18, 'TRANS': 514} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 77 Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'XMO': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'XMO': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'XMO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.55, per 1000 atoms: 0.48 Number of scatterers: 24297 At special positions: 0 Unit cell: (128.52, 126.36, 76.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 87 16.00 O 2115 8.00 N 1923 7.00 C 8103 6.00 H 12069 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: 20.07 Conformation dependent library (CDL) restraints added in 2.6 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: 80 helices and 0 sheets defined 80.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.66 Creating SS restraints... Processing helix chain 'B' and resid 91 through 102 Processing helix chain 'B' and resid 104 through 129 Processing helix chain 'B' and resid 133 through 156 Proline residue: B 136 - end of helix Processing helix chain 'B' and resid 158 through 174 Proline residue: B 167 - end of helix Processing helix chain 'B' and resid 176 through 202 removed outlier: 4.718A pdb=" N TRP B 181 " --> pdb=" O PHE B 177 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL B 182 " --> pdb=" O TRP B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 222 removed outlier: 4.018A pdb=" N PHE B 210 " --> pdb=" O GLN B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 251 Processing helix chain 'B' and resid 253 through 281 removed outlier: 3.526A pdb=" N ALA B 258 " --> pdb=" O PRO B 254 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE B 259 " --> pdb=" O GLY B 255 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP B 260 " --> pdb=" O PHE B 256 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA B 277 " --> pdb=" O SER B 273 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER B 278 " --> pdb=" O ASP B 274 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N PHE B 279 " --> pdb=" O ALA B 275 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N VAL B 280 " --> pdb=" O GLY B 276 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE B 281 " --> pdb=" O ALA B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 287 No H-bonds generated for 'chain 'B' and resid 285 through 287' Processing helix chain 'B' and resid 289 through 311 removed outlier: 4.164A pdb=" N LEU B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) Proline residue: B 296 - end of helix Processing helix chain 'B' and resid 314 through 328 Processing helix chain 'B' and resid 333 through 343 removed outlier: 3.817A pdb=" N ILE B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 353 Proline residue: B 351 - end of helix No H-bonds generated for 'chain 'B' and resid 347 through 353' Processing helix chain 'B' and resid 355 through 360 Proline residue: B 359 - end of helix Processing helix chain 'B' and resid 363 through 374 Processing helix chain 'B' and resid 380 through 388 removed outlier: 4.305A pdb=" N ALA B 384 " --> pdb=" O SER B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 413 removed outlier: 4.064A 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: 3.783A pdb=" N SER B 449 " --> pdb=" O GLY B 445 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE B 450 " --> pdb=" O ALA B 446 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N SER B 451 " --> pdb=" O SER B 447 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LEU B 452 " --> pdb=" O SER B 448 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA B 454 " --> pdb=" O ILE B 450 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N MET B 480 " --> pdb=" O TRP B 476 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N PHE B 481 " --> pdb=" O LEU B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 495 removed outlier: 3.587A 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: 4.259A pdb=" N PHE B 511 " --> pdb=" O TRP B 507 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N MET B 512 " --> pdb=" O GLN B 508 " (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 574 through 585 Processing helix chain 'B' and resid 587 through 595 removed outlier: 4.547A pdb=" N ARG B 591 " --> pdb=" O SER B 588 " (cutoff:3.500A) removed outlier: 3.882A 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 'A' and resid 91 through 102 Processing helix chain 'A' and resid 104 through 129 Processing helix chain 'A' and resid 133 through 156 Proline residue: A 136 - end of helix Processing helix chain 'A' and resid 158 through 174 Proline residue: A 167 - end of helix Processing helix chain 'A' and resid 176 through 202 removed outlier: 4.713A pdb=" N TRP A 181 " --> pdb=" O PHE A 177 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL A 182 " --> pdb=" O TRP A 178 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS A 201 " --> pdb=" O PHE A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 222 removed outlier: 3.663A pdb=" N SER A 