Starting phenix.real_space_refine on Fri Feb 16 02:05:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m22_30058/02_2024/6m22_30058_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m22_30058/02_2024/6m22_30058.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m22_30058/02_2024/6m22_30058.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m22_30058/02_2024/6m22_30058.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m22_30058/02_2024/6m22_30058_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m22_30058/02_2024/6m22_30058_updated.pdb" } resolution = 2.7 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= 0.003 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 K 2 8.98 5 S 96 5.16 5 Cl 8 4.86 5 C 9090 2.51 5 N 2290 2.21 5 O 2542 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 116": "OE1" <-> "OE2" Residue "A GLU 394": "OE1" <-> "OE2" Residue "A PHE 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 557": "NH1" <-> "NH2" Residue "A GLU 567": "OE1" <-> "OE2" Residue "A ARG 688": "NH1" <-> "NH2" Residue "A ARG 693": "NH1" <-> "NH2" Residue "A GLU 696": "OE1" <-> "OE2" Residue "A ARG 705": "NH1" <-> "NH2" Residue "A TYR 753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 814": "NH1" <-> "NH2" Residue "A ARG 891": "NH1" <-> "NH2" Residue "A PHE 893": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 917": "NH1" <-> "NH2" Residue "A GLU 923": "OE1" <-> "OE2" Residue "A GLU 926": "OE1" <-> "OE2" Residue "A ARG 1032": "NH1" <-> "NH2" Residue "A ARG 1062": "NH1" <-> "NH2" Residue "A GLU 1065": "OE1" <-> "OE2" Residue "A ARG 1088": "NH1" <-> "NH2" Residue "B GLU 116": "OE1" <-> "OE2" Residue "B GLU 394": "OE1" <-> "OE2" Residue "B PHE 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 557": "NH1" <-> "NH2" Residue "B GLU 567": "OE1" <-> "OE2" Residue "B ARG 688": "NH1" <-> "NH2" Residue "B ARG 693": "NH1" <-> "NH2" Residue "B GLU 696": "OE1" <-> "OE2" Residue "B ARG 705": "NH1" <-> "NH2" Residue "B TYR 753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 814": "NH1" <-> "NH2" Residue "B ARG 891": "NH1" <-> "NH2" Residue "B PHE 893": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 917": "NH1" <-> "NH2" Residue "B GLU 923": "OE1" <-> "OE2" Residue "B GLU 926": "OE1" <-> "OE2" Residue "B ARG 1032": "NH1" <-> "NH2" Residue "B ARG 1062": "NH1" <-> "NH2" Residue "B GLU 1065": "OE1" <-> "OE2" Residue "B ARG 1088": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14028 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 6853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 885, 6853 Classifications: {'peptide': 885} Link IDs: {'PTRANS': 32, 'TRANS': 852} Chain breaks: 2 Chain: "B" Number of atoms: 6853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 885, 6853 Classifications: {'peptide': 885} Link IDs: {'PTRANS': 32, 'TRANS': 852} Chain breaks: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 57 Unusual residues: {' K': 1, ' CL': 2, 'EZC': 1, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 57 Unusual residues: {' K': 1, ' CL': 2, 'EZC': 1, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "B" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Time building chain proxies: 8.35, per 1000 atoms: 0.60 Number of scatterers: 14028 At special positions: 0 Unit cell: (92.395, 114.135, 155.441, 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) K 2 19.00 Cl 8 17.00 S 96 16.00 O 2542 8.00 N 2290 7.00 C 9090 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 324 " - pdb=" SG CYS A 339 " distance=2.04 Simple disulfide: pdb=" SG CYS B 324 " - pdb=" SG CYS B 339 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A1110 " - " ASN A 347 " " NAG A1111 " - " ASN A 360 " " NAG B1110 " - " ASN B 347 " " NAG B1111 " - " ASN B 360 " " NAG C 1 " - " ASN A 328 " " NAG D 1 " - " ASN A 366 " " NAG E 1 " - " ASN A 377 " " NAG F 1 " - " ASN B 328 " " NAG G 1 " - " ASN B 366 " " NAG H 1 " - " ASN B 377 " Time building additional restraints: 5.27 Conformation dependent library (CDL) restraints added in 2.6 seconds 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3256 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 72 helices and 4 sheets defined 50.3% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.85 Creating SS restraints... Processing helix chain 'A' and resid 136 through 139 No H-bonds