Starting phenix.real_space_refine on Wed Jul 24 01:46:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz9_41738/07_2024/8tz9_41738_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz9_41738/07_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_41738/07_2024/8tz9_41738.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz9_41738/07_2024/8tz9_41738.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz9_41738/07_2024/8tz9_41738_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz9_41738/07_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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 11.13, per 1000 atoms: 0.46 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: 18.39 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: 1.71 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: 8.68 Time building geometry restraints manager: 19.43 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 1.850 nonbonded pdb=" O LEU B 195 " pdb=" HG1 THR B 199 " model vdw 1.569 1.850 nonbonded pdb=" O LEU C 195 " pdb=" HG1 THR C 199 " model vdw 1.573 1.850 nonbonded pdb=" O LEU B 248 " pdb=" HG1 THR B 252 " model vdw 1.584 1.850 nonbonded pdb=" O LEU A 248 " pdb=" HG1 THR A 252 " model vdw 1.588 1.850 ... (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 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: 1.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.390 Extract box with map and model: 0.900 Check model and map are aligned: 0.170 Set scattering table: 0.230 Process input model: 74.150 Find NCS groups from input model: 0.750 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: 0.010 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.090 ------------------------------------------------------------------------------- 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 : 1.768 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: 0.4584 time to fit residues: 264.0934 Evaluate side-chains 213 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 210 time to evaluate : 1.814 ------------------------------------------------------------------------------- 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: 0.6980 chunk 64 optimal weight: 8.9990 chunk 124 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 144 optimal weight: 4.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 12564 Z= 0.241 Angle : 0.566 4.878 17118 Z= 0.310 Chirality : 0.037 0.131 1986 Planarity : 0.004 0.043 2082 Dihedral : 7.727 82.261 1770 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.24 % Allowed : 10.98 % Favored : 86.78 % 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: 3.25 (0.21), residues: 1593 helix: 2.75 (0.14), residues: 1311 sheet: None (None), residues: 0 loop : -0.93 (0.30), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 316 HIS 0.003 0.001 HIS C 152 PHE 0.015 0.002 PHE A 138 TYR 0.011 0.001 TYR A 564 ARG 0.004 0.001 ARG C 163 *********************** 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 239 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 211 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: 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: C 482 ASP cc_start: 0.8175 (t0) cc_final: 0.7873 (t0) REVERT: C 483 TYR cc_start: 0.7772 (t80) cc_final: 0.7316 (m-80) outliers start: 28 outliers final: 18 residues processed: 234 average time/residue: 0.4174 time to fit residues: 150.7822 Evaluate side-chains 187 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 169 time to evaluate : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 506 ASP Chi-restraints excluded: chain B residue 571 ASN Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 506 ASP Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain A residue 611 THR 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 506 ASP 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: 0.5980 chunk 120 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 39 optimal weight: 0.7980 chunk 144 optimal weight: 4.9990 chunk 156 optimal weight: 6.9990 chunk 128 optimal weight: 0.2980 chunk 143 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 116 optimal weight: 6.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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: 0.7715 moved from start: 0.4846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12564 Z= 0.172 Angle : 0.488 6.250 17118 Z= 0.262 Chirality : 0.035 0.120 1986 Planarity : 0.003 0.042 2082 Dihedral : 5.981 82.830 1770 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.48 % Allowed : 11.14 % 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: 3.76 (0.21), residues: 1593 helix: 3.12 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -0.95 (0.31), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 176 HIS 0.004 0.001 HIS B 288 PHE 0.016 0.001 PHE C 221 TYR 0.009 0.001 TYR B 564 ARG 0.003 0.000 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue 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 208 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 177 time to evaluate : 1.764 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: B 585 MET cc_start: 0.7369 (mtt) cc_final: 0.7086 (mtt) REVERT: C 482 ASP cc_start: 0.8206 (t0) cc_final: 0.7932 (t0) REVERT: C 483 TYR cc_start: 0.7563 (t80) cc_final: 0.7252 (m-80) REVERT: C 554 MET cc_start: 0.7037 (ptm) cc_final: 0.6797 (ptm) outliers start: 31 outliers final: 24 residues processed: 203 average time/residue: 0.3939 time to fit residues: 128.4187 Evaluate side-chains 173 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 149 time to evaluate : 1.