Starting phenix.real_space_refine on Thu Aug 8 23:09:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz9_41738/08_2024/8tz9_41738_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz9_41738/08_2024/8tz9_41738.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz9_41738/08_2024/8tz9_41738.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz9_41738/08_2024/8tz9_41738.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz9_41738/08_2024/8tz9_41738_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz9_41738/08_2024/8tz9_41738_trim.cif" } resolution = 3.67 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= 0.008 sd= 0.045 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 PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 11.94, per 1000 atoms: 0.49 Number of scatterers: 24297 At special positions: 0 Unit cell: (128.52, 130.68, 75.6, 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: 19.95 Conformation dependent library (CDL) restraints added in 2.7 seconds 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2946 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 0 sheets defined 90.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.87 Creating SS restraints... Processing helix chain 'B' and resid 90 through 103 Processing helix chain 'B' and resid 103 through 130 Processing helix chain 'B' and resid 130 through 157 Proline residue: B 136 - end of helix Processing helix chain 'B' and resid 157 through 203 Proline residue: B 167 - end of helix removed outlier: 4.683A pdb=" N PHE B 177 " --> pdb=" O ASP B 173 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N TRP B 178 " --> pdb=" O SER B 174 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N TRP B 181 " --> pdb=" O PHE B 177 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL B 182 " --> pdb=" O TRP B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 223 removed outlier: 3.711A pdb=" N LEU B 207 " --> pdb=" O GLY B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 252 removed outlier: 4.437A pdb=" N VAL B 235 " --> pdb=" O TYR B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 277 removed outlier: 3.534A pdb=" N ALA B 258 " --> pdb=" O PRO B 254 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE B 259 " --> pdb=" O GLY B 255 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP B 260 " --> pdb=" O PHE B 256 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER B 273 " --> pdb=" O PHE B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 282 Processing helix chain 'B' and resid 283 through 287 removed outlier: 4.369A pdb=" N THR B 286 " --> pdb=" O GLU B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 293 Processing helix chain 'B' and resid 293 through 312 Processing helix chain 'B' and resid 313 through 330 removed outlier: 3.511A pdb=" N GLY B 330 " --> pdb=" O LEU B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 343 Processing helix chain 'B' and resid 349 through 361 Proline residue: B 356 - end of helix Proline residue: B 359 - end of helix Processing helix chain 'B' and resid 362 through 376 removed outlier: 3.563A pdb=" N THR B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 389 removed outlier: 3.978A pdb=" N GLY B 383 " --> pdb=" O GLY B 379 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ALA B 384 " --> pdb=" O SER B 380 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY B 389 " --> pdb=" O TYR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 414 removed outlier: 3.981A pdb=" N ALA B 403 " --> pdb=" O SER B 399 " (cutoff:3.500A) Proline residue: B 404 - end of helix Processing helix chain 'B' and resid 423 through 429 Processing helix chain 'B' and resid 437 through 481 removed outlier: 3.660A pdb=" N SER B 449 " --> pdb=" O GLY B 445 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE B 450 " --> pdb=" O ALA B 446 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N SER B 451 " --> pdb=" O SER B 447 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU B 452 " --> pdb=" O SER B 448 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA B 454 " --> pdb=" O ILE B 450 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N MET B 480 " --> pdb=" O TRP B 476 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N PHE B 481 " --> pdb=" O LEU B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 496 removed outlier: 3.522A pdb=" N TYR B 494 " --> pdb=" O VAL B 490 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE B 496 " --> pdb=" O CYS B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 503 Processing helix chain 'B' and resid 506 through 523 removed outlier: 4.227A pdb=" N PHE B 511 " --> pdb=" O TRP B 507 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N MET B 512 " --> pdb=" O