generated for 'chain 'A' and resid 136 through 139' Processing helix chain 'A' and resid 141 through 148 removed outlier: 3.567A pdb=" N ASN A 147 " --> pdb=" O PRO A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 155 Processing helix chain 'A' and resid 157 through 162 Processing helix chain 'A' and resid 165 through 190 removed outlier: 3.547A pdb=" N ALA A 171 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR A 180 " --> pdb=" O CYS A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 208 removed outlier: 3.507A pdb=" N ALA A 208 " --> pdb=" O MET A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 241 removed outlier: 3.572A pdb=" N ALA A 230 " --> pdb=" O THR A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 284 Processing helix chain 'A' and resid 287 through 291 Processing helix chain 'A' and resid 293 through 315 removed outlier: 3.616A pdb=" N VAL A 300 " --> pdb=" O PHE A 296 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER A 303 " --> pdb=" O CYS A 299 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER A 314 " --> pdb=" O GLY A 310 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N SER A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 357 removed outlier: 3.588A pdb=" N PHE A 357 " --> pdb=" O LYS A 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 353 through 357' Processing helix chain 'A' and resid 391 through 394 Processing helix chain 'A' and resid 434 through 444 removed outlier: 3.557A pdb=" N GLY A 439 " --> pdb=" O THR A 435 " (cutoff:3.500A) Proline residue: A 443 - end of helix Processing helix chain 'A' and resid 448 through 452 removed outlier: 3.834A pdb=" N GLY A 451 " --> pdb=" O ILE A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 457 No H-bonds generated for 'chain 'A' and resid 455 through 457' Processing helix chain 'A' and resid 461 through 490 Proline residue: A 466 - end of helix removed outlier: 3.768A pdb=" N VAL A 485 " --> pdb=" O LEU A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 496 No H-bonds generated for 'chain 'A' and resid 493 through 496' Processing helix chain 'A' and resid 499 through 501 No H-bonds generated for 'chain 'A' and resid 499 through 501' Processing helix chain 'A' and resid 509 through 513 removed outlier: 3.743A pdb=" N LEU A 513 " --> pdb=" O VAL A 509 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 509 through 513' Processing helix chain 'A' and resid 519 through 548 Proline residue: A 541 - end of helix Processing helix chain 'A' and resid 554 through 559 removed outlier: 3.517A pdb=" N ARG A 557 " --> pdb=" O PRO A 554 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N VAL A 558 " --> pdb=" O PHE A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 584 removed outlier: 3.507A pdb=" N LEU A 581 " --> pdb=" O ALA A 577 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY A 582 " --> pdb=" O ILE A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 615 Proline residue: A 593 - end of helix removed outlier: 3.632A pdb=" N PHE A 598 " --> pdb=" O ILE A 594 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR A 614 " --> pdb=" O CYS A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 645 Processing helix chain 'A' and resid 650 through 674 removed outlier: 3.693A pdb=" N VAL A 654 " --> pdb=" O TYR A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 693 removed outlier: 3.867A pdb=" N SER A 683 " --> pdb=" O ILE A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 733 removed outlier: 3.597A pdb=" N PHE A 728 " --> pdb=" O LEU A 725 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA A 729 " --> pdb=" O LEU A 726 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS A 733 " --> pdb=" O SER A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 769 removed outlier: 3.605A pdb=" N GLN A 761 " --> pdb=" O LEU A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 793 Processing helix chain 'A' and resid 821 through 834 removed outlier: 3.840A pdb=" N PHE A 825 " --> pdb=" O ALA A 821 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE A 826 " --> pdb=" O TRP A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 847 No H-bonds generated for 'chain 'A' and resid 845 through 847' Processing helix chain 'A' and resid 869 through 881 Proline residue: A 876 - end of helix removed outlier: 3.997A pdb=" N