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 479 ASN Chi-restraints excluded: chain B residue 506 ASP Chi-restraints excluded: chain B residue 571 ASN Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 350 SER 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 506 ASP Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 305 MET 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 487 SER Chi-restraints excluded: chain C residue 506 ASP 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: 0.6980 chunk 108 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 chunk 153 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 127 optimal weight: 3.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.5574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12564 Z= 0.307 Angle : 0.563 7.165 17118 Z= 0.311 Chirality : 0.037 0.124 1986 Planarity : 0.004 0.040 2082 Dihedral : 6.390 74.125 1770 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.37 % Allowed : 11.54 % Favored : 85.10 % 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: 3.21 (0.21), residues: 1593 helix: 2.73 (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 0.007 0.001 TRP B 176 HIS 0.005 0.001 HIS A 367 PHE 0.015 0.002 PHE A 138 TYR 0.013 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 192 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 150 time to evaluate : 1.836 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 207 LEU cc_start: 0.8746 (mt) cc_final: 0.8523 (tt) REVERT: B 569 PHE cc_start: 0.8453 (m-10) cc_final: 0.7977 (m-10) REVERT: C 207 LEU cc_start: 0.8634 (mt) cc_final: 0.8365 (tt) REVERT: C 283 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7244 (mp0) outliers start: 42 outliers final: 34 residues processed: 189 average time/residue: 0.3817 time to fit residues: 116.5573 Evaluate side-chains 173 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 138 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain B residue 506 ASP 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 327 VAL Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 350 SER 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 506 ASP 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 283 GLU Chi-restraints excluded: chain C residue 305 MET 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 506 ASP Chi-restraints excluded: chain C residue 571 ASN Chi-restraints excluded: chain C residue 583 THR Chi-restraints excluded: chain C residue 611 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: 10.0000 chunk 114 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 chunk 131 optimal weight: 0.6980 chunk 106 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 78 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- 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: 0.7897 moved from start: 0.6175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 12564 Z= 0.302 Angle : 0.548 8.068 17118 Z= 0.304 Chirality : 0.036 0.138 1986 Planarity : 0.004 0.041 2082 Dihedral : 6.231 72.461 1770 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.53 % Allowed : 12.42 % Favored : 84.05 % 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: 2.99 (0.21), residues: 1593 helix: 2.60 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -1.20 (0.33), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 176 HIS 0.004 0.001 HIS B 367 PHE 0.019 0.002 PHE A 501 TYR 0.014 0.001 TYR B 564 ARG 0.003 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue 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 185 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 141 time to evaluate : 1.935 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: B 207 LEU cc_start: 0.8773 (mt) cc_final: 0.8559 (tt) REVERT: B 257 MET cc_start: 0.7118 (tmm) cc_final: 0.6826 (tmm) REVERT: A 257 MET cc_start: 0.7237 (tmm) cc_final: 0.6971 (tmm) REVERT: C 207 LEU cc_start: 0.8671 (mt) cc_final: 0.8365 (tt) REVERT: C 283 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7292 (mp0) outliers start: 44 outliers final: 34 residues processed: 177 average time/residue: 0.3917 time to fit residues: 112.1057 Evaluate side-chains 173 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 138 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain B residue 506 ASP 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 327 VAL Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 350 SER 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 506 ASP 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 283 GLU Chi-restraints excluded: chain C residue 328 THR 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 506 ASP Chi-restraints excluded: chain C residue 571 ASN Chi-restraints excluded: chain C residue 583 THR Chi-restraints excluded: chain C residue 611 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 138 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 chunk 148 optimal weight: 0.6980 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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: 0.7842 moved from start: 0.6330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12564 Z= 0.180 Angle : 0.475 8.112 17118 Z= 0.253 Chirality : 0.034 0.125 1986 Planarity : 0.003 0.043 2082 Dihedral : 5.466 70.817 1768 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.72 % Allowed : 13.94 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.42 (0.21), residues: 1593 helix: 2.92 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -1.21 (0.32), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 176 HIS 0.003 0.001 HIS B 367 PHE 0.015 0.001 PHE B 221 TYR 0.011 0.001 TYR B 564 ARG 0.001 0.000 ARG B 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 178 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 144 time to evaluate : 1.673 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: 0.7053 (tmm) cc_final: 0.6736 (tmm) REVERT: B 585 MET cc_start: 0.7386 (mtt) cc_final: 0.7171 (mtt) REVERT: A 257 MET cc_start: 0.7149 (tmm) cc_final: 0.6850 (tmm) outliers start: 34 outliers final: 29 residues processed: 172 average time/residue: 0.3968 time to fit residues: 108.7188 Evaluate side-chains 171 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 142 time to evaluate : 1.