GLN B 508 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU B 516 " --> pdb=" O MET B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 542 removed outlier: 3.969A pdb=" N ALA B 528 " --> pdb=" O ASN B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 566 Processing helix chain 'B' and resid 571 through 586 Processing helix chain 'B' and resid 589 through 619 removed outlier: 3.595A pdb=" N MET B 598 " --> pdb=" O THR B 594 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG B 599 " --> pdb=" O ALA B 595 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA B 612 " --> pdb=" O CYS B 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 103 Processing helix chain 'A' and resid 103 through 130 Processing helix chain 'A' and resid 130 through 157 Proline residue: A 136 - end of helix Processing helix chain 'A' and resid 157 through 203 Proline residue: A 167 - end of helix removed outlier: 4.683A pdb=" N PHE A 177 " --> pdb=" O ASP A 173 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N TRP A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N TRP A 181 " --> pdb=" O PHE A 177 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL A 182 " --> pdb=" O TRP A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 223 removed outlier: 3.712A pdb=" N LEU A 207 " --> pdb=" O GLY A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 252 removed outlier: 4.436A pdb=" N VAL A 235 " --> pdb=" O TYR A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 277 removed outlier: 3.535A pdb=" N ALA A 258 " --> pdb=" O PRO A 254 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE A 259 " --> pdb=" O GLY A 255 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP A 260 " --> pdb=" O PHE A 256 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER A 273 " --> pdb=" O PHE A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 Processing helix chain 'A' and resid 283 through 287 removed outlier: 4.368A pdb=" N THR A 286 " --> pdb=" O GLU A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 293 Processing helix chain 'A' and resid 293 through 312 Processing helix chain 'A' and resid 313 through 330 removed outlier: 3.510A pdb=" N GLY A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 343 Processing helix chain 'A' and resid 349 through 361 Proline residue: A 356 - end of helix Proline residue: A 359 - end of helix Processing helix chain 'A' and resid 362 through 376 removed outlier: 3.563A pdb=" N THR A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 389 removed outlier: 3.978A pdb=" N GLY A 383 " --> pdb=" O GLY A 379 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA A 384 " --> pdb=" O SER A 380 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY A 389 " --> pdb=" O TYR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 414 removed outlier: 3.981A pdb=" N ALA A 403 " --> pdb=" O SER A 399 " (cutoff:3.500A) Proline residue: A 404 - end of helix Processing helix chain 'A' and resid 423 through 429 Processing helix chain 'A' and resid 437 through 481 removed outlier: 3.659A pdb=" N SER A 449 " --> pdb=" O GLY A 445 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE A 450 " --> pdb=" O ALA A 446 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N SER A 451 " --> pdb=" O SER A 447 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU A 452 " --> pdb=" O SER A 448 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA A 454 " --> pdb=" O ILE A 450 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET A 480 " --> pdb=" O TRP A 476 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE A 481 " --> pdb=" O LEU A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 496 removed outlier: 3.521A pdb=" N TYR A 494 " --> pdb=" O VAL A 490 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE A 496 " --> pdb=" O CYS A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 503 Processing helix chain 'A' and resid 506 through 523 removed outlier: 4.227A pdb=" N PHE A 511 " --> pdb=" O TRP A 507 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N MET A 512 " --> pdb=" O GLN A 508 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 516 " --> pdb=" O MET A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 542 removed outlier: 3.971A pdb=" N ALA A 528 " --> pdb=" O ASN A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 566 Processing helix chain 'A' and resid 571 through 586 Processing helix chain 'A' and resid 589 through 619 removed outlier: 3.595A pdb=" N MET A 598 " --> pdb=" O THR A 594 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG A 599 " --> pdb=" O ALA A 595 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA A 612 " --> pdb=" O CYS A 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 