Starting phenix.real_space_refine on Tue Apr 9 09:40:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3s_36858/04_2024/8k3s_36858_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3s_36858/04_2024/8k3s_36858.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3s_36858/04_2024/8k3s_36858.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3s_36858/04_2024/8k3s_36858.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3s_36858/04_2024/8k3s_36858_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3s_36858/04_2024/8k3s_36858_neut_trim_updated.pdb" } resolution = 3.0 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= 0.000 sd= 0.006 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: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 P 4 5.49 5 S 80 5.16 5 C 10424 2.51 5 N 2444 2.21 5 O 2808 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 289": "OD1" <-> "OD2" Residue "A ASP 346": "OD1" <-> "OD2" Residue "A GLU 371": "OE1" <-> "OE2" Residue "A ASP 373": "OD1" <-> "OD2" Residue "A TYR 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 676": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 684": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 278": "OD1" <-> "OD2" Residue "B GLU 312": "OE1" <-> "OE2" Residue "B ASP 346": "OD1" <-> "OD2" Residue "B PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 676": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 684": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 278": "OD1" <-> "OD2" Residue "C ASP 346": "OD1" <-> "OD2" Residue "C ASP 425": "OD1" <-> "OD2" Residue "C PHE 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 654": "NH1" <-> "NH2" Residue "C PHE 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 676": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 684": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 278": "OD1" <-> "OD2" Residue "D ASP 289": "OD1" <-> "OD2" Residue "D ASP 346": "OD1" <-> "OD2" Residue "D ASP 425": "OD1" <-> "OD2" Residue "D PHE 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 648": "OE1" <-> "OE2" Residue "D PHE 676": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 15761 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3856 Classifications: {'peptide': 466} Link IDs: {'PTRANS': 12, 'TRANS': 453} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3856 Classifications: {'peptide': 466} Link IDs: {'PTRANS': 12, 'TRANS': 453} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 3856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3856 Classifications: {'peptide': 466} Link IDs: {'PTRANS': 12, 'TRANS': 453} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 3856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3856 Classifications: {'peptide': 466} Link IDs: {'PTRANS': 12, 'TRANS': 453} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 85 Unusual residues: {' CA': 1, 'NAG': 3, 'PEF': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 84 Unusual residues: {'NAG': 3, 'PEF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 84 Unusual residues: {'NAG': 3, 'PEF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 84 Unusual residues: {'NAG': 3, 'PEF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 8.51, per 1000 atoms: 0.54 Number of scatterers: 15761 At special positions: 0 Unit cell: (107.613, 107.613, 96.743, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 S 80 16.00 P 4 15.00 O 2808 8.00 N 2444 7.00 C 10424 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 344 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 344 " distance=2.03 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 344 " distance=2.03 Simple disulfide: pdb=" SG CYS D 331 " - pdb=" SG CYS D 344 " distance=2.03 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=3, symmetry=0 Links applied NAG-ASN " NAG A 802 " - " ASN A 328 " " NAG A 803 " - " ASN A 362 " " NAG A 804 " - " ASN A 375 " " NAG B 802 " - " ASN B 328 " " NAG B 803 " - " ASN B 362 " " NAG B 804 " - " ASN B 375 " " NAG C 802 " - " ASN C 328 " " NAG C 803 " - " ASN C 362 " " NAG C 804 " - " ASN C 375 " " NAG D 802 " - " ASN D 328 " " NAG D 803 " - " ASN D 362 " " NAG D 804 " - " ASN D 375 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.15 Conformation dependent library (CDL) restraints added in 2.5 seconds 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3568 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 64 helices and 7 sheets defined 48.9% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.81 Creating SS restraints... Processing helix chain 'A' and resid 216 through 241 Processing helix chain 'A' and resid 247 through 258 Processing helix chain 'A' and resid 276 through 283 Processing helix chain 'A' and resid 286 through 289 No H-bonds generated for 'chain 'A' and resid 286 through 289' Processing helix chain 'A' and resid 309 through 311 No H-bonds generated for 'chain 'A' and resid 309 through 311' Processing helix chain 'A' and resid 399 through 411 Processing helix chain 'A' and resid 468 through 492 Processing helix chain 'A' and resid 510 through 528 Processing helix chain 'A' and resid 535 through 539 removed outlier: 4.265A pdb=" N PHE A 538 " --> pdb=" O LEU A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 577 removed outlier: 3.895A pdb=" N LEU A 573 " --> pdb=" O VAL A 569 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N PHE A 574 " --> pdb=" O TRP A 570 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N LYS A 575 " --> pdb=" O ILE A 571 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N PHE A 576 " --> pdb=" O LYS A 572 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE A 577 " --> pdb=" O LEU A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 591 removed outlier: 4.031A pdb=" N SER A 584 " --> pdb=" O ARG A 581 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER A 587 " --> pdb=" O SER A 584 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N THR A 588 " --> pdb=" O GLN A 585 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N THR A 589 " --> pdb=" O LEU A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 599 No H-bonds generated for 'chain 'A' and resid 596 through 599' Processing helix chain 'A' and resid 602 through 618 Processing helix chain 'A' and resid 629 through 641 Processing helix chain 'A' and resid 646 through 652 Processing helix chain 'A' and resid 656 through 685 removed outlier: 3.774A pdb=" N PHE A 669 " --> pdb=" O VAL A 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 241 Processing helix chain 'B' and resid 247 through 258 Processing helix chain 'B' and resid 276 through 283 Processing helix chain 'B' and resid 286 through 289 No H-bonds generated for 'chain 'B' and resid 286 through 289' Processing helix chain 'B' and resid 309 through 311 No H-bonds generated for 'chain 'B' and resid 309 through 311' Processing helix chain 