209 " --> pdb=" O GLN A 205 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE A 210 " --> pdb=" O GLN A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 251 Processing helix chain 'A' and resid 253 through 281 removed outlier: 3.523A pdb=" N ALA A 258 " --> pdb=" O PRO A 254 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE A 259 " --> pdb=" O GLY A 255 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER A 273 " --> pdb=" O PHE A 269 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER A 278 " --> pdb=" O ASP A 274 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N PHE A 279 " --> pdb=" O ALA A 275 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N VAL A 280 " --> pdb=" O GLY A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 287 No H-bonds generated for 'chain 'A' and resid 285 through 287' Processing helix chain 'A' and resid 289 through 311 removed outlier: 4.292A pdb=" N LEU A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) Proline residue: A 296 - end of helix Processing helix chain 'A' and resid 314 through 329 Processing helix chain 'A' and resid 333 through 343 removed outlier: 3.789A pdb=" N ILE A 343 " --> pdb=" O ALA A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 353 Proline residue: A 351 - end of helix No H-bonds generated for 'chain 'A' and resid 347 through 353' Processing helix chain 'A' and resid 355 through 360 Proline residue: A 359 - end of helix Processing helix chain 'A' and resid 363 through 374 Processing helix chain 'A' and resid 380 through 388 removed outlier: 4.223A pdb=" N ALA A 384 " --> pdb=" O SER A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 413 removed outlier: 4.170A 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: 3.613A pdb=" N SER A 449 " --> pdb=" O GLY A 445 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE A 450 " --> pdb=" O ALA A 446 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N SER A 451 " --> pdb=" O SER A 447 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU A 452 " --> pdb=" O SER A 448 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N MET A 480 " --> pdb=" O TRP A 476 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE A 481 " --> pdb=" O LEU A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 495 removed outlier: 3.566A 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: 4.290A pdb=" N PHE A 511 " --> pdb=" O TRP A 507 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N MET A 512 " --> pdb=" O GLN A 508 " (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 574 through 585 Processing helix chain 'A' and resid 590 through 595 Processing helix chain 'A' and resid 597 through 618 Processing helix chain 'C' and resid 91 through 102 Processing helix chain 'C' and resid 104 through 129 Processing helix chain 'C' and resid 133 through 156 Proline residue: C 136 - end of helix Processing helix chain 'C' and resid 158 through 174 Proline residue: C 167 - end of helix Processing helix chain 'C' and resid 176 through 202 removed outlier: 4.695A pdb=" N TRP C 181 " --> pdb=" O PHE C 177 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL C 182 " --> pdb=" O TRP C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 222 removed outlier: 3.775A pdb=" N PHE C 210 " --> pdb=" O GLN C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 251 Processing helix chain 'C' and resid 253 through 281 removed outlier: 3.681A pdb=" N PHE C 259 " --> pdb=" O GLY C 255 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER C 273 " --> pdb=" O PHE C 269 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER C 278 " --> pdb=" O ASP C 274 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N PHE C 279 " --> pdb=" O ALA C 275 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N VAL C 280 " --> pdb=" O GLY C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 287 No H-bonds generated for 'chain 'C' and resid 285 through 287' Processing helix chain 'C' and resid 289 through 311 removed outlier: 3.536A pdb=" N VAL C 294 " --> pdb=" O PHE C 290 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LEU C 295 " --> pdb=" O ALA C 291 " (cutoff:3.500A) Proline residue: C 296 - end of helix Processing helix chain 'C' and resid 314 through 328 Processing helix chain 'C' and resid 333 through 343 removed outlier: 3.819A pdb=" N ILE C 343 " --> pdb=" O ALA C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 360 Proline residue: C 351 - end of helix removed outlier: 4.712A 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 380 through 388 removed outlier: 4.299A pdb=" N ALA C 384 " --> pdb=" O SER C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 413 removed outlier: 4.137A 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: 3.713A pdb=" N SER C 449 " --> pdb=" O GLY C 445 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ILE C 450 " --> pdb=" O ALA C 446 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N SER C 451 " --> pdb=" O SER C 447 