103 Processing helix chain 'C' and resid 103 through 130 Processing helix chain 'C' and resid 130 through 157 Proline residue: C 136 - end of helix Processing helix chain 'C' and resid 157 through 201 Proline residue: C 167 - end of helix removed outlier: 4.682A pdb=" N PHE C 177 " --> pdb=" O ASP C 173 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N TRP C 178 " --> pdb=" O SER C 174 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N TRP C 181 " --> pdb=" O PHE C 177 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL C 182 " --> pdb=" O TRP C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 223 removed outlier: 3.712A pdb=" N LEU C 207 " --> pdb=" O GLY C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 252 removed outlier: 4.438A pdb=" N VAL C 235 " --> pdb=" O TYR C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 277 removed outlier: 3.534A pdb=" N ALA C 258 " --> pdb=" O PRO C 254 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE C 259 " --> pdb=" O GLY C 255 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP C 260 " --> pdb=" O PHE C 256 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER C 273 " --> pdb=" O PHE C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 282 Processing helix chain 'C' and resid 283 through 287 removed outlier: 4.369A pdb=" N THR C 286 " --> pdb=" O GLU C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 293 Processing helix chain 'C' and resid 293 through 312 Processing helix chain 'C' and resid 313 through 330 removed outlier: 3.511A pdb=" N GLY C 330 " --> pdb=" O LEU C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 343 Processing helix chain 'C' and resid 349 through 361 Proline residue: C 356 - end of helix Proline residue: C 359 - end of helix Processing helix chain 'C' and resid 362 through 376 removed outlier: 3.564A pdb=" N THR C 376 " --> pdb=" O ALA C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 389 removed outlier: 3.978A pdb=" N GLY C 383 " --> pdb=" O GLY C 379 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA C 384 " --> pdb=" O SER C 380 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY C 389 " --> pdb=" O TYR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 414 removed outlier: 3.980A pdb=" N ALA C 403 " --> pdb=" O SER C 399 " (cutoff:3.500A) Proline residue: C 404 - end of helix Processing helix chain 'C' and resid 423 through 429 Processing helix chain 'C' and resid 437 through 481 removed outlier: 3.660A pdb=" N SER C 449 " --> pdb=" O GLY C 445 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE C 450 " --> pdb=" O ALA C 446 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N SER C 451 " --> pdb=" O SER C 447 " (cutoff:3.500A) removed outlier: 4.229A 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: 3.721A pdb=" N MET C 480 " --> pdb=" O TRP C 476 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE C 481 " --> pdb=" O LEU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 496 removed outlier: 3.522A pdb=" N TYR C 494 " --> pdb=" O VAL C 490 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE C 496 " --> pdb=" O CYS C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 503 Processing helix chain 'C' and resid 506 through 523 removed outlier: 4.226A pdb=" N PHE C 511 " --> pdb=" O TRP C 507 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N MET C 512 " --> pdb=" O GLN C 508 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU C 516 " --> pdb=" O MET C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 542 removed outlier: 3.971A pdb=" N ALA C 528 " --> pdb=" O ASN C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 566 Processing helix chain 'C' and resid 571 through 586 Processing helix chain 'C' and resid 589 through 619 removed outlier: 3.593A pdb=" N MET C 598 " --> pdb=" O THR C 594 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG C 599 " --> pdb=" O ALA C 595 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA C 612 " --> pdb=" O CYS C 608 " (cutoff:3.500A) 992 hydrogen bonds defined for protein. 