'B' and resid 399 through 411 Processing helix chain 'B' and resid 468 through 492 Processing helix chain 'B' and resid 510 through 528 Processing helix chain 'B' and resid 535 through 539 removed outlier: 4.255A pdb=" N PHE B 538 " --> pdb=" O LEU B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 579 removed outlier: 3.931A pdb=" N LEU B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N PHE B 574 " --> pdb=" O TRP B 570 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N LYS B 575 " --> pdb=" O ILE B 571 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N PHE B 576 " --> pdb=" O LYS B 572 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE B 577 " --> pdb=" O LEU B 573 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE B 579 " --> pdb=" O LYS B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 591 removed outlier: 4.032A pdb=" N SER B 584 " --> pdb=" O ARG B 581 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU B 586 " --> pdb=" O MET B 583 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N SER B 587 " --> pdb=" O SER B 584 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR B 588 " --> pdb=" O GLN B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 599 No H-bonds generated for 'chain 'B' and resid 596 through 599' Processing helix chain 'B' and resid 602 through 618 Processing helix chain 'B' and resid 629 through 641 Processing helix chain 'B' and resid 646 through 652 Processing helix chain 'B' and resid 656 through 685 removed outlier: 3.762A pdb=" N PHE B 669 " --> pdb=" O VAL B 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 241 Processing helix chain 'C' and resid 247 through 258 Processing helix chain 'C' and resid 276 through 283 Processing helix chain 'C' and resid 286 through 289 No H-bonds generated for 'chain 'C' and resid 286 through 289' Processing helix chain 'C' and resid 309 through 311 No H-bonds generated for 'chain 'C' and resid 309 through 311' Processing helix chain 'C' and resid 399 through 411 Processing helix chain 'C' and resid 468 through 492 Processing helix chain 'C' and resid 510 through 528 Processing helix chain 'C' and resid 535 through 539 removed outlier: 4.244A pdb=" N PHE C 538 " --> pdb=" O LEU C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 579 removed outlier: 3.946A pdb=" N LEU C 573 " --> pdb=" O VAL C 569 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N PHE C 574 " --> pdb=" O TRP C 570 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LYS C 575 " --> pdb=" O ILE C 571 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N PHE C 576 " --> pdb=" O LYS C 572 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE C 577 " --> pdb=" O LEU C 573 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N PHE C 579 " --> pdb=" O LYS C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 592 removed outlier: 3.988A pdb=" N SER C 584 " --> pdb=" O ARG C 581 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU C 586 " --> pdb=" O MET C 583 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N SER C 587 " --> pdb=" O SER C 584 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR C 588 " --> pdb=" O GLN C 585 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR C 589 " --> pdb=" O LEU C 586 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ARG C 592 " --> pdb=" O THR C 589 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 599 No H-bonds generated for 'chain 'C' and resid 596 through 599' Processing helix chain 'C' and resid 602 through 618 Processing helix chain 'C' and resid 629 through 641 Processing helix chain 'C' and resid 646 through 652 Processing helix chain 'C' and resid 656 through 685 removed outlier: 3.807A pdb=" N PHE C 669 " --> pdb=" O VAL C 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 241 Processing helix chain 'D' and resid 247 through 258 Processing helix chain 'D' and resid 276 through 283 Processing helix chain 'D' and resid 286 through 289 No H-bonds generated for 'chain 'D' and resid 286 through 289' Processing helix chain 'D' and resid 309 through 311 No H-bonds generated for 'chain 'D' and resid 309 through 311' Processing helix chain 'D' and resid 399 through 411 Processing helix chain 'D' and resid 468 through 492 Processing helix chain 'D' and resid 510 through 528 Processing helix chain 'D' and resid 535 through 539 removed outlier: 4.269A pdb=" N PHE D 538 " --> pdb=" O LEU D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 579 removed outlier: 3.873A pdb=" N LEU D 573 " --> pdb=" O VAL D 569 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N PHE D 574 " --> pdb=" O TRP D 570 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N LYS D 575 " --> pdb=" O ILE D 571 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N PHE D 576 " --> pdb=" O LYS D 572 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE D 577 " --> pdb=" O LEU D 573 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N PHE D 579 " --> pdb=" O LYS D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 591 removed outlier: 4.051A pdb=" N SER D 584 " --> pdb=" O ARG D 581 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER D 587 " --> pdb=" O SER D 584 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N THR D 588 " --> pdb=" O GLN D 585 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR D 589 " --> pdb=" O LEU D 586 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER D 591 " --> pdb=" O THR D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 596 through 599 No H-bonds generated for 'chain 'D' and resid 596 through 599' Processing helix chain 'D' and resid 602 through 618 Processing helix chain 'D' and resid 629 through 641 Processing helix chain 'D' and resid 646 through 652 Processing helix chain 'D' and resid 656 through 685 removed outlier: 3.753A pdb=" N PHE D 669 " --> pdb=" O VAL D 665 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 391 through 394 removed outlier: 3.681A pdb=" N ALA A 421 " --> pdb=" O LEU A 324 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU A 435 " --> pdb=" O ASN A 430 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 391 through 394 removed outlier: 3.661A pdb=" N ALA B 421 " --> pdb=" O LEU B 324 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU B 435 " --> pdb=" O ASN B 430 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 442 through 444 Processing sheet with id= D, first strand: chain 'C' and resid 391 through 394 removed outlier: 3.687A pdb=" N ALA C 421 " --> pdb=" O LEU C 324 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU C 435 " --> pdb=" O ASN C 430 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 441 through 444 Processing sheet with id= F, first strand: chain 'D' and resid 391 through 394 removed outlier: 3.687A pdb=" N ALA D 421 " --> pdb=" O LEU D 324 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU D 435 " --> pdb=" O ASN D 430 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 442 through 444 727 hydrogen bonds defined for protein. 