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LEU C 452 " --> pdb=" O SER C 448 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA C 454 " --> pdb=" O ILE C 450 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N MET C 480 " --> pdb=" O TRP C 476 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N PHE C 481 " --> pdb=" O LEU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 495 removed outlier: 3.577A 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: 4.284A pdb=" N PHE C 511 " --> pdb=" O TRP C 507 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N MET C 512 " --> pdb=" O GLN C 508 " (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 573 through 585 removed outlier: 3.679A pdb=" N GLY C 576 " --> pdb=" O GLY C 573 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE C 577 " --> pdb=" O SER C 574 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL C 578 " --> pdb=" O LEU C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 595 removed outlier: 4.678A pdb=" N ARG C 591 " --> pdb=" O SER C 588 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR C 594 " --> pdb=" O ARG C 591 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA C 595 " --> pdb=" O ASP C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 597 through 618 844 hydrogen bonds defined for protein. 2322 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.64 Time building geometry restraints manager: 20.90 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: 12051 1.03 - 1.23: 24 1.23 - 1.42: 5331 1.42 - 1.61: 7068 1.61 - 1.81: 159 Bond restraints: 24633 Sorted by residual: bond pdb=" C04 XMO A 801 " pdb=" O06 XMO A 801 " ideal model delta sigma weight residual 1.416 1.479 -0.063 2.00e-02 2.50e+03 9.92e+00 bond pdb=" C04 XMO C 801 " pdb=" O06 XMO C 801 " ideal model delta sigma weight residual 1.416 1.478 -0.062 2.00e-02 2.50e+03 9.54e+00 bond pdb=" C04 XMO B 801 " pdb=" O06 XMO B 801 " ideal model delta sigma weight residual 1.416 1.477 -0.061 2.00e-02 2.50e+03 9.29e+00 bond pdb=" C10 XMO C 801 " pdb=" O22 XMO C 801 " ideal model delta sigma weight residual 1.514 1.458 0.056 2.00e-02 2.50e+03 7.92e+00 bond pdb=" C10 XMO B 801 " pdb=" O22 XMO B 801 " ideal model delta sigma weight residual 1.514 1.458 0.056 2.00e-02 2.50e+03 7.75e+00 ... (remaining 24628 not shown) Histogram of bond angle deviations from ideal: 100.03 - 106.82: 411 106.82 - 113.61: 28485 113.61 - 120.41: 8719 120.41 - 127.20: 6657 127.20 - 134.00: 164 Bond angle restraints: 44436 Sorted by residual: angle pdb=" N ASP B 548 " pdb=" CA ASP B 548 " pdb=" C ASP B 548 " ideal model delta sigma weight residual 108.19 105.39 2.80 1.29e+00 6.01e-01 4.70e+00 angle pdb=" N ASP A 548 " pdb=" CA ASP A 548 " pdb=" C ASP A 548 " ideal model delta sigma weight residual 108.19 105.46 2.73 1.29e+00 6.01e-01 4.49e+00 angle pdb=" N ASP C 548 " pdb=" CA ASP C 548 " pdb=" C ASP C 548 " ideal model delta sigma weight residual 108.19 105.48 2.71 1.29e+00 6.01e-01 4.42e+00 angle pdb=" CA ASP B 548 " pdb=" C ASP B 548 " pdb=" N GLY B 549 " ideal model delta sigma weight residual 116.47 118.85 -2.38 1.19e+00 7.06e-01 4.02e+00 angle pdb=" CA ASP A 548 " pdb=" C ASP A 548 " pdb=" N GLY A 549 " ideal model delta sigma weight residual 116.47 118.77 -2.30 1.19e+00 7.06e-01 3.75e+00 ... (remaining 44431 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.09: 11099 21.09 - 42.18: 353 42.18 - 63.27: 221 63.27 - 84.35: 7 84.35 - 105.44: 2 Dihedral angle restraints: 11682 sinusoidal: 5952 harmonic: 5730 Sorted by residual: dihedral pdb=" C01 XMO A 801 " pdb=" C02 XMO A 801 " pdb=" C04 XMO A 801 " pdb=" O06 XMO A 801 " ideal model delta sinusoidal sigma weight residual 259.35 153.91 105.44 1 3.00e+01 1.11e-03 1.35e+01 dihedral pdb=" CA LYS C 293 " pdb=" C LYS C 293 " pdb=" N VAL C 294 " pdb=" CA VAL C 294 " ideal model delta harmonic sigma weight residual -180.00 -163.16 -16.84 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA LYS A 293 " pdb=" C LYS A 293 " pdb=" N VAL A 294 " pdb=" CA VAL A 294 " ideal model delta harmonic sigma weight residual -180.00 -163.34 -16.66 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 11679 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1294 0.027 - 0.053: 423 0.053 - 0.080: 182 0.080 - 0.107: 77 0.107 - 0.133: 10 Chirality restraints: 1986 Sorted by residual: chirality pdb=" CA PRO B 296 " pdb=" N PRO B 296 " pdb=" C PRO B 296 " pdb=" CB PRO B 296 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" CA PRO C 296 " pdb=" N PRO C 296 " pdb=" C PRO C 296 " pdb=" CB PRO C 296 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.06e-01 chirality pdb=" CA PRO A 296 " pdb=" N PRO A 296 " pdb=" C PRO A 296 " pdb=" CB PRO A 296 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.05e-01 ... (remaining 1983 not shown) Planarity restraints: 3624 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 295 " -0.045 5.00e-02 4.00e+02 6.79e-02 7.38e+00 pdb=" N PRO B 296 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO B 296 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 296 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 295 " 0.044 5.00e-02 4.00e+02 6.57e-02 6.90e+00 pdb=" N PRO C 296 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO C 296 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 296 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 295 " -0.043 5.00e-02 4.00e+02 6.46e-02 6.68e+00 pdb=" N PRO A 296 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 296 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 296 " -0.036 5.00e-02 4.00e+02 ... (remaining 3621 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 712 2.16 - 2.77: 45218 2.77 - 3.38: 69234 3.38 - 3.99: 84348 3.99 - 4.60: 136739 Nonbonded interactions: 336251 Sorted by model distance: nonbonded pdb=" O LEU A 195 " pdb=" HG1 THR A 199 " model vdw 1.547 1.850 nonbonded pdb=" OE1 GLU B 525 " pdb=" H GLU B 525 " model vdw 1.596 1.850 nonbonded pdb=" O LEU C 195 " pdb=" HG1 THR C 199 " model vdw 1.598 1.850 nonbonded pdb=" O LEU B 195 " pdb=" HG1 THR B 199 " model vdw 1.606 1.850 nonbonded pdb=" O HIS B 103 " pdb=" H LEU B 107 " model vdw 1.620 1.850 ... (remaining 336246 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: 0.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.380 Extract box with map and model: 4.860 Check model and map are aligned: 0.380 Set scattering table: 0.230 Process input model: 79.640 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 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 : 0.003 0.063 12564 Z= 0.211 Angle : 0.447 4.856 17118 Z= 0.249 Chirality : 0.035 0.133 1986 Planarity : 0.004 0.068 2082 Dihedral : 10.702 105.442 4212 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % 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: 4.14 (0.21), residues: 1593 helix: 3.45 (0.14), residues: 1302 sheet: None (None), residues: 0 loop : -0.97 (0.29), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 194 HIS 0.002 0.001 HIS A 288 PHE 0.011 0.001 PHE C 269 TYR 0.007 0.001 TYR A 216 ARG 0.001 0.000 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 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 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 THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 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 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 THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 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. Evaluate side-chains 342 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 342 time to evaluate : 1.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 182 VAL cc_start: 0.9102 (t) cc_final: 0.8664 (t) REVERT: B 186 CYS cc_start: 0.8040 (m) cc_final: 0.7645 (m) REVERT: B 370 MET cc_start: 0.7923 (mtp) cc_final: 0.7623 (mtm) REVERT: A 154 MET cc_start: 0.7706 (mmm) cc_final: 0.6835 (mtp) REVERT: A 176 TRP cc_start: 0.7178 (t-100) cc_final: 0.6904 (t-100) REVERT: A 497 MET cc_start: 0.7754 (tmt) cc_final: 0.7552 (tmm) REVERT: C 119 TYR cc_start: 0.7805 (t80) cc_final: 0.7540 (t80) REVERT: C 130 ASN cc_start: 0.6308 (t0) cc_final: 0.5985 (m-40) REVERT: C 428 MET cc_start: 0.8759 (mmt) cc_final: 0.8385 (mmt) outliers start: 0 outliers final: 0 residues processed: 342 average time/residue: 0.4819 time to fit residues: 244.3632 Evaluate side-chains 201 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 1.884 ------------------------------------------------------------------------------- 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: 2.9990 chunk 66 optimal weight: 0.0470 chunk 41 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 overall best weight: 2.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 206 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12564 Z= 0.305 Angle : 0.536 6.215 17118 Z= 0.302 Chirality : 0.037 0.123 1986 Planarity : 0.005 0.050 2082 Dihedral : 5.688 93.640 1701 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.00 % Allowed : 9.38 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.88 (0.21), residues: 1593 helix: 2.52 (0.14), residues: 1305 sheet: None (None), residues: 0 loop : -1.11 (0.30), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 184 HIS 0.003 0.001 HIS B 152 PHE 0.016 0.001 PHE B 259 TYR 0.011 0.001 TYR A 519 ARG 0.010 0.001 ARG B 589 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 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 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 THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 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 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 THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 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. Evaluate side-chains 223 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 198 time to evaluate : 1.