2931 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: 8.81 Time building geometry restraints manager: 20.75 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: 27 1.23 - 1.42: 5325 1.42 - 1.62: 7071 1.62 - 1.81: 159 Bond restraints: 24633 Sorted by residual: bond pdb=" C11 XMO B 801 " pdb=" O12 XMO B 801 " ideal model delta sigma weight residual 1.398 1.678 -0.280 2.00e-02 2.50e+03 1.96e+02 bond pdb=" C11 XMO A 801 " pdb=" O12 XMO A 801 " ideal model delta sigma weight residual 1.398 1.677 -0.279 2.00e-02 2.50e+03 1.95e+02 bond pdb=" C11 XMO C 801 " pdb=" O12 XMO C 801 " ideal model delta sigma weight residual 1.398 1.677 -0.279 2.00e-02 2.50e+03 1.95e+02 bond pdb=" C10 XMO B 801 " pdb=" C11 XMO B 801 " ideal model delta sigma weight residual 1.534 1.287 0.247 2.00e-02 2.50e+03 1.52e+02 bond pdb=" C10 XMO A 801 " pdb=" C11 XMO A 801 " ideal model delta sigma weight residual 1.534 1.288 0.246 2.00e-02 2.50e+03 1.52e+02 ... (remaining 24628 not shown) Histogram of bond angle deviations from ideal: 99.57 - 106.46: 408 106.46 - 113.36: 28344 113.36 - 120.26: 8373 120.26 - 127.16: 7140 127.16 - 134.05: 171 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 108.19 103.35 4.84 1.29e+00 6.01e-01 1.41e+01 angle pdb=" N ASP A 548 " pdb=" CA ASP A 548 " pdb=" C ASP A 548 " ideal model delta sigma weight residual 108.19 103.35 4.84 1.29e+00 6.01e-01 1.41e+01 angle pdb=" N ASP C 548 " pdb=" CA ASP C 548 " pdb=" C ASP C 548 " ideal model delta sigma weight residual 108.19 103.40 4.79 1.29e+00 6.01e-01 1.38e+01 angle pdb=" C THR B 252 " pdb=" N GLU B 253 " pdb=" CA GLU B 253 " ideal model delta sigma weight residual 119.78 124.07 -4.29 1.24e+00 6.50e-01 1.20e+01 angle pdb=" C THR A 252 " pdb=" N GLU A 253 " pdb=" CA GLU A 253 " ideal model delta sigma weight residual 119.78 124.07 -4.29 1.24e+00 6.50e-01 1.20e+01 ... (remaining 44431 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.35: 11306 32.35 - 64.70: 409 64.70 - 97.06: 15 97.06 - 129.41: 3 129.41 - 161.76: 12 Dihedral angle restraints: 11745 sinusoidal: 6015 harmonic: 5730 Sorted by residual: dihedral pdb=" C01 XMO B 801 " pdb=" C02 XMO B 801 " pdb=" C04 XMO B 801 " pdb=" O06 XMO B 801 " ideal model delta sinusoidal sigma weight residual 296.92 135.16 161.76 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" C01 XMO C 801 " pdb=" C02 XMO C 801 " pdb=" C04 XMO C 801 " pdb=" O06 XMO C 801 " ideal model delta sinusoidal sigma weight residual 296.92 135.23 161.69 1 3.00e+01 1.11e-03 2.08e+01 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 296.92 135.31 161.61 1 3.00e+01 1.11e-03 2.08e+01 ... (remaining 11742 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1764 0.067 - 0.135: 219 0.135 - 0.202: 0 0.202 - 0.270: 0 0.270 - 0.337: 3 Chirality restraints: 1986 Sorted by residual: chirality pdb=" C10 XMO B 801 " pdb=" C09 XMO B 801 " pdb=" C11 XMO B 801 " pdb=" O22 XMO B 801 " both_signs ideal model delta sigma weight residual False 2.74 2.40 0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" C10 XMO A 801 " pdb=" C09 XMO A 801 " pdb=" C11 XMO A 801 " pdb=" O22 XMO A 801 " both_signs ideal model delta sigma weight residual False 2.74 2.40 0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" C10 XMO C 801 " pdb=" C09 XMO C 801 " pdb=" C11 XMO C 801 " pdb=" O22 XMO C 801 " both_signs ideal model delta sigma weight residual False 2.74 2.40 0.33 2.00e-01 2.50e+01 2.80e+00 ... (remaining 1983 not shown) Planarity restraints: 3624 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 196 " -0.008 2.00e-02 2.50e+03 1.65e-02 2.73e+00 pdb=" C VAL C 196 " 0.029 2.00e-02 2.50e+03 pdb=" O VAL C 196 " -0.011 2.00e-02 2.50e+03 pdb=" N PHE C 197 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 196 " 0.008 2.00e-02 2.50e+03 1.61e-02 2.60e+00 pdb=" C VAL B 196 " -0.028 2.00e-02 2.50e+03 pdb=" O VAL B 196 " 0.010 2.00e-02 2.50e+03 pdb=" N PHE B 197 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 196 " -0.008 2.00e-02 2.50e+03 1.59e-02 2.54e+00 pdb=" C VAL A 196 " 0.028 2.00e-02 2.50e+03 pdb=" O VAL A 196 " -0.010 2.00e-02 2.50e+03 pdb=" N PHE A 197 " -0.009 2.00e-02 2.50e+03 ... (remaining 3621 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 942 2.18 - 2.78: 46802 2.78 - 3.39: 67605 3.39 - 3.99: 84316 3.99 - 4.60: 134630 Nonbonded interactions: 334295 Sorted by model distance: nonbonded pdb=" O LEU A 195 " pdb=" HG1 THR A 199 " model vdw 1.569 2.450 nonbonded pdb=" O LEU B 195 " pdb=" HG1 THR B 199 " model vdw 1.569 2.450 nonbonded pdb=" O LEU C 195 " pdb=" HG1 THR C 199 " model vdw 1.573 2.450 nonbonded pdb=" O LEU B 248 " pdb=" HG1 THR B 252 " model vdw 1.584 2.450 nonbonded pdb=" O LEU A 248 " pdb=" HG1 THR A 252 " model vdw 1.588 2.450 ... (remaining 334290 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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 group one per residue 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: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.370 Extract box with map and model: 0.950 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 78.610 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.070 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 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 : 0.009 0.280 12564 Z= 0.566 Angle : 0.604 8.962 17118 Z= 0.337 Chirality : 0.041 0.337 1986 Planarity : 0.003 0.036 2082 Dihedral : 15.653 161.760 4275 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.72 % Allowed : 4.57 % Favored : 94.