1959 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: 4.08 Time building geometry restraints manager: 6.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2396 1.31 - 1.43: 4858 1.43 - 1.56: 8785 1.56 - 1.69: 13 1.69 - 1.81: 124 Bond restraints: 16176 Sorted by residual: bond pdb=" C10 PEF A 801 " pdb=" O2 PEF A 801 " ideal model delta sigma weight residual 1.330 1.399 -0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C10 PEF D 801 " pdb=" O2 PEF D 801 " ideal model delta sigma weight residual 1.330 1.399 -0.069 2.00e-02 2.50e+03 1.17e+01 bond pdb=" C10 PEF C 801 " pdb=" O2 PEF C 801 " ideal model delta sigma weight residual 1.330 1.398 -0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" C10 PEF B 801 " pdb=" O2 PEF B 801 " ideal model delta sigma weight residual 1.330 1.398 -0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" C30 PEF B 801 " pdb=" O3 PEF B 801 " ideal model delta sigma weight residual 1.333 1.398 -0.065 2.00e-02 2.50e+03 1.07e+01 ... (remaining 16171 not shown) Histogram of bond angle deviations from ideal: 99.41 - 106.34: 277 106.34 - 113.26: 8473 113.26 - 120.19: 6266 120.19 - 127.12: 6767 127.12 - 134.05: 133 Bond angle restraints: 21916 Sorted by residual: angle pdb=" CA PRO B 604 " pdb=" N PRO B 604 " pdb=" CD PRO B 604 " ideal model delta sigma weight residual 112.00 103.43 8.57 1.40e+00 5.10e-01 3.74e+01 angle pdb=" CA PRO C 604 " pdb=" N PRO C 604 " pdb=" CD PRO C 604 " ideal model delta sigma weight residual 112.00 103.63 8.37 1.40e+00 5.10e-01 3.57e+01 angle pdb=" CA PRO A 604 " pdb=" N PRO A 604 " pdb=" CD PRO A 604 " ideal model delta sigma weight residual 112.00 103.97 8.03 1.40e+00 5.10e-01 3.29e+01 angle pdb=" CA PRO D 604 " pdb=" N PRO D 604 " pdb=" CD PRO D 604 " ideal model delta sigma weight residual 112.00 104.05 7.95 1.40e+00 5.10e-01 3.22e+01 angle pdb=" O3P PEF C 801 " pdb=" P PEF C 801 " pdb=" O4P PEF C 801 " ideal model delta sigma weight residual 93.96 110.01 -16.05 3.00e+00 1.11e-01 2.86e+01 ... (remaining 21911 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 8622 17.99 - 35.99: 732 35.99 - 53.98: 167 53.98 - 71.97: 41 71.97 - 89.97: 10 Dihedral angle restraints: 9572 sinusoidal: 4048 harmonic: 5524 Sorted by residual: dihedral pdb=" CA ASP D 416 " pdb=" C ASP D 416 " pdb=" N ARG D 417 " pdb=" CA ARG D 417 " ideal model delta harmonic sigma weight residual 180.00 159.33 20.67 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA ASP C 416 " pdb=" C ASP C 416 " pdb=" N ARG C 417 " pdb=" CA ARG C 417 " ideal model delta harmonic sigma weight residual 180.00 159.36 20.64 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA ASP A 416 " pdb=" C ASP A 416 " pdb=" N ARG A 417 " pdb=" CA ARG A 417 " ideal model delta harmonic sigma weight residual 180.00 159.38 20.62 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 9569 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2055 0.057 - 0.113: 351 0.113 - 0.170: 45 0.170 - 0.227: 3 0.227 - 0.283: 2 Chirality restraints: 2456 Sorted by residual: chirality pdb=" CA MET A 590 " pdb=" N MET A 590 " pdb=" C MET A 590 " pdb=" CB MET A 590 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CA LEU D 586 " pdb=" N LEU D 586 " pdb=" C LEU D 586 " pdb=" CB LEU D 586 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA ILE C 679 " pdb=" N ILE C 679 " pdb=" C ILE C 679 " pdb=" CB ILE C 679 " both_signs ideal model delta sigma weight residual False 2.43 2.22 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 2453 not shown) Planarity restraints: 2708 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 603 " -0.088 5.00e-02 4.00e+02 1.29e-01 2.65e+01 pdb=" N PRO B 604 " 0.222 5.00e-02 4.00e+02 pdb=" CA PRO B 604 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO B 604 " -0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET C 603 " -0.088 5.00e-02 4.00e+02 1.28e-01 2.60e+01 pdb=" N PRO C 604 " 0.220 5.00e-02 4.00e+02 pdb=" CA PRO C 604 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO C 604 " -0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 603 " 0.085 5.00e-02 4.00e+02 1.24e-01 2.46e+01 pdb=" N PRO A 604 " -0.214 5.00e-02 4.00e+02 pdb=" CA PRO A 604 " 0.063 5.00e-02 4.00e+02 pdb=" CD PRO A 604 " 0.066 5.00e-02 4.00e+02 ... (remaining 2705 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.32: 31 2.32 - 2.96: 7556 2.96 - 3.61: 22303 3.61 - 4.25: 34558 4.25 - 4.90: 60854 Nonbonded interactions: 125302 Sorted by model distance: nonbonded pdb=" O SER D 587 " pdb=" OG SER D 591 " model vdw 1.671 2.440 nonbonded pdb=" OD1 ASN A 681 " pdb=" CG2 THR B 683 " model vdw 1.707 3.460 nonbonded pdb=" NH2 ARG D 440 " pdb=" N PEF D 801 " model vdw 1.750 2.560 nonbonded pdb=" ND2 ASN C 578 " pdb=" CD2 LEU C 586 " model vdw 1.752 3.540 nonbonded pdb=" OD1 ASN B 681 " pdb=" CG2 THR C 683 " model vdw 1.900 3.460 ... (remaining 125297 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' and (resid 215 through 686 or resid 801 through 804)) selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 3.920 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 41.130 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 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 : 0.004 0.097 16176 Z= 0.233 Angle : 0.757 16.047 21916 Z= 0.407 Chirality : 0.044 0.283 2456 Planarity : 0.006 0.129 2696 Dihedral : 14.320 89.967 5992 Min Nonbonded Distance : 1.671 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.28 % Favored : 93.51 % Rotamer: Outliers : 0.77 % Allowed : 1.18 % Favored : 98.05 % 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: -0.59 (0.20), residues: 1848 helix: 0.66 (0.17), residues: 972 sheet: -1.34 (0.36), residues: 200 loop : -1.57 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 414 HIS 0.004 0.001 HIS B 379 PHE 0.033 0.001 PHE C 600 TYR 0.017 0.001 TYR D 249 ARG 0.006 0.000 ARG C 306 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 340 time to evaluate : 1.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 583 MET cc_start: 0.6266 (pmm) cc_final: 0.5385 (tpt) REVERT: A 684 TYR cc_start: 0.5167 (OUTLIER) cc_final: 0.3338 (m-10) REVERT: B 583 MET cc_start: 0.5745 (pmm) cc_final: 0.5064 (tpt) REVERT: B 585 GLN cc_start: 0.7584 (OUTLIER) cc_final: 0.7095 (mp10) REVERT: B 684 TYR cc_start: 0.5583 (OUTLIER) cc_final: 0.4750 (t80) REVERT: C 227 TYR cc_start: 0.7810 (t80) cc_final: 0.7604 (t80) REVERT: C 495 ILE cc_start: 0.8127 (tt) cc_final: 0.7911 (mt) REVERT: C 508 ASN cc_start: 0.8504 (m110) cc_final: 0.8196 (m-40) REVERT: C 583 MET cc_start: 0.5902 (pmm) cc_final: 0.5163 (tpt) REVERT: D 508 ASN cc_start: 0.8519 (m110) cc_final: 0.8296 (m-40) REVERT: D 583 MET cc_start: 0.6227 (pmm) cc_final: 0.5298 (tpt) outliers start: 13 outliers final: 6 residues processed: 353 average time/residue: 1.0747 time to fit residues: 426.2160 Evaluate side-chains 247 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 238 time to evaluate : 1.