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 186 CYS cc_start: 0.8298 (m) cc_final: 0.7880 (m) REVERT: B 206 GLN cc_start: 0.8652 (mp10) cc_final: 0.8367 (mp10) REVERT: B 503 MET cc_start: 0.8541 (mtm) cc_final: 0.8236 (mtm) REVERT: A 154 MET cc_start: 0.7886 (mmm) cc_final: 0.7560 (mmm) REVERT: A 176 TRP cc_start: 0.7180 (t-100) cc_final: 0.6972 (t-100) REVERT: A 617 MET cc_start: 0.7920 (ttt) cc_final: 0.7654 (ttt) REVERT: C 119 TYR cc_start: 0.7693 (t80) cc_final: 0.7435 (t80) REVERT: C 428 MET cc_start: 0.8905 (mmt) cc_final: 0.8288 (mmt) outliers start: 25 outliers final: 22 residues processed: 220 average time/residue: 0.4245 time to fit residues: 145.3114 Evaluate side-chains 187 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 165 time to evaluate : 1.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 342 ASN Chi-restraints excluded: chain C residue 482 ASP Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 550 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 98 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 chunk 144 optimal weight: 3.9990 chunk 156 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 116 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: C 571 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12564 Z= 0.240 Angle : 0.474 4.678 17118 Z= 0.263 Chirality : 0.035 0.122 1986 Planarity : 0.004 0.039 2082 Dihedral : 5.407 64.381 1701 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.40 % Allowed : 10.98 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.75 (0.21), residues: 1593 helix: 2.46 (0.14), residues: 1275 sheet: None (None), residues: 0 loop : -0.94 (0.31), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 316 HIS 0.002 0.001 HIS B 152 PHE 0.011 0.001 PHE A 413 TYR 0.011 0.001 TYR A 519 ARG 0.004 0.000 ARG B 589 *********************** 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 THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 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 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 THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 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 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 THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 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. Evaluate side-chains 199 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 169 time to evaluate : 1.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 186 CYS cc_start: 0.8325 (m) cc_final: 0.7874 (m) REVERT: B 503 MET cc_start: 0.8554 (mtm) cc_final: 0.8247 (mtm) REVERT: A 154 MET cc_start: 0.7971 (mmm) cc_final: 0.6811 (mtp) REVERT: A 257 MET cc_start: 0.6725 (ptt) cc_final: 0.6454 (ptm) REVERT: A 617 MET cc_start: 0.7993 (ttt) cc_final: 0.7733 (ttt) outliers start: 30 outliers final: 22 residues processed: 192 average time/residue: 0.4224 time to fit residues: 126.9946 Evaluate side-chains 176 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 154 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 592 ASP Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 482 ASP Chi-restraints excluded: chain C residue 541 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 142 optimal weight: 1.9990 chunk 108 optimal weight: 9.9990 chunk 75 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 145 optimal weight: 5.9990 chunk 153 optimal weight: 3.9990 chunk 137 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 342 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12564 Z= 0.279 Angle : 0.494 4.984 17118 Z= 0.276 Chirality : 0.036 0.118 1986 Planarity : 0.004 0.036 2082 Dihedral : 5.352 77.352 1701 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.56 % Allowed : 11.54 % Favored : 85.90 % 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: 2.41 (0.21), residues: 1593 helix: 2.21 (0.15), residues: 1272 sheet: None (None), residues: 0 loop : -0.99 (0.31), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 316 HIS 0.003 0.001 HIS B 152 PHE 0.014 0.001 PHE A 413 TYR 0.014 0.001 TYR A 119 ARG 0.003 0.001 ARG B 589 *********************** 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 THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 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 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 THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 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 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 THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 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. Evaluate side-chains 193 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 161 time to evaluate : 1.