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.31 (0.21), residues: 1593 helix: 2.78 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -0.89 (0.31), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 316 HIS 0.004 0.001 HIS C 394 PHE 0.012 0.001 PHE A 413 TYR 0.007 0.001 TYR C 519 ARG 0.002 0.000 ARG B 557 *********************** 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 379 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 370 time to evaluate : 1.981 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: 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: 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: A 149 VAL cc_start: 0.9005 (t) cc_final: 0.8775 (p) outliers start: 9 outliers final: 3 residues processed: 378 average time/residue: 0.4960 time to fit residues: 287.2390 Evaluate side-chains 213 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 210 time to evaluate : 1.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 571 ASN Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain C residue 571 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 81 optimal weight: 0.7980 chunk 64 optimal weight: 8.9990 chunk 124 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 144 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 530 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12564 Z= 0.210 Angle : 0.559 4.921 17118 Z= 0.304 Chirality : 0.037 0.134 1986 Planarity : 0.003 0.043 2082 Dihedral : 8.104 76.003 1770 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.84 % Allowed : 11.30 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.47 (0.21), residues: 1593 helix: 2.89 (0.14), residues: 1329 sheet: None (None), residues: 0 loop : -1.09 (0.31), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 323 HIS 0.003 0.001 HIS B 132 PHE 0.014 0.001 PHE A 138 TYR 0.009 0.001 TYR A 564 ARG 0.003 0.001 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue 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 237 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 214 time to evaluate : 1.848 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 440 GLU cc_start: 0.7450 (tp30) cc_final: 0.7123 (tp30) REVERT: C 482 ASP cc_start: 0.8232 (t0) cc_final: 0.7905 (t0) REVERT: C 483 TYR cc_start: 0.7646 (t80) cc_final: 0.7304 (m-80) outliers start: 23 outliers final: 13 residues processed: 230 average time/residue: 0.4239 time to fit residues: 149.5743 Evaluate side-chains 184 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 171 time to evaluate : 1.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain B residue 479 ASN Chi-restraints excluded: chain B residue 571 ASN Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 571 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 144 optimal weight: 0.8980 chunk 156 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 143 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 HIS A 175 HIS C 175 HIS C 530 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.5072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12564 Z= 0.267 Angle : 0.557 6.316 17118 Z= 0.307 Chirality : 0.036 0.125 1986 Planarity : 0.003 0.040 2082 Dihedral : 6.465 86.286 1770 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.12 % Allowed : 10.50 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.35 (0.21), residues: 1593 helix: 2.81 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -0.88 (0.32), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 176 HIS 0.004 0.001 HIS B 367 PHE 0.025 0.002 PHE B 301 TYR 0.011 0.001 TYR B 310 ARG 0.003 0.001 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue 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 213 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 174 time to evaluate : 1.934 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: C 283 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7313 (mp0) REVERT: C 482 ASP cc_start: 0.8290 (t0) cc_final: 0.7968 (t0) REVERT: C 483 TYR cc_start: 0.7580 (t80) cc_final: 0.7207 (m-80) outliers start: 39 outliers final: 29 residues processed: 208 average time/residue: 0.4162 time to fit residues: 138.4949 Evaluate side-chains 176 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 146 time to evaluate : 2.