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 585 GLN Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 684 TYR Chi-restraints excluded: chain D residue 684 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 chunk 77 optimal weight: 0.1980 chunk 47 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 chunk 74 optimal weight: 9.9990 chunk 144 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 107 optimal weight: 0.0170 chunk 167 optimal weight: 2.9990 overall best weight: 1.0222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 ASN B 305 ASN B 543 ASN C 305 ASN C 543 ASN D 305 ASN D 379 HIS D 543 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16176 Z= 0.172 Angle : 0.568 7.646 21916 Z= 0.302 Chirality : 0.041 0.176 2456 Planarity : 0.006 0.190 2696 Dihedral : 10.146 89.328 2477 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.33 % Favored : 93.61 % Rotamer: Outliers : 3.14 % Allowed : 11.55 % Favored : 85.31 % 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: -0.48 (0.20), residues: 1848 helix: 0.74 (0.17), residues: 984 sheet: -0.87 (0.39), residues: 200 loop : -1.72 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 414 HIS 0.002 0.001 HIS C 498 PHE 0.022 0.001 PHE D 670 TYR 0.018 0.001 TYR C 249 ARG 0.026 0.000 ARG D 440 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 267 time to evaluate : 1.755 Fit side-chains REVERT: A 229 LEU cc_start: 0.8520 (mt) cc_final: 0.8282 (mp) REVERT: A 236 ILE cc_start: 0.9070 (OUTLIER) cc_final: 0.8817 (tp) REVERT: A 305 ASN cc_start: 0.7154 (p0) cc_final: 0.6852 (p0) REVERT: A 583 MET cc_start: 0.5734 (pmm) cc_final: 0.5226 (tpt) REVERT: A 602 ILE cc_start: 0.8104 (OUTLIER) cc_final: 0.7455 (tt) REVERT: A 684 TYR cc_start: 0.5229 (OUTLIER) cc_final: 0.3190 (m-10) REVERT: B 229 LEU cc_start: 0.8550 (mt) cc_final: 0.8271 (mp) REVERT: B 252 MET cc_start: 0.7563 (OUTLIER) cc_final: 0.7232 (mpp) REVERT: B 583 MET cc_start: 0.6236 (pmm) cc_final: 0.5538 (tpt) REVERT: B 602 ILE cc_start: 0.8146 (OUTLIER) cc_final: 0.7490 (tt) REVERT: B 651 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7171 (tm-30) REVERT: C 229 LEU cc_start: 0.8482 (mt) cc_final: 0.8211 (mp) REVERT: C 252 MET cc_start: 0.7586 (OUTLIER) cc_final: 0.7244 (mpp) REVERT: C 305 ASN cc_start: 0.6942 (OUTLIER) cc_final: 0.6705 (p0) REVERT: C 508 ASN cc_start: 0.8532 (m110) cc_final: 0.8282 (m-40) REVERT: C 583 MET cc_start: 0.6273 (pmm) cc_final: 0.5518 (tpt) REVERT: C 590 MET cc_start: 0.3816 (mtp) cc_final: 0.3058 (mmt) REVERT: C 651 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.6979 (tm-30) REVERT: D 229 LEU cc_start: 0.8431 (mt) cc_final: 0.8185 (mp) REVERT: D 252 MET cc_start: 0.7595 (OUTLIER) cc_final: 0.7264 (mpp) REVERT: D 583 MET cc_start: 0.6097 (pmm) cc_final: 0.5551 (tpt) REVERT: D 602 ILE cc_start: 0.7932 (OUTLIER) cc_final: 0.7320 (tt) outliers start: 53 outliers final: 11 residues processed: 290 average time/residue: 0.8893 time to fit residues: 297.1175 Evaluate side-chains 251 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 229 time to evaluate : 2.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 651 GLU Chi-restraints excluded: chain B residue 677 LEU Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 305 ASN Chi-restraints excluded: chain C residue 482 PHE Chi-restraints excluded: chain C residue 651 GLU Chi-restraints excluded: chain C residue 677 LEU Chi-restraints excluded: chain D residue 252 MET Chi-restraints excluded: chain D residue 482 PHE Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 683 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 46 optimal weight: 10.0000 chunk 167 optimal weight: 0.7980 chunk 180 optimal weight: 0.6980 chunk 149 optimal weight: 7.9990 chunk 165 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 chunk 134 optimal weight: 6.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 ASN B 305 ASN B 543 ASN C 543 ASN D 305 ASN D 543 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16176 Z= 0.241 Angle : 0.597 7.465 21916 Z= 0.318 Chirality : 0.042 0.186 2456 Planarity : 0.005 0.110 2696 Dihedral : 9.344 87.232 2462 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.03 % Favored : 92.80 % Rotamer: Outliers : 3.61 % Allowed : 14.93 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.20), residues: 1848 helix: 0.73 (0.17), residues: 984 sheet: -0.92 (0.38), residues: 200 loop : -1.53 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 414 HIS 0.003 0.001 HIS C 498 PHE 0.015 0.001 PHE B 538 TYR 0.022 0.002 TYR A 249 ARG 0.013 0.001 ARG D 440 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 246 time to evaluate : 1.832 Fit side-chains REVERT: A 229 LEU cc_start: 0.8540 (mt) cc_final: 0.8284 (mp) REVERT: A 252 MET cc_start: 0.7616 (OUTLIER) cc_final: 0.7193 (mpp) REVERT: A 305 ASN cc_start: 0.7072 (p0) cc_final: 0.6635 (p0) REVERT: A 583 MET cc_start: 0.5972 (pmm) cc_final: 0.5682 (tpt) REVERT: A 651 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7163 (tm-30) REVERT: A 684 TYR cc_start: 0.5227 (OUTLIER) cc_final: 0.3208 (m-10) REVERT: B 252 MET cc_start: 0.7636 (OUTLIER) cc_final: 0.7148 (mpp) REVERT: B 305 ASN cc_start: 0.7016 (OUTLIER) cc_final: 0.6629 (p0) REVERT: B 583 MET cc_start: 0.6319 (pmm) cc_final: 0.5505 (tpt) REVERT: B 590 MET cc_start: 0.4067 (mtp) cc_final: 0.3684 (mtm) REVERT: B 602 ILE cc_start: 0.8327 (OUTLIER) cc_final: 0.7749 (tt) REVERT: B 651 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7307 (tm-30) REVERT: C 252 MET cc_start: 0.7656 (OUTLIER) cc_final: 0.7144 (mpp) REVERT: C 583 MET cc_start: 0.6391 (pmm) cc_final: 0.5514 (tpt) REVERT: C 590 MET cc_start: 0.4020 (mtp) cc_final: 0.3364 (mmt) REVERT: C 651 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7074 (tm-30) REVERT: D 252 MET cc_start: 0.7667 (OUTLIER) cc_final: 0.7189 (mpp) REVERT: D 305 ASN cc_start: 0.7045 (OUTLIER) cc_final: 0.6832 (p0) REVERT: D 312 GLU cc_start: 0.8005 (pm20) cc_final: 0.7785 (pm20) REVERT: D 583 MET cc_start: 0.5984 (pmm) cc_final: 0.5452 (tpt) REVERT: D 602 ILE cc_start: 0.8094 (OUTLIER) cc_final: 0.7519 (tt) outliers start: 61 outliers final: 20 residues processed: 270 average time/residue: 0.9196 time to fit residues: 286.4137 Evaluate side-chains 262 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 230 time to evaluate : 1.