GLN A 881 " --> pdb=" O PHE A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 914 Processing helix chain 'A' and resid 1032 through 1035 No H-bonds generated for 'chain 'A' and resid 1032 through 1035' Processing helix chain 'A' and resid 1037 through 1047 removed outlier: 3.554A pdb=" N VAL A1042 " --> pdb=" O LYS A1038 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1077 Processing helix chain 'B' and resid 136 through 139 No H-bonds generated for 'chain 'B' and resid 136 through 139' Processing helix chain 'B' and resid 141 through 148 removed outlier: 3.567A pdb=" N ASN B 147 " --> pdb=" O PRO B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 155 Processing helix chain 'B' and resid 157 through 162 Processing helix chain 'B' and resid 165 through 190 removed outlier: 3.547A pdb=" N ALA B 171 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR B 180 " --> pdb=" O CYS B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 208 removed outlier: 3.507A pdb=" N ALA B 208 " --> pdb=" O MET B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 241 removed outlier: 3.572A pdb=" N ALA B 230 " --> pdb=" O THR B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 284 Processing helix chain 'B' and resid 287 through 291 Processing helix chain 'B' and resid 293 through 315 removed outlier: 3.616A pdb=" N VAL B 300 " --> pdb=" O PHE B 296 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER B 303 " --> pdb=" O CYS B 299 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER B 314 " --> pdb=" O GLY B 310 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N SER B 315 " --> pdb=" O ALA B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 357 removed outlier: 3.588A pdb=" N PHE B 357 " --> pdb=" O LYS B 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 353 through 357' Processing helix chain 'B' and resid 391 through 394 Processing helix chain 'B' and resid 434 through 444 removed outlier: 3.557A pdb=" N GLY B 439 " --> pdb=" O THR B 435 " (cutoff:3.500A) Proline residue: B 443 - end of helix Processing helix chain 'B' and resid 448 through 452 removed outlier: 3.834A pdb=" N GLY B 451 " --> pdb=" O ILE B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 457 No H-bonds generated for 'chain 'B' and resid 455 through 457' Processing helix chain 'B' and resid 461 through 490 Proline residue: B 466 - end of helix removed outlier: 3.768A pdb=" N VAL B 485 " --> pdb=" O LEU B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 496 No H-bonds generated for 'chain 'B' and resid 493 through 496' Processing helix chain 'B' and resid 499 through 501 No H-bonds generated for 'chain 'B' and resid 499 through 501' Processing helix chain 'B' and resid 509 through 513 removed outlier: 3.743A pdb=" N LEU B 513 " --> pdb=" O VAL B 509 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 509 through 513' Processing helix chain 'B' and resid 519 through 548 Proline residue: B 541 - end of helix Processing helix chain 'B' and resid 554 through 559 removed outlier: 3.517A pdb=" N ARG B 557 " --> pdb=" O PRO B 554 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N VAL B 558 " --> pdb=" O PHE B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 584 removed outlier: 3.507A pdb=" N LEU B 581 " --> pdb=" O ALA B 577 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY B 582 " --> pdb=" O ILE B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 615 Proline residue: B 593 - end of helix removed outlier: 3.632A pdb=" N PHE B 598 " --> pdb=" O ILE B 594 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR B 614 " --> pdb=" O CYS B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 645 Processing helix chain 'B' and resid 650 through 674 removed outlier: 3.693A pdb=" N VAL B 654 " --> pdb=" O TYR B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 693 removed outlier: 3.867A pdb=" N SER B 683 " --> pdb=" O ILE B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 733 removed outlier: 3.597A pdb=" N PHE B 728 " --> pdb=" O LEU B 725 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA B 729 " --> pdb=" O LEU B 726 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS B 733 " --> pdb=" O SER B 730 " (cutoff:3.500A) Processing helix chain 'B' and resid 753 through 769 removed outlier: 3.605A pdb=" N GLN B 761 " --> pdb=" O LEU