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain B residue 571 ASN Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 479 ASN Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 571 ASN Chi-restraints excluded: chain C residue 583 THR 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: 0.5980 chunk 69 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 145 optimal weight: 5.9990 chunk 153 optimal weight: 4.9990 chunk 137 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- 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: 0.7820 moved from start: 0.5573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12564 Z= 0.228 Angle : 0.516 6.763 17118 Z= 0.280 Chirality : 0.035 0.116 1986 Planarity : 0.003 0.040 2082 Dihedral : 5.965 74.424 1770 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.40 % Allowed : 12.42 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.44 (0.21), residues: 1593 helix: 2.88 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -0.94 (0.33), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 176 HIS 0.003 0.001 HIS C 367 PHE 0.013 0.001 PHE B 138 TYR 0.012 0.001 TYR B 564 ARG 0.002 0.000 ARG B 163 *********************** 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 178 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 148 time to evaluate : 1.912 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: A 257 MET cc_start: 0.7060 (tmm) cc_final: 0.6751 (tmm) outliers start: 30 outliers final: 23 residues processed: 175 average time/residue: 0.3938 time to fit residues: 111.0623 Evaluate side-chains 163 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 140 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 479 ASN Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 583 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 87 optimal weight: 8.9990 chunk 2 optimal weight: 9.9990 chunk 114 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 106 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 78 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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: 0.6214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 12564 Z= 0.391 Angle : 0.613 7.880 17118 Z= 0.346 Chirality : 0.039 0.131 1986 Planarity : 0.004 0.036 2082 Dihedral : 6.875 72.446 1766 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.12 % Allowed : 13.30 % 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: 2.66 (0.21), residues: 1593 helix: 2.29 (0.14), residues: 1329 sheet: None (None), residues: 0 loop : -1.05 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 316 HIS 0.005 0.001 HIS B 367 PHE 0.015 0.002 PHE C 221 TYR 0.014 0.002 TYR B 310 ARG 0.003 0.001 ARG B 599 *********************** 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 180 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 141 time to evaluate : 2.060 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 257 MET cc_start: 0.7170 (tmm) cc_final: 0.6881 (tmm) REVERT: A 257 MET cc_start: 0.7150 (tmm) cc_final: 0.6858 (tmm) REVERT: C 283 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7265 (mp0) outliers start: 39 outliers final: 29 residues processed: 173 average time/residue: 0.3973 time to fit residues: 109.9036 Evaluate side-chains 165 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 135 time to evaluate : 1.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain B residue 571 ASN Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 479 ASN Chi-restraints excluded: chain A residue 554 MET Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 571 ASN Chi-restraints excluded: chain C residue 583 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 138 optimal weight: 0.9990 chunk 30 optimal weight: 0.3980 chunk 90 optimal weight: 0.4980 chunk 37 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 127 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 80 optimal weight: 0.7980 chunk 148 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 552 GLN A 552 GLN C 552 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.6312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12564 Z= 0.154 Angle : 0.474 7.811 17118 Z= 0.249 Chirality : 0.034 0.122 1986 Planarity : 0.003 0.041 2082 Dihedral : 5.331 73.456 1764 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.60 % Allowed : 14.26 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.47 (0.21), residues: 1593 helix: 2.93 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -1.06 (0.33), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 176 HIS 0.004 0.001 HIS C 288 PHE 0.013 0.001 PHE B 138 TYR 0.009 0.001 TYR B 564 ARG 0.001 0.000 ARG C 163 *********************** 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 175 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 155 time to evaluate : 1.926 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 257 MET cc_start: 0.6998 (tmm) cc_final: 0.6691 (tmm) REVERT: B 585 MET cc_start: 0.7335 (mtt) cc_final: 0.7124 (mtt) REVERT: A 257 MET cc_start: 0.7181 (tmm) cc_final: 0.6866 (tmm) outliers start: 20 outliers final: 17 residues processed: 172 average time/residue: 0.4083 time to fit residues: 110.2462 Evaluate side-chains 158 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 141 time to evaluate : 2.