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 264 LYS Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 651 GLU Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 264 LYS Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 651 GLU Chi-restraints excluded: chain B residue 677 LEU Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 482 PHE Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 651 GLU Chi-restraints excluded: chain C residue 677 LEU Chi-restraints excluded: chain D residue 252 MET Chi-restraints excluded: chain D residue 305 ASN Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 482 PHE Chi-restraints excluded: chain D residue 582 THR Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 677 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 8.9990 chunk 125 optimal weight: 5.9990 chunk 86 optimal weight: 0.0270 chunk 18 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 167 optimal weight: 4.9990 chunk 177 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 159 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 overall best weight: 1.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 ASN B 305 ASN B 543 ASN C 508 ASN C 543 ASN D 305 ASN D 543 ASN D 580 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16176 Z= 0.161 Angle : 0.544 7.244 21916 Z= 0.289 Chirality : 0.040 0.160 2456 Planarity : 0.006 0.222 2696 Dihedral : 8.986 88.860 2462 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.60 % Favored : 93.34 % Rotamer: Outliers : 3.08 % Allowed : 17.00 % Favored : 79.92 % 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: -0.35 (0.20), residues: 1848 helix: 0.80 (0.17), residues: 984 sheet: -0.88 (0.38), residues: 200 loop : -1.55 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 414 HIS 0.002 0.000 HIS D 498 PHE 0.022 0.001 PHE A 670 TYR 0.022 0.001 TYR B 527 ARG 0.013 0.000 ARG D 440 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 253 time to evaluate : 1.982 Fit side-chains revert: symmetry clash REVERT: A 229 LEU cc_start: 0.8542 (mt) cc_final: 0.8331 (mp) REVERT: A 252 MET cc_start: 0.7589 (OUTLIER) cc_final: 0.7138 (mpp) REVERT: A 305 ASN cc_start: 0.6965 (p0) cc_final: 0.6532 (p0) REVERT: A 590 MET cc_start: 0.6488 (mmt) cc_final: 0.5966 (ptm) REVERT: A 602 ILE cc_start: 0.8345 (OUTLIER) cc_final: 0.8012 (pp) REVERT: A 651 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7083 (tm-30) REVERT: A 684 TYR cc_start: 0.5182 (OUTLIER) cc_final: 0.3158 (m-10) REVERT: B 229 LEU cc_start: 0.8541 (mt) cc_final: 0.8273 (mp) REVERT: B 252 MET cc_start: 0.7616 (OUTLIER) cc_final: 0.7128 (mpp) REVERT: B 305 ASN cc_start: 0.6914 (OUTLIER) cc_final: 0.6373 (p0) REVERT: B 312 GLU cc_start: 0.7922 (pm20) cc_final: 0.7697 (pm20) REVERT: B 343 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7295 (mp0) REVERT: B 583 MET cc_start: 0.6392 (pmm) cc_final: 0.5529 (tpt) REVERT: B 590 MET cc_start: 0.4119 (mtp) cc_final: 0.3653 (mtm) REVERT: B 602 ILE cc_start: 0.8355 (OUTLIER) cc_final: 0.7733 (tt) REVERT: B 651 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7218 (tm-30) REVERT: C 252 MET cc_start: 0.7628 (OUTLIER) cc_final: 0.7139 (mpp) REVERT: C 343 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7328 (mp0) REVERT: C 583 MET cc_start: 0.6319 (pmm) cc_final: 0.5376 (tpt) REVERT: C 590 MET cc_start: 0.4288 (mtp) cc_final: 0.3713 (ptt) REVERT: C 651 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.6982 (tm-30) REVERT: D 252 MET cc_start: 0.7648 (OUTLIER) cc_final: 0.7167 (mpp) REVERT: D 305 ASN cc_start: 0.6962 (OUTLIER) cc_final: 0.6617 (p0) REVERT: D 343 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7316 (mp0) REVERT: D 583 MET cc_start: 0.5862 (pmm) cc_final: 0.5370 (tpt) REVERT: D 602 ILE cc_start: 0.8133 (OUTLIER) cc_final: 0.7566 (tt) outliers start: 52 outliers final: 18 residues processed: 278 average time/residue: 0.9227 time to fit residues: 294.3729 Evaluate side-chains 264 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 230 time to evaluate : 1.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 651 GLU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 651 GLU Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 482 PHE Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 651 GLU Chi-restraints excluded: chain D residue 252 MET Chi-restraints excluded: chain D residue 305 ASN Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 482 PHE Chi-restraints excluded: chain D residue 582 THR Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 624 ASP Chi-restraints excluded: chain D residue 683 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 5.9990 chunk 100 optimal weight: 0.0030 chunk 2 optimal weight: 6.9990 chunk 132 optimal weight: 0.0670 chunk 73 optimal weight: 5.9990 chunk 151 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 90 optimal weight: 0.9980 chunk 159 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 overall best weight: 0.8130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 305 ASN B 543 ASN C 543 ASN D 305 ASN D 543 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16176 Z= 0.147 Angle : 0.532 7.188 21916 Z= 0.282 Chirality : 0.039 0.150 2456 Planarity : 0.005 0.216 2696 Dihedral : 8.404 89.164 2462 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.76 % Favored : 93.18 % Rotamer: Outliers : 3.02 % Allowed : 17.12 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.20), residues: 1848 helix: 1.12 (0.17), residues: 940 sheet: -0.82 (0.39), residues: 200 loop : -1.61 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 414 HIS 0.002 0.000 HIS D 379 PHE 0.016 0.001 PHE B 538 TYR 0.020 0.001 TYR B 527 ARG 0.010 0.000 ARG D 440 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 251 time to evaluate : 1.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 MET cc_start: 0.7542 (OUTLIER) cc_final: 0.7076 (mpp) REVERT: A 305 ASN cc_start: 0.6960 (p0) cc_final: 0.6509 (p0) REVERT: A 602 ILE cc_start: 0.8414 (OUTLIER) cc_final: 0.8056 (pp) REVERT: A 684 TYR cc_start: 0.5163 (OUTLIER) cc_final: 0.3149 (m-10) REVERT: B 252 MET cc_start: 0.7559 (OUTLIER) cc_final: 0.7074 (mpp) REVERT: B 305 ASN cc_start: 0.6899 (OUTLIER) cc_final: 0.6263 (p0) REVERT: B 343 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7277 (mp0) REVERT: B 583 MET cc_start: 0.6455 (pmm) cc_final: 0.5478 (tpt) REVERT: B 590 MET cc_start: 0.4289 (mtp) cc_final: 0.3588 (mtm) REVERT: B 602 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.7784 (tt) REVERT: B 651 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7193 (tm-30) REVERT: C 252 MET cc_start: 0.7584 (OUTLIER) cc_final: 0.7086 (mpp) REVERT: C 305 ASN cc_start: 0.6871 (p0) cc_final: 0.6183 (p0) REVERT: C 343 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7323 (mp0) REVERT: C 583 MET cc_start: 0.6105 (pmm) cc_final: 0.5268 (tpt) REVERT: C 590 MET cc_start: 0.4270 (mtp) cc_final: 0.3524 (ptm) REVERT: C 609 LEU cc_start: 0.8582 (mt) cc_final: 0.8179 (mp) REVERT: D 252 MET cc_start: 0.7600 (OUTLIER) cc_final: 0.7121 (mpp) REVERT: D 305 ASN cc_start: 0.6942 (OUTLIER) cc_final: 0.6522 (p0) REVERT: D 343 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7281 (mp0) REVERT: D 583 MET cc_start: 0.5894 (pmm) cc_final: 0.5564 (tpt) REVERT: D 590 MET cc_start: 0.5332 (ptt) cc_final: 0.4950 (ppp) REVERT: D 602 ILE cc_start: 0.8072 (OUTLIER) cc_final: 0.7432 (tt) REVERT: D 603 MET cc_start: 0.7175 (ttp) cc_final: 0.6705 (ttt) outliers start: 51 outliers final: 21 residues processed: 275 average time/residue: 0.9284 time to fit residues: 292.8343 Evaluate side-chains 262 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 227 time to evaluate : 1.