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 186 CYS cc_start: 0.8305 (m) cc_final: 0.7844 (m) REVERT: B 503 MET cc_start: 0.8552 (mtm) cc_final: 0.8251 (mtm) REVERT: A 154 MET cc_start: 0.7965 (mmm) cc_final: 0.7663 (mmm) REVERT: A 176 TRP cc_start: 0.7106 (t-100) cc_final: 0.6768 (t-100) REVERT: A 257 MET cc_start: 0.6727 (ptt) cc_final: 0.6427 (ptm) REVERT: A 305 MET cc_start: 0.8425 (tpp) cc_final: 0.8029 (mmp) REVERT: A 617 MET cc_start: 0.8013 (ttt) cc_final: 0.7740 (ttt) outliers start: 32 outliers final: 23 residues processed: 187 average time/residue: 0.4261 time to fit residues: 124.8583 Evaluate side-chains 167 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 144 time to evaluate : 1.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 342 ASN Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 571 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 87 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 chunk 131 optimal weight: 3.9990 chunk 106 optimal weight: 20.0000 chunk 0 optimal weight: 40.0000 chunk 78 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 226 HIS ** C 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 479 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.4703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 12564 Z= 0.392 Angle : 0.541 6.742 17118 Z= 0.307 Chirality : 0.037 0.137 1986 Planarity : 0.004 0.043 2082 Dihedral : 5.474 78.109 1701 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.72 % Allowed : 12.82 % Favored : 84.46 % 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: 1.92 (0.21), residues: 1593 helix: 1.87 (0.14), residues: 1272 sheet: None (None), residues: 0 loop : -1.16 (0.31), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 150 HIS 0.004 0.001 HIS C 226 PHE 0.015 0.001 PHE A 413 TYR 0.012 0.001 TYR A 119 ARG 0.003 0.001 ARG B 589 *********************** 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 THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 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 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 THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 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 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 THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 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. Evaluate side-chains 176 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 142 time to evaluate : 1.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 186 CYS cc_start: 0.8292 (m) cc_final: 0.7836 (m) REVERT: B 509 ASP cc_start: 0.8531 (OUTLIER) cc_final: 0.8314 (m-30) REVERT: A 154 MET cc_start: 0.8091 (mmm) cc_final: 0.7813 (mmm) REVERT: A 257 MET cc_start: 0.6882 (ptt) cc_final: 0.6590 (ptm) REVERT: A 305 MET cc_start: 0.8476 (tpp) cc_final: 0.8150 (mmp) REVERT: C 482 ASP cc_start: 0.8559 (OUTLIER) cc_final: 0.8329 (t0) outliers start: 34 outliers final: 26 residues processed: 168 average time/residue: 0.4201 time to fit residues: 112.4901 Evaluate side-chains 165 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 137 time to evaluate : 1.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 619 THR Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 482 ASP Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 571 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 138 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 153 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 148 optimal weight: 0.9980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12564 Z= 0.199 Angle : 0.443 4.482 17118 Z= 0.243 Chirality : 0.034 0.117 1986 Planarity : 0.004 0.037 2082 Dihedral : 5.087 78.304 1701 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.92 % Allowed : 13.78 % Favored : 84.29 % 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: 2.42 (0.21), residues: 1593 helix: 2.23 (0.15), residues: 1263 sheet: None (None), residues: 0 loop : -0.91 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 316 HIS 0.002 0.001 HIS C 394 PHE 0.009 0.001 PHE C 259 TYR 0.013 0.001 TYR A 119 ARG 0.002 0.000 ARG C 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 THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 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 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 THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 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 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 THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 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. Evaluate side-chains 171 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 147 time to evaluate : 1.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 186 CYS cc_start: 0.8225 (m) cc_final: 0.7756 (m) REVERT: B 503 MET cc_start: 0.8550 (mtm) cc_final: 0.8248 (mtm) REVERT: A 154 MET cc_start: 0.8114 (mmm) cc_final: 0.7823 (mmm) REVERT: A 257 MET cc_start: 0.6662 (ptt) cc_final: 0.6417 (ptm) REVERT: C 222 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8660 (mp) outliers start: 24 outliers final: 21 residues processed: 166 average time/residue: 0.4140 time to fit residues: 108.8599 Evaluate side-chains 163 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 141 time to evaluate : 2.