B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 793 Processing helix chain 'B' and resid 821 through 834 removed outlier: 3.840A pdb=" N PHE B 825 " --> pdb=" O ALA B 821 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE B 826 " --> pdb=" O TRP B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 845 through 847 No H-bonds generated for 'chain 'B' and resid 845 through 847' Processing helix chain 'B' and resid 869 through 881 Proline residue: B 876 - end of helix removed outlier: 3.997A pdb=" N GLN B 881 " --> pdb=" O PHE B 877 " (cutoff:3.500A) Processing helix chain 'B' and resid 903 through 914 Processing helix chain 'B' and resid 1032 through 1035 No H-bonds generated for 'chain 'B' and resid 1032 through 1035' Processing helix chain 'B' and resid 1037 through 1047 removed outlier: 3.554A pdb=" N VAL B1042 " --> pdb=" O LYS B1038 " (cutoff:3.500A) Processing helix chain 'B' and resid 1067 through 1077 Processing sheet with id= A, first strand: chain 'A' and resid 322 through 326 Processing sheet with id= B, first strand: chain 'A' and resid 920 through 926 removed outlier: 6.988A pdb=" N ILE A 890 " --> pdb=" O GLU A 921 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N GLU A 923 " --> pdb=" O ILE A 890 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ILE A 892 " --> pdb=" O GLU A 923 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N VAL A 925 " --> pdb=" O ILE A 892 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N THR A 894 " --> pdb=" O VAL A 925 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N VAL A 895 " --> pdb=" O TRP A 864 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASN A1056 " --> pdb=" O TRP A 863 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL A1084 " --> pdb=" O LYS A 843 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N GLY A 808 " --> pdb=" O LEU A 711 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N VAL A 744 " --> pdb=" O LEU A 712 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N PHE A 775 " --> pdb=" O VAL A 741 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N SER A 743 " --> pdb=" O PHE A 775 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLN A 777 " --> pdb=" O SER A 743 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N ILE A 745 " --> pdb=" O GLN A 777 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL A 779 " --> pdb=" O ILE A 745 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 322 through 326 Processing sheet with id= D, first strand: chain 'B' and resid 920 through 926 removed outlier: 6.988A pdb=" N ILE B 890 " --> pdb=" O GLU B 921 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N GLU B 923 " --> pdb=" O ILE B 890 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ILE B 892 " --> pdb=" O GLU B 923 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N VAL B 925 " --> pdb=" O ILE B 892 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N THR B 894 " --> pdb=" O VAL B 925 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N VAL B 895 " --> pdb=" O TRP B 864 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASN B1056 " --> pdb=" O TRP B 863 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL B1084 " --> pdb=" O LYS B 843 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N GLY B 808 " --> pdb=" O LEU B 711 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N VAL B 744 " --> pdb=" O LEU B 712 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N PHE B 775 " --> pdb=" O VAL B 741 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N SER B 743 " --> pdb=" O PHE B 775 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLN B 777 " --> pdb=" O SER B 743 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N ILE B 745 " --> pdb=" O GLN B 777 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL B 779 " --> pdb=" O ILE B 745 " (cutoff:3.500A) 588 hydrogen bonds defined for protein. 1716 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: 4.76 Time building geometry restraints manager: 5.