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 651 GLU Chi-restraints excluded: chain B residue 677 LEU Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain C residue 482 PHE Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 677 LEU Chi-restraints excluded: chain D residue 252 MET Chi-restraints excluded: chain D residue 305 ASN Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 482 PHE Chi-restraints excluded: chain D residue 582 THR Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 624 ASP Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 683 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 178 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 82 optimal weight: 20.0000 chunk 14 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 305 ASN B 543 ASN C 543 ASN D 305 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16176 Z= 0.223 Angle : 0.581 7.387 21916 Z= 0.305 Chirality : 0.042 0.152 2456 Planarity : 0.005 0.144 2696 Dihedral : 8.289 85.962 2462 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.14 % Favored : 92.80 % Rotamer: Outliers : 3.08 % Allowed : 17.65 % Favored : 79.27 % 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: -0.26 (0.20), residues: 1848 helix: 0.90 (0.17), residues: 964 sheet: -0.80 (0.39), residues: 200 loop : -1.50 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 414 HIS 0.002 0.001 HIS D 498 PHE 0.026 0.001 PHE A 670 TYR 0.022 0.002 TYR B 527 ARG 0.006 0.000 ARG D 440 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 244 time to evaluate : 1.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.8532 (mt) cc_final: 0.8277 (mp) REVERT: A 252 MET cc_start: 0.7616 (OUTLIER) cc_final: 0.7159 (mpp) REVERT: A 305 ASN cc_start: 0.7032 (p0) cc_final: 0.6531 (p0) REVERT: A 602 ILE cc_start: 0.8488 (OUTLIER) cc_final: 0.8130 (pp) REVERT: A 609 LEU cc_start: 0.8551 (mt) cc_final: 0.8348 (mp) REVERT: A 684 TYR cc_start: 0.5238 (OUTLIER) cc_final: 0.3233 (m-10) REVERT: B 252 MET cc_start: 0.7616 (OUTLIER) cc_final: 0.7149 (mpp) REVERT: B 305 ASN cc_start: 0.6947 (OUTLIER) cc_final: 0.6123 (p0) REVERT: B 343 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7379 (mp0) REVERT: B 538 PHE cc_start: 0.8311 (OUTLIER) cc_final: 0.8045 (t80) REVERT: B 583 MET cc_start: 0.6463 (pmm) cc_final: 0.5469 (tpt) REVERT: B 590 MET cc_start: 0.4243 (mtp) cc_final: 0.3246 (ptm) REVERT: B 651 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7262 (tm-30) REVERT: C 252 MET cc_start: 0.7614 (OUTLIER) cc_final: 0.7146 (mpp) REVERT: C 305 ASN cc_start: 0.6892 (p0) cc_final: 0.6092 (p0) REVERT: C 583 MET cc_start: 0.6159 (pmm) cc_final: 0.5354 (tpt) REVERT: C 590 MET cc_start: 0.4295 (mtp) cc_final: 0.3476 (ptm) REVERT: C 609 LEU cc_start: 0.8637 (mt) cc_final: 0.8369 (mp) REVERT: D 252 MET cc_start: 0.7644 (OUTLIER) cc_final: 0.7179 (mpp) REVERT: D 305 ASN cc_start: 0.7141 (OUTLIER) cc_final: 0.6638 (p0) REVERT: D 343 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7378 (mp0) REVERT: D 583 MET cc_start: 0.5768 (pmm) cc_final: 0.5553 (tpt) REVERT: D 590 MET cc_start: 0.5483 (ptt) cc_final: 0.5011 (ppp) REVERT: D 602 ILE cc_start: 0.8143 (OUTLIER) cc_final: 0.7508 (tt) REVERT: D 609 LEU cc_start: 0.8600 (mt) cc_final: 0.8391 (mp) outliers start: 52 outliers final: 24 residues processed: 267 average time/residue: 0.8899 time to fit residues: 274.6677 Evaluate side-chains 265 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 228 time to evaluate : 2.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 538 PHE Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 651 GLU Chi-restraints excluded: chain B residue 677 LEU Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 482 PHE Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 677 LEU Chi-restraints excluded: chain D residue 252 MET Chi-restraints excluded: chain D residue 305 ASN Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 482 PHE Chi-restraints excluded: chain D residue 582 THR Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 624 ASP Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 683 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 149 optimal weight: 6.9990 chunk 99 optimal weight: 0.9980 chunk 177 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 81 optimal weight: 0.0170 overall best weight: 2.0024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 ASN B 305 ASN B 543 ASN C 543 ASN D 543 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16176 Z= 0.247 Angle : 0.599 7.822 21916 Z= 0.315 Chirality : 0.042 0.156 2456 Planarity : 0.005 0.119 2696 Dihedral : 8.191 86.433 2462 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.03 % Favored : 92.91 % Rotamer: Outliers : 3.14 % Allowed : 18.25 % Favored : 78.61 % 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: -0.30 (0.20), residues: 1848 helix: 0.85 (0.17), residues: 964 sheet: -0.80 (0.39), residues: 200 loop : -1.49 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 414 HIS 0.002 0.001 HIS C 498 PHE 0.013 0.001 PHE A 480 TYR 0.022 0.002 TYR B 527 ARG 0.004 0.000 ARG D 440 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 238 time to evaluate : 1.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 TYR cc_start: 0.7975 (t80) cc_final: 0.7478 (t80) REVERT: A 252 MET cc_start: 0.7643 (OUTLIER) cc_final: 0.7206 (mpp) REVERT: A 305 ASN cc_start: 0.7017 (p0) cc_final: 0.6563 (p0) REVERT: A 602 ILE cc_start: 0.8507 (OUTLIER) cc_final: 0.8155 (pp) REVERT: A 684 TYR cc_start: 0.5265 (OUTLIER) cc_final: 0.3281 (m-10) REVERT: B 252 MET cc_start: 0.7618 (OUTLIER) cc_final: 0.7162 (mpp) REVERT: B 305 ASN cc_start: 0.7023 (OUTLIER) cc_final: 0.6167 (p0) REVERT: B 343 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7395 (mp0) REVERT: B 583 MET cc_start: 0.6438 (pmm) cc_final: 0.5484 (tpt) REVERT: B 590 MET cc_start: 0.4369 (mtp) cc_final: 0.3350 (ptp) REVERT: B 602 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.8232 (pp) REVERT: B 651 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7246 (tm-30) REVERT: C 252 MET cc_start: 0.7638 (OUTLIER) cc_final: 0.7155 (mpp) REVERT: C 305 ASN cc_start: 0.6941 (p0) cc_final: 0.6119 (p0) REVERT: C 543 ASN cc_start: 0.8715 (OUTLIER) cc_final: 0.8515 (t0) REVERT: C 583 MET cc_start: 0.6209 (pmm) cc_final: 0.5297 (tpt) REVERT: C 590 MET cc_start: 0.4221 (mtp) cc_final: 0.3438 (ptm) REVERT: C 651 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7211 (tm-30) REVERT: D 252 MET cc_start: 0.7647 (OUTLIER) cc_final: 0.7189 (mpp) REVERT: D 343 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7388 (mp0) REVERT: D 456 GLN cc_start: 0.7240 (OUTLIER) cc_final: 0.6802 (tt0) REVERT: D 583 MET cc_start: 0.5677 (pmm) cc_final: 0.5465 (tpt) REVERT: D 590 MET cc_start: 0.5332 (ptt) cc_final: 0.4863 (ppp) REVERT: D 597 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7312 (mp) REVERT: D 602 ILE cc_start: 0.8249 (OUTLIER) cc_final: 0.7630 (tt) outliers start: 53 outliers final: 25 residues processed: 262 average time/residue: 0.9157 time to fit residues: 275.0104 Evaluate side-chains 270 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 229 time to evaluate : 1.