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 541 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 17 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 112 optimal weight: 6.9990 chunk 129 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 chunk 61 optimal weight: 7.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 571 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.4856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12564 Z= 0.205 Angle : 0.441 4.420 17118 Z= 0.244 Chirality : 0.034 0.131 1986 Planarity : 0.004 0.036 2082 Dihedral : 4.989 75.891 1701 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.16 % Allowed : 13.54 % Favored : 84.29 % 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: 2.30 (0.15), residues: 1263 sheet: None (None), residues: 0 loop : -0.84 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 316 HIS 0.002 0.001 HIS C 394 PHE 0.009 0.001 PHE C 259 TYR 0.012 0.001 TYR A 119 ARG 0.001 0.000 ARG B 589 *********************** 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 THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 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 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 THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 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 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 THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 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. Evaluate side-chains 172 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 145 time to evaluate : 1.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 186 CYS cc_start: 0.8191 (m) cc_final: 0.7753 (m) REVERT: B 598 MET cc_start: 0.8128 (mmm) cc_final: 0.7918 (mmm) REVERT: A 154 MET cc_start: 0.8122 (mmm) cc_final: 0.7829 (mmm) REVERT: A 257 MET cc_start: 0.6454 (ptt) cc_final: 0.6201 (ptm) REVERT: A 305 MET cc_start: 0.8289 (tpp) cc_final: 0.7919 (mmp) REVERT: C 222 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8663 (mp) outliers start: 27 outliers final: 22 residues processed: 166 average time/residue: 0.4411 time to fit residues: 116.5237 Evaluate side-chains 161 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 138 time to evaluate : 1.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 571 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 91 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 120 optimal weight: 2.9990 chunk 139 optimal weight: 0.3980 chunk 146 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.4882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 12564 Z= 0.140 Angle : 0.407 4.211 17118 Z= 0.220 Chirality : 0.033 0.118 1986 Planarity : 0.004 0.037 2082 Dihedral : 4.822 73.710 1701 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.52 % Allowed : 14.50 % Favored : 83.97 % 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: 2.86 (0.22), residues: 1593 helix: 2.50 (0.15), residues: 1272 sheet: None (None), residues: 0 loop : -0.68 (0.33), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 150 HIS 0.002 0.001 HIS B 394 PHE 0.008 0.001 PHE A 501 TYR 0.011 0.001 TYR A 119 ARG 0.001 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 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 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 THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 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 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 THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 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. Evaluate side-chains 173 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 154 time to evaluate : 1.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 186 CYS cc_start: 0.8189 (m) cc_final: 0.7759 (m) REVERT: A 154 MET cc_start: 0.8134 (mmm) cc_final: 0.7824 (mmm) REVERT: A 257 MET cc_start: 0.6431 (ptt) cc_final: 0.6193 (ptm) REVERT: A 305 MET cc_start: 0.8285 (tpp) cc_final: 0.7886 (mmp) REVERT: C 222 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8654 (mp) REVERT: C 349 GLU cc_start: 0.6926 (tm-30) cc_final: 0.6576 (tm-30) outliers start: 19 outliers final: 17 residues processed: 169 average time/residue: 0.4469 time to fit residues: 122.4921 Evaluate side-chains 162 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 144 time to evaluate : 1.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain C residue 222 LEU 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: 2.9990 chunk 142 optimal weight: 2.9990 chunk 146 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 112 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 chunk 151 optimal weight: 5.