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 479 ASN Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain C residue 583 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 17 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 112 optimal weight: 10.0000 chunk 129 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 153 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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: 0.7880 moved from start: 0.6542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12564 Z= 0.251 Angle : 0.516 7.645 17118 Z= 0.282 Chirality : 0.035 0.121 1986 Planarity : 0.003 0.039 2082 Dihedral : 5.666 66.090 1764 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.76 % Allowed : 14.34 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.27 (0.21), residues: 1593 helix: 2.79 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -1.12 (0.33), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 176 HIS 0.004 0.001 HIS B 367 PHE 0.022 0.002 PHE C 301 TYR 0.014 0.001 TYR C 564 ARG 0.002 0.000 ARG B 163 *********************** 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 163 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 141 time to evaluate : 1.920 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 257 MET cc_start: 0.7103 (tmm) cc_final: 0.6788 (tmm) REVERT: B 585 MET cc_start: 0.7455 (mtt) cc_final: 0.7231 (mtt) REVERT: A 257 MET cc_start: 0.7125 (tmm) cc_final: 0.6798 (tmm) REVERT: A 501 PHE cc_start: 0.8796 (t80) cc_final: 0.8571 (t80) outliers start: 22 outliers final: 19 residues processed: 159 average time/residue: 0.3883 time to fit residues: 98.5528 Evaluate side-chains 154 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 135 time to evaluate : 1.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 479 ASN Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 583 THR 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: 6.9990 chunk 30 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 139 optimal weight: 6.9990 chunk 146 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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: 0.7901 moved from start: 0.6762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12564 Z= 0.276 Angle : 0.530 7.857 17118 Z= 0.292 Chirality : 0.036 0.120 1986 Planarity : 0.004 0.038 2082 Dihedral : 5.726 68.026 1764 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.48 % Allowed : 14.58 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.05 (0.21), residues: 1593 helix: 2.63 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -1.19 (0.32), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 176 HIS 0.005 0.001 HIS B 367 PHE 0.020 0.002 PHE C 301 TYR 0.013 0.001 TYR B 564 ARG 0.002 0.000 ARG B 163 *********************** 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 170 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 139 time to evaluate : 2.061 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 257 MET cc_start: 0.7169 (tmm) cc_final: 0.6902 (tmm) REVERT: B 585 MET cc_start: 0.7501 (mtt) cc_final: 0.7273 (mtt) REVERT: A 221 PHE cc_start: 0.8789 (t80) cc_final: 0.8580 (t80) REVERT: A 257 MET cc_start: 0.7238 (tmm) cc_final: 0.6926 (tmm) outliers start: 31 outliers final: 31 residues processed: 164 average time/residue: 0.3923 time to fit residues: 102.8493 Evaluate side-chains 166 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 135 time to evaluate : 2.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain B residue 554 MET Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 479 ASN Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 554 MET Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 571 ASN Chi-restraints excluded: chain C residue 583 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 133 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 146 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 112 optimal weight: 9.9990 chunk 43 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 chunk 151 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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: 0.7846 moved from start: 0.6825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12564 Z= 0.178 Angle : 0.484 8.508 17118 Z= 0.257 Chirality : 0.034 0.123 1986 Planarity : 0.003 0.041 2082 Dihedral : 5.151 65.921 1764 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.08 % Allowed : 15.14 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.38 (0.21), residues: 1593 helix: 2.89 