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 464 ARG Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 651 GLU Chi-restraints excluded: chain B residue 677 LEU Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 482 PHE Chi-restraints excluded: chain C residue 543 ASN Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 651 GLU Chi-restraints excluded: chain C residue 677 LEU Chi-restraints excluded: chain D residue 252 MET Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 456 GLN Chi-restraints excluded: chain D residue 482 PHE Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 582 THR Chi-restraints excluded: chain D residue 597 LEU Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 624 ASP Chi-restraints excluded: chain D residue 677 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 105 optimal weight: 0.5980 chunk 53 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 120 optimal weight: 10.0000 chunk 87 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 139 optimal weight: 0.8980 chunk 161 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 305 ASN B 543 ASN ** B 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 543 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16176 Z= 0.257 Angle : 0.609 8.211 21916 Z= 0.320 Chirality : 0.043 0.158 2456 Planarity : 0.005 0.106 2696 Dihedral : 8.169 89.512 2462 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.98 % Favored : 92.97 % Rotamer: Outliers : 3.02 % Allowed : 18.90 % Favored : 78.08 % 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: -0.34 (0.20), residues: 1848 helix: 0.81 (0.17), residues: 964 sheet: -0.82 (0.39), residues: 200 loop : -1.50 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 414 HIS 0.002 0.001 HIS C 498 PHE 0.027 0.002 PHE A 670 TYR 0.022 0.002 TYR B 527 ARG 0.003 0.000 ARG D 440 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 247 time to evaluate : 1.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 TYR cc_start: 0.8017 (t80) cc_final: 0.7465 (t80) REVERT: A 252 MET cc_start: 0.7645 (OUTLIER) cc_final: 0.7243 (mpp) REVERT: A 305 ASN cc_start: 0.7031 (p0) cc_final: 0.6572 (p0) REVERT: A 602 ILE cc_start: 0.8523 (OUTLIER) cc_final: 0.8178 (pp) REVERT: A 684 TYR cc_start: 0.5271 (OUTLIER) cc_final: 0.3286 (m-10) REVERT: B 252 MET cc_start: 0.7625 (OUTLIER) cc_final: 0.7164 (mpp) REVERT: B 305 ASN cc_start: 0.7085 (OUTLIER) cc_final: 0.6165 (p0) REVERT: B 583 MET cc_start: 0.6426 (pmm) cc_final: 0.5494 (tpt) REVERT: B 590 MET cc_start: 0.4404 (mtp) cc_final: 0.3392 (ptp) REVERT: B 602 ILE cc_start: 0.8522 (OUTLIER) cc_final: 0.7987 (tt) REVERT: B 651 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7301 (tm-30) REVERT: C 252 MET cc_start: 0.7640 (OUTLIER) cc_final: 0.7171 (mpp) REVERT: C 305 ASN cc_start: 0.6872 (p0) cc_final: 0.6028 (p0) REVERT: C 583 MET cc_start: 0.6188 (pmm) cc_final: 0.5267 (tpt) REVERT: C 590 MET cc_start: 0.3852 (mtp) cc_final: 0.3218 (ptm) REVERT: C 602 ILE cc_start: 0.8579 (OUTLIER) cc_final: 0.8003 (tt) REVERT: C 651 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7204 (tm-30) REVERT: D 252 MET cc_start: 0.7653 (OUTLIER) cc_final: 0.7194 (mpp) REVERT: D 456 GLN cc_start: 0.7324 (OUTLIER) cc_final: 0.6866 (tt0) REVERT: D 583 MET cc_start: 0.5717 (pmm) cc_final: 0.5503 (tpt) REVERT: D 590 MET cc_start: 0.5285 (ptt) cc_final: 0.4819 (ppp) REVERT: D 602 ILE cc_start: 0.8267 (OUTLIER) cc_final: 0.7722 (tt) outliers start: 51 outliers final: 26 residues processed: 271 average time/residue: 0.9308 time to fit residues: 289.0552 Evaluate side-chains 272 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 233 time to evaluate : 1.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 464 ARG Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 651 GLU Chi-restraints excluded: chain B residue 677 LEU Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 482 PHE Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 602 ILE Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 651 GLU Chi-restraints excluded: chain C residue 677 LEU Chi-restraints excluded: chain D residue 252 MET Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 456 GLN Chi-restraints excluded: chain D residue 482 PHE Chi-restraints excluded: chain D residue 582 THR Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 624 ASP Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 683 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 6.9990 chunk 155 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 129 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 149 optimal weight: 0.0770 chunk 156 optimal weight: 0.7980 chunk 164 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 overall best weight: 1.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 305 ASN C 543 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16176 Z= 0.181 Angle : 0.578 11.323 21916 Z= 0.302 Chirality : 0.041 0.140 2456 Planarity : 0.004 0.080 2696 Dihedral : 7.899 89.572 2462 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.82 % Favored : 93.13 % Rotamer: Outliers : 2.43 % Allowed : 19.96 % Favored : 77.61 % 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: -0.25 (0.20), residues: 1848 helix: 0.93 (0.17), residues: 964 sheet: -0.78 (0.39), residues: 200 loop : -1.52 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 414 HIS 0.001 0.000 HIS D 498 PHE 0.019 0.001 PHE B 485 TYR 0.021 0.001 TYR B 527 ARG 0.003 0.000 ARG B 306 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 240 time to evaluate : 1.