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.4972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12564 Z= 0.177 Angle : 0.424 4.845 17118 Z= 0.232 Chirality : 0.034 0.121 1986 Planarity : 0.004 0.034 2082 Dihedral : 4.837 72.521 1701 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.68 % Allowed : 14.74 % Favored : 83.57 % 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: 2.83 (0.22), residues: 1593 helix: 2.43 (0.15), residues: 1281 sheet: None (None), residues: 0 loop : -0.57 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 150 HIS 0.002 0.001 HIS B 152 PHE 0.009 0.001 PHE A 413 TYR 0.011 0.001 TYR A 119 ARG 0.001 0.000 ARG A 539 *********************** 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 THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 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 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 THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 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 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 THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 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. Evaluate side-chains 167 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 146 time to evaluate : 2.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 186 CYS cc_start: 0.8184 (m) cc_final: 0.7760 (m) REVERT: A 154 MET cc_start: 0.8146 (mmm) cc_final: 0.7826 (mmm) REVERT: A 257 MET cc_start: 0.6397 (ptt) cc_final: 0.6157 (ptm) REVERT: A 305 MET cc_start: 0.8227 (tpp) cc_final: 0.7876 (mmp) REVERT: C 222 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8663 (mp) REVERT: C 349 GLU cc_start: 0.7061 (tm-30) cc_final: 0.6632 (tm-30) outliers start: 21 outliers final: 18 residues processed: 163 average time/residue: 0.4134 time to fit residues: 107.3350 Evaluate side-chains 163 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 144 time to evaluate : 2.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 571 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 92 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.5099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12564 Z= 0.233 Angle : 0.454 4.648 17118 Z= 0.253 Chirality : 0.035 0.120 1986 Planarity : 0.004 0.034 2082 Dihedral : 5.038 75.329 1701 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.52 % Allowed : 14.74 % Favored : 83.73 % 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: 2.61 (0.22), residues: 1593 helix: 2.30 (0.15), residues: 1272 sheet: None (None), residues: 0 loop : -0.66 (0.33), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 150 HIS 0.002 0.001 HIS C 226 PHE 0.011 0.001 PHE A 413 TYR 0.011 0.001 TYR A 119 ARG 0.002 0.000 ARG A 539 ********************** 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 THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 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 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 THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 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 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 THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 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. Evaluate side-chains 165 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 146 time to evaluate : 1.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 186 CYS cc_start: 0.8185 (m) cc_final: 0.7760 (m) REVERT: A 154 MET cc_start: 0.8160 (mmm) cc_final: 0.7847 (mmm) REVERT: A 257 MET cc_start: 0.6505 (ptt) cc_final: 0.6284 (ptm) REVERT: A 305 MET cc_start: 0.8363 (tpp) cc_final: 0.7982 (mmp) REVERT: C 222 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8666 (mp) outliers start: 19 outliers final: 18 residues processed: 163 average time/residue: 0.4077 time to fit residues: 105.2718 Evaluate side-chains 159 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 140 time to evaluate : 1.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 571 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 38 optimal weight: 4.9990 chunk 116 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 126 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 chunk 7 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.126931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.104390 restraints weight = 55372.457| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.66 r_work: 0.3183 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.5097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12564 Z= 0.153 Angle : 0.414 5.101 17118 Z= 0.225 Chirality : 0.033 0.119 1986 Planarity : 0.004 0.036 2082 Dihedral : 4.857 72.834 1701 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.52 % Allowed : 14.98 % Favored : 83.49 % 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: 2.88 (0.22), residues: 1593 helix: 2.46 (0.15), residues: 1290 sheet: None (None), residues: 0 loop : -0.61 (0.34), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 150 HIS 0.002 0.001 HIS B 394 PHE 0.007 0.001 PHE C 259 TYR 0.011 0.001 TYR A 119 ARG 0.001 0.000 ARG A 355 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4856.58 seconds wall clock time: 90 minutes 18.41 seconds (5418.41 seconds total)