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 2178 1.30 - 1.43: 3856 1.43 - 1.56: 8094 1.56 - 1.69: 16 1.69 - 1.82: 158 Bond restraints: 14302 Sorted by residual: bond pdb=" C07 EZC A1112 " pdb=" C11 EZC A1112 " ideal model delta sigma weight residual 1.543 1.330 0.213 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C07 EZC B1112 " pdb=" C11 EZC B1112 " ideal model delta sigma weight residual 1.543 1.330 0.213 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C08 EZC A1112 " pdb=" C10 EZC A1112 " ideal model delta sigma weight residual 1.537 1.345 0.192 2.00e-02 2.50e+03 9.19e+01 bond pdb=" C08 EZC B1112 " pdb=" C10 EZC B1112 " ideal model delta sigma weight residual 1.537 1.349 0.188 2.00e-02 2.50e+03 8.85e+01 bond pdb=" C13 EZC B1112 " pdb=" C14 EZC B1112 " ideal model delta sigma weight residual 1.540 1.369 0.171 2.00e-02 2.50e+03 7.32e+01 ... (remaining 14297 not shown) Histogram of bond angle deviations from ideal: 98.89 - 106.73: 424 106.73 - 114.57: 8498 114.57 - 122.41: 8526 122.41 - 130.25: 1870 130.25 - 138.09: 104 Bond angle restraints: 19422 Sorted by residual: angle pdb=" N LEU B 708 " pdb=" CA LEU B 708 " pdb=" C LEU B 708 " ideal model delta sigma weight residual 110.48 123.69 -13.21 1.48e+00 4.57e-01 7.96e+01 angle pdb=" N LEU A 708 " pdb=" CA LEU A 708 " pdb=" C LEU A 708 " ideal model delta sigma weight residual 110.48 123.69 -13.21 1.48e+00 4.57e-01 7.96e+01 angle pdb=" N VAL B 374 " pdb=" CA VAL B 374 " pdb=" C VAL B 374 " ideal model delta sigma weight residual 110.62 105.12 5.50 1.02e+00 9.61e-01 2.90e+01 angle pdb=" N VAL A 374 " pdb=" CA VAL A 374 " pdb=" C VAL A 374 " ideal model delta sigma weight residual 110.62 105.12 5.50 1.02e+00 9.61e-01 2.90e+01 angle pdb=" N LEU A 709 " pdb=" CA LEU A 709 " pdb=" C LEU A 709 " ideal model delta sigma weight residual 108.02 98.89 9.13 1.78e+00 3.16e-01 2.63e+01 ... (remaining 19417 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.32: 8049 22.32 - 44.63: 513 44.63 - 66.95: 60 66.95 - 89.26: 6 89.26 - 111.58: 6 Dihedral angle restraints: 8634 sinusoidal: 3564 harmonic: 5070 Sorted by residual: dihedral pdb=" CA ALA B 216 " pdb=" C ALA B 216 " pdb=" N VAL B 217 " pdb=" CA VAL B 217 " ideal model delta harmonic sigma weight residual 180.00 153.73 26.27 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA ALA A 216 " pdb=" C ALA A 216 " pdb=" N VAL A 217 " pdb=" CA VAL A 217 " ideal model delta harmonic sigma weight residual 180.00 153.73 26.27 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA GLU B 716 " pdb=" C GLU B 716 " pdb=" N ASP B 717 " pdb=" CA ASP B 717 " ideal model delta harmonic sigma weight residual -180.00 -154.93 -25.07 0 5.00e+00 4.00e-02 2.51e+01 ... (remaining 8631 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1820 0.066 - 0.132: 403 0.132 - 0.198: 53 0.198 - 0.264: 12 0.264 - 0.330: 8 Chirality restraints: 2296 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.71 0.31 2.00e-02 2.50e+03 2.40e+02 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.71 0.31 2.00e-02 2.50e+03 2.40e+02 chirality pdb=" CA LEU A 708 " pdb=" N LEU A 708 " pdb=" C LEU A 708 " pdb=" CB LEU A 708 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.73e+00 ... (remaining 2293 not shown) Planarity restraints: 2400 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 377 " 0.058 2.00e-02 2.50e+03 1.10e-01 1.50e+02 pdb=" CG ASN A 377 " -0.034 2.00e-02 2.50e+03 pdb=" OD1 ASN A 377 " 0.047 2.00e-02 2.50e+03 pdb=" ND2 ASN A 377 " -0.195 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " 0.124 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 377 " -0.058 2.00e-02 2.50e+03 1.10e-01 1.50e+02 pdb=" CG ASN B 377 " 0.034 2.00e-02 2.50e+03 pdb=" OD1 ASN B 377 " -0.047 2.00e-02 2.50e+03 pdb=" ND2 ASN B 377 " 0.195 2.00e-02 2.50e+03 pdb=" C1 NAG H 1 " -0.124 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 328 " -0.022 2.00e-02 2.50e+03 6.25e-02 4.89e+01 pdb=" CG ASN A 328 " 0.021 2.00e-02 2.50e+03 pdb=" OD1 ASN A 328 " -0.046 2.00e-02 2.50e+03 pdb=" ND2 ASN A 328 " 0.111 2.00e-02 2.50e+03 pdb=" C1 NAG C 1 " -0.064 2.00e-02 2.50e+03 ... (remaining 2397 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.60: 102 2.60 - 3.23: 12693 3.23 - 3.87: 26435 3.87 - 4.50: 36454 4.50 - 5.14: 56754 Nonbonded interactions: 132438 Sorted by model distance: nonbonded pdb=" OE1 GLU B1065 " pdb=" N GLY B1066 " model vdw 1.962 2.520 nonbonded pdb=" OE1 GLU A1065 " pdb=" N GLY A1066 " model vdw 1.962 2.520 nonbonded pdb=" N ASN A1063 " pdb=" OD1 ASN A1063 " model vdw 2.297 2.520 nonbonded pdb=" N ASN B1063 " pdb=" OD1 ASN B1063 " model vdw 2.297 2.520 nonbonded pdb=" OH TYR B 372 " pdb=" OG SER