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 MET cc_start: 0.7607 (OUTLIER) cc_final: 0.7169 (mpp) REVERT: A 305 ASN cc_start: 0.6964 (p0) cc_final: 0.6539 (p0) REVERT: A 602 ILE cc_start: 0.8476 (OUTLIER) cc_final: 0.8153 (pp) REVERT: B 252 MET cc_start: 0.7596 (OUTLIER) cc_final: 0.7122 (mpp) REVERT: B 305 ASN cc_start: 0.7252 (OUTLIER) cc_final: 0.6344 (p0) REVERT: B 455 TRP cc_start: 0.8352 (OUTLIER) cc_final: 0.7714 (p90) REVERT: B 583 MET cc_start: 0.6273 (pmm) cc_final: 0.5435 (tpt) REVERT: B 590 MET cc_start: 0.4336 (mtp) cc_final: 0.3495 (ptp) REVERT: B 602 ILE cc_start: 0.8470 (OUTLIER) cc_final: 0.7903 (tt) REVERT: B 651 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7223 (tm-30) REVERT: C 252 MET cc_start: 0.7614 (OUTLIER) cc_final: 0.7123 (mpp) REVERT: C 305 ASN cc_start: 0.6855 (p0) cc_final: 0.5956 (p0) REVERT: C 543 ASN cc_start: 0.8770 (OUTLIER) cc_final: 0.8518 (t0) REVERT: C 583 MET cc_start: 0.5767 (pmm) cc_final: 0.5173 (tpt) REVERT: C 590 MET cc_start: 0.3827 (mtp) cc_final: 0.3221 (ptm) REVERT: C 602 ILE cc_start: 0.8546 (OUTLIER) cc_final: 0.7922 (tt) REVERT: D 252 MET cc_start: 0.7637 (OUTLIER) cc_final: 0.7164 (mpp) REVERT: D 456 GLN cc_start: 0.7236 (OUTLIER) cc_final: 0.6924 (tt0) REVERT: D 590 MET cc_start: 0.5342 (ptt) cc_final: 0.4860 (ppp) REVERT: D 602 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.7781 (tt) outliers start: 41 outliers final: 22 residues processed: 255 average time/residue: 0.9588 time to fit residues: 282.2023 Evaluate side-chains 263 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 228 time to evaluate : 1.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 464 ARG Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 455 TRP Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 651 GLU Chi-restraints excluded: chain B residue 677 LEU Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 482 PHE Chi-restraints excluded: chain C residue 543 ASN Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 602 ILE Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 677 LEU Chi-restraints excluded: chain D residue 252 MET Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 456 GLN Chi-restraints excluded: chain D residue 482 PHE Chi-restraints excluded: chain D residue 582 THR Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 624 ASP Chi-restraints excluded: chain D residue 683 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 8.9990 chunk 106 optimal weight: 0.0770 chunk 82 optimal weight: 4.9990 chunk 121 optimal weight: 0.9990 chunk 183 optimal weight: 0.7980 chunk 168 optimal weight: 5.9990 chunk 145 optimal weight: 4.9990 chunk 15 optimal weight: 0.0770 chunk 112 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 overall best weight: 0.9900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 305 ASN ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 543 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.193 16176 Z= 0.240 Angle : 0.785 59.147 21916 Z= 0.447 Chirality : 0.041 0.196 2456 Planarity : 0.004 0.083 2696 Dihedral : 7.895 89.643 2460 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.98 % Favored : 92.97 % Rotamer: Outliers : 2.25 % Allowed : 20.50 % Favored : 77.25 % Cbeta Deviations : 0.06 % 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: -0.24 (0.20), residues: 1848 helix: 0.93 (0.17), residues: 964 sheet: -0.78 (0.39), residues: 200 loop : -1.52 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 414 HIS 0.002 0.000 HIS D 379 PHE 0.014 0.001 PHE B 471 TYR 0.020 0.001 TYR B 527 ARG 0.005 0.000 ARG D 440 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 226 time to evaluate : 1.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 MET cc_start: 0.7604 (OUTLIER) cc_final: 0.7169 (mpp) REVERT: A 305 ASN cc_start: 0.6997 (p0) cc_final: 0.6570 (p0) REVERT: A 602 ILE cc_start: 0.8476 (OUTLIER) cc_final: 0.8151 (pp) REVERT: B 252 MET cc_start: 0.7594 (OUTLIER) cc_final: 0.7122 (mpp) REVERT: B 305 ASN cc_start: 0.7135 (OUTLIER) cc_final: 0.6603 (p0) REVERT: B 455 TRP cc_start: 0.8351 (OUTLIER) cc_final: 0.7712 (p90) REVERT: B 583 MET cc_start: 0.6270 (pmm) cc_final: 0.5434 (tpt) REVERT: B 590 MET cc_start: 0.4335 (mtp) cc_final: 0.3496 (ptp) REVERT: B 602 ILE cc_start: 0.8471 (OUTLIER) cc_final: 0.7901 (tt) REVERT: B 651 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7222 (tm-30) REVERT: C 252 MET cc_start: 0.7614 (OUTLIER) cc_final: 0.7120 (mpp) REVERT: C 305 ASN cc_start: 0.6856 (p0) cc_final: 0.5950 (p0) REVERT: C 543 ASN cc_start: 0.8603 (OUTLIER) cc_final: 0.7632 (t0) REVERT: C 583 MET cc_start: 0.5763 (pmm) cc_final: 0.5173 (tpt) REVERT: C 590 MET cc_start: 0.3822 (mtp) cc_final: 0.3220 (ptm) REVERT: C 602 ILE cc_start: 0.8545 (OUTLIER) cc_final: 0.7921 (tt) REVERT: D 252 MET cc_start: 0.7641 (OUTLIER) cc_final: 0.7163 (mpp) REVERT: D 456 GLN cc_start: 0.7301 (OUTLIER) cc_final: 0.6932 (tt0) REVERT: D 590 MET cc_start: 0.5359 (ptt) cc_final: 0.4859 (ppp) REVERT: D 602 ILE cc_start: 0.8313 (OUTLIER) cc_final: 0.7780 (tt) outliers start: 38 outliers final: 22 residues processed: 238 average time/residue: 0.8877 time to fit residues: 243.6798 Evaluate side-chains 258 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 223 time to evaluate : 1.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 464 ARG Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 455 TRP Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 651 GLU Chi-restraints excluded: chain B residue 677 LEU Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 482 PHE Chi-restraints excluded: chain C residue 543 ASN Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 602 ILE Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 677 LEU Chi-restraints excluded: chain D residue 252 MET Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 456 GLN Chi-restraints excluded: chain D residue 482 PHE Chi-restraints excluded: chain D residue 582 THR Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 624 ASP Chi-restraints excluded: chain D residue 683 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 134 optimal weight: 0.0470 chunk 21 optimal weight: 4.9990 chunk 40 optimal weight: 0.2980 chunk 146 optimal weight: 4.9990 chunk 61 optimal weight: 0.0020 chunk 150 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 128 optimal weight: 20.0000 overall best weight: 0.4288 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 543 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.159883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.110936 restraints weight = 18495.968| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.24 r_work: 0.3123 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.584 16176 Z= 0.403 Angle : 0.721 42.153 21916 Z= 0.460 Chirality : 0.042 0.571 2456 Planarity : 0.006 0.182 2696 Dihedral : 7.895 89.643 2460 Min Nonbonded Distance : 1.673 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.98 % Favored : 92.97 % Rotamer: Outliers : 2.01 % Allowed : 20.73 % Favored : 77.25 % Cbeta Deviations : 0.06 % 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: -0.24 (0.20), residues: 1848 helix: 0.93 (0.17), residues: 964 sheet: -0.78 (0.39), residues: 200 loop : -1.52 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 414 HIS 0.002 0.000 HIS D 379 PHE 0.014 0.001 PHE B 471 TYR 0.020 0.001 TYR B 527 ARG 0.005 0.000 ARG D 440 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5356.10 seconds wall clock time: 96 minutes 57.02 seconds (5817.02 seconds total)