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain B residue 506 ASP 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 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 438 LEU Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 479 ASN Chi-restraints excluded: chain A residue 506 ASP 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 307 MET Chi-restraints excluded: chain C residue 328 THR 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 506 ASP Chi-restraints excluded: chain C residue 554 MET Chi-restraints excluded: chain C residue 571 ASN Chi-restraints excluded: chain C residue 583 THR Chi-restraints excluded: chain C residue 611 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 17 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 112 optimal weight: 9.9990 chunk 129 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 153 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 61 optimal weight: 10.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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: 0.7860 moved from start: 0.6567 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= 0.206 Angle : 0.485 7.985 17118 Z= 0.261 Chirality : 0.034 0.121 1986 Planarity : 0.003 0.044 2082 Dihedral : 5.384 65.595 1766 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.56 % Allowed : 14.10 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.41 (0.21), residues: 1593 helix: 2.91 (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 0.008 0.001 TRP B 176 HIS 0.004 0.001 HIS B 367 PHE 0.020 0.001 PHE A 501 TYR 0.011 0.001 TYR B 564 ARG 0.001 0.000 ARG A 251 *********************** 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 179 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 147 time to evaluate : 1.882 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: 0.7054 (tmm) cc_final: 0.6695 (tmm) REVERT: B 329 MET cc_start: 0.8294 (OUTLIER) cc_final: 0.8021 (mtt) REVERT: B 585 MET cc_start: 0.7426 (mtt) cc_final: 0.7205 (mtt) REVERT: A 257 MET cc_start: 0.7156 (tmm) cc_final: 0.6841 (tmm) REVERT: C 430 MET cc_start: 0.8598 (ptp) cc_final: 0.8201 (mtm) outliers start: 32 outliers final: 30 residues processed: 172 average time/residue: 0.4141 time to fit residues: 112.5014 Evaluate side-chains 167 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 136 time to evaluate : 1.928 ------------------------------------------------------------------------------- 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 329 MET Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain B residue 506 ASP 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 260 ASP Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 479 ASN Chi-restraints excluded: chain A residue 506 ASP 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 307 MET Chi-restraints excluded: chain C residue 328 THR 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 506 ASP Chi-restraints excluded: chain C residue 583 THR Chi-restraints excluded: chain C residue 611 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 91 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 120 optimal weight: 0.6980 chunk 139 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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: 0.7866 moved from start: 0.6738 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= 0.212 Angle : 0.489 8.181 17118 Z= 0.263 Chirality : 0.034 0.118 1986 Planarity : 0.003 0.044 2082 Dihedral : 5.235 65.130 1764 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.04 % Allowed : 13.86 % Favored : 83.09 % 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: 2.91 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -1.34 (0.30), 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 0.021 0.001 PHE C 221 TYR 0.010 0.001 TYR B 564 ARG 0.001 0.000 ARG A 251 *********************** 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 181 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 143 time to evaluate : 2.398 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: 0.7139 (tmm) cc_final: 0.6799 (tmm) REVERT: B 329 MET cc_start: 0.8313 (OUTLIER) cc_final: 0.8036 (mtt) REVERT: B 585 MET cc_start: 0.7389 (mtt) cc_final: 0.7172 (mtt) REVERT: A 257 MET cc_start: 0.7173 (tmm) cc_final: 0.6858 (tmm) outliers start: 38 outliers final: 35 residues processed: 171 average time/residue: 0.3925 time to fit residues: 109.4597 Evaluate side-chains 173 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 137 time to evaluate : 1.810 ------------------------------------------------------------------------------- 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 328 THR Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain B residue 506 ASP 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 260 ASP Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 479 ASN Chi-restraints excluded: chain A residue 506 ASP 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 307 MET Chi-restraints excluded: chain C residue 328 THR 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 506 ASP Chi-restraints excluded: chain C residue 554 MET Chi-restraints excluded: chain C residue 583 THR Chi-restraints excluded: chain C residue 611 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: 2.9990 chunk 146 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 112 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 135 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 151 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 552 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.6888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12564 Z= 0.232 Angle : 0.503 8.826 17118 Z= 0.272 Chirality : 0.035 0.120 1986 Planarity : 0.003 0.043 2082 Dihedral : 5.300 63.829 1764 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.04 % Allowed : 14.42 % Favored : 82.53 % 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: 3.25 (0.21), residues: 1593 helix: 2.82 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -1.37 (0.30), 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 0.031 0.002 PHE A 221 TYR 0.015 0.001 TYR B 564 ARG 0.002 0.000 ARG B 557 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue 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 179 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 141 time to evaluate : 1.