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -1.23 (0.31), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 176 HIS 0.003 0.001 HIS B 367 PHE 0.021 0.001 PHE A 501 TYR 0.010 0.001 TYR B 564 ARG 0.002 0.000 ARG C 163 *********************** 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 174 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 148 time to evaluate : 1.782 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 257 MET cc_start: 0.7094 (tmm) cc_final: 0.6767 (tmm) REVERT: B 585 MET cc_start: 0.7456 (mtt) cc_final: 0.7244 (mtt) REVERT: A 257 MET cc_start: 0.7125 (tmm) cc_final: 0.6807 (tmm) REVERT: C 205 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8134 (mp10) REVERT: C 377 ILE cc_start: 0.8679 (pt) cc_final: 0.8474 (pt) outliers start: 26 outliers final: 22 residues processed: 170 average time/residue: 0.3799 time to fit residues: 103.6853 Evaluate side-chains 164 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 141 time to evaluate : 2.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain B residue 554 MET Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 479 ASN Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 205 GLN Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 583 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 92 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 145 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 134 optimal weight: 0.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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: 0.7883 moved from start: 0.6972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12564 Z= 0.236 Angle : 0.517 8.559 17118 Z= 0.280 Chirality : 0.035 0.126 1986 Planarity : 0.003 0.041 2082 Dihedral : 5.335 63.072 1764 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.16 % Allowed : 15.46 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.19 (0.21), residues: 1593 helix: 2.77 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -1.33 (0.31), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 176 HIS 0.004 0.001 HIS B 367 PHE 0.030 0.002 PHE A 221 TYR 0.014 0.001 TYR B 564 ARG 0.002 0.000 ARG B 557 ********************** 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 172 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 145 time to evaluate : 1.949 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 257 MET cc_start: 0.7118 (tmm) cc_final: 0.6796 (tmm) REVERT: B 585 MET cc_start: 0.7474 (mtt) cc_final: 0.7261 (mtt) REVERT: A 257 MET cc_start: 0.7191 (tmm) cc_final: 0.6859 (tmm) REVERT: C 205 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.8126 (mp10) REVERT: C 377 ILE cc_start: 0.8687 (pt) cc_final: 0.8462 (pt) outliers start: 27 outliers final: 26 residues processed: 166 average time/residue: 0.3863 time to fit residues: 103.1869 Evaluate side-chains 168 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 141 time to evaluate : 1.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain B residue 554 MET Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 479 ASN Chi-restraints excluded: chain A residue 554 MET Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 205 GLN Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 583 THR 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: 5.9990 chunk 18 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 126 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 0.0670 chunk 110 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 overall best weight: 2.0126 ------------------------------------------------------------------------------- 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 = 0.3577 r_free = 0.3577 target = 0.103551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.083038 restraints weight = 88394.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.086501 restraints weight = 34213.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.088632 restraints weight = 18960.170| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.7020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12564 Z= 0.208 Angle : 0.503 8.797 17118 Z= 0.270 Chirality : 0.035 0.125 1986 Planarity : 0.003 0.041 2082 Dihedral : 5.147 63.868 1764 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.08 % Allowed : 15.87 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.22 (0.21), residues: 1593 helix: 2.81 (0.14), residues: 1311 sheet: None (None), residues: 0 loop : -1.41 (0.31), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 176 HIS 0.004 0.001 HIS B 367 PHE 0.028 0.001 PHE C 301 TYR 0.012 0.001 TYR B 564 ARG 0.002 0.000 ARG B 163 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4360.00 seconds wall clock time: 77 minutes 24.48 seconds (4644.48 seconds total)