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 257 MET cc_start: 0.7149 (tmm) cc_final: 0.6813 (tmm) REVERT: B 329 MET cc_start: 0.8337 (OUTLIER) cc_final: 0.8062 (mtt) REVERT: B 585 MET cc_start: 0.7493 (mtt) cc_final: 0.7272 (mtt) REVERT: A 257 MET cc_start: 0.7210 (tmm) cc_final: 0.6887 (tmm) outliers start: 38 outliers final: 36 residues processed: 170 average time/residue: 0.3781 time to fit residues: 104.0976 Evaluate side-chains 174 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 137 time to evaluate : 1.733 ------------------------------------------------------------------------------- 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 328 THR Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain B residue 506 ASP 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 218 SER Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 350 SER 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 506 ASP 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 307 MET Chi-restraints excluded: chain C residue 328 THR 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 506 ASP Chi-restraints excluded: chain C residue 583 THR Chi-restraints excluded: chain C residue 611 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 92 optimal weight: 0.0040 chunk 71 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 chunk 145 optimal weight: 0.2980 chunk 126 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 overall best weight: 1.6196 ------------------------------------------------------------------------------- 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: 0.7853 moved from start: 0.6941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12564 Z= 0.182 Angle : 0.481 8.808 17118 Z= 0.256 Chirality : 0.034 0.137 1986 Planarity : 0.003 0.044 2082 Dihedral : 5.014 63.791 1764 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.88 % Allowed : 15.14 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.41 (0.21), residues: 1593 helix: 2.95 (0.14), residues: 1311 sheet: None (None), residues: 0 loop : -1.38 (0.30), residues: 282 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 0.030 0.001 PHE A 221 TYR 0.012 0.001 TYR B 564 ARG 0.001 0.000 ARG B 163 ********************** 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 181 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 145 time to evaluate : 1.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 257 MET cc_start: 0.7143 (tmm) cc_final: 0.6805 (tmm) REVERT: B 329 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.7996 (mtt) REVERT: B 430 MET cc_start: 0.8228 (mtt) cc_final: 0.7998 (mtt) REVERT: B 585 MET cc_start: 0.7444 (mtt) cc_final: 0.7234 (mtt) REVERT: A 257 MET cc_start: 0.7144 (tmm) cc_final: 0.6818 (tmm) REVERT: A 501 PHE cc_start: 0.8796 (t80) cc_final: 0.8560 (t80) outliers start: 36 outliers final: 34 residues processed: 172 average time/residue: 0.3789 time to fit residues: 105.0155 Evaluate side-chains 176 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 141 time to evaluate : 1.814 ------------------------------------------------------------------------------- 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 328 THR Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain B residue 506 ASP 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 260 ASP Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 479 ASN Chi-restraints excluded: chain A residue 506 ASP 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 307 MET Chi-restraints excluded: chain C residue 328 THR 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 506 ASP Chi-restraints excluded: chain C residue 554 MET Chi-restraints excluded: chain C residue 583 THR Chi-restraints excluded: chain C residue 611 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: 4.9990 chunk 126 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 129 optimal weight: 0.2980 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 110 optimal weight: 0.8980 chunk 7 optimal weight: 6.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 552 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.104850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.084196 restraints weight = 87975.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.087682 restraints weight = 33944.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.089899 restraints weight = 18821.258| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.7014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12564 Z= 0.172 Angle : 0.477 8.780 17118 Z= 0.253 Chirality : 0.034 0.146 1986 Planarity : 0.003 0.045 2082 Dihedral : 4.871 61.596 1764 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.96 % Allowed : 15.38 % Favored : 81.65 % 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: 2.99 (0.14), residues: 1311 sheet: None (None), residues: 0 loop : -1.39 (0.30), residues: 282 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 0.030 0.001 PHE A 221 TYR 0.012 0.001 TYR B 564 ARG 0.003 0.000 ARG A 539 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4221.80 seconds wall clock time: 74 minutes 46.27 seconds (4486.27 seconds total)