B 414 " model vdw 2.297 2.440 ... (remaining 132433 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.700 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 41.100 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.213 14302 Z= 0.573 Angle : 1.045 13.207 19422 Z= 0.573 Chirality : 0.059 0.330 2296 Planarity : 0.007 0.096 2390 Dihedral : 14.669 111.579 5372 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.80 % Allowed : 7.51 % Favored : 91.70 % Rotamer: Outliers : 1.22 % Allowed : 4.06 % Favored : 94.72 % 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: -5.21 (0.14), residues: 1758 helix: -4.11 (0.07), residues: 914 sheet: 0.08 (0.37), residues: 168 loop : -3.20 (0.19), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 649 HIS 0.008 0.001 HIS B 252 PHE 0.015 0.002 PHE B 555 TYR 0.020 0.002 TYR B 372 ARG 0.009 0.001 ARG B 622 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 256 time to evaluate : 1.738 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 703 ASN cc_start: 0.7459 (m-40) cc_final: 0.7173 (t0) REVERT: B 703 ASN cc_start: 0.7467 (m-40) cc_final: 0.7180 (t0) outliers start: 18 outliers final: 6 residues processed: 270 average time/residue: 1.4020 time to fit residues: 411.7229 Evaluate side-chains 154 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 148 time to evaluate : 1.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 1063 ASN Chi-restraints excluded: chain A residue 1065 GLU Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 1063 ASN Chi-restraints excluded: chain B residue 1065 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 0.6980 chunk 133 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 89 optimal weight: 5.9990 chunk 71 optimal weight: 0.6980 chunk 137 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 159 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN A 507 ASN A 607 ASN A 613 GLN A 629 HIS A 707 GLN A 882 HIS A1056 ASN ** A1069 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 GLN B 507 ASN B 607 ASN B 613 GLN B 629 HIS B 707 GLN B 882 HIS B1056 ASN ** B1069 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14302 Z= 0.196 Angle : 0.659 8.827 19422 Z= 0.343 Chirality : 0.045 0.269 2296 Planarity : 0.006 0.073 2390 Dihedral : 9.326 95.713 2294 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.74 % Favored : 92.04 % Rotamer: Outliers : 2.98 % Allowed : 11.10 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.17), residues: 1758 helix: -1.23 (0.15), residues: 906 sheet: 0.31 (0.39), residues: 170 loop : -3.02 (0.19), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 397 HIS 0.003 0.001 HIS A 867 PHE 0.011 0.001 PHE B 555 TYR 0.012 0.001 TYR B 650 ARG 0.004 0.001 ARG B 557 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 156 time to evaluate : 1.697 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 703 ASN cc_start: 0.7911 (m-40) cc_final: 0.7417 (t0) REVERT: A 873 MET cc_start: 0.7560 (OUTLIER) cc_final: 0.7099 (mtt) REVERT: B 703 ASN cc_start: 0.7922 (m-40) cc_final: 0.7423 (t0) REVERT: B 873 MET cc_start: 0.7557 (OUTLIER) cc_final: 0.7099 (mtt) outliers start: 44 outliers final: 12 residues processed: 180 average time/residue: 1.3945 time to fit residues: 273.1936 Evaluate side-chains 154 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 140 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 873 MET Chi-restraints excluded: chain A residue 908 ASP Chi-restraints excluded: chain A residue 1063 ASN Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 873 MET Chi-restraints excluded: chain B residue 908 ASP Chi-restraints excluded: chain B residue 1063 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 88 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 172 optimal weight: 5.9990 chunk 142 optimal weight: 0.5980 chunk 158 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1069 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1069 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14302 Z= 0.223 Angle : 0.634 10.464 19422 Z= 0.327 Chirality : 0.044 0.219 2296 Planarity : 0.005 0.070 2390 Dihedral : 7.850 81.300 2288 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.91 % Favored : 91.87 % Rotamer: Outliers : 2.23 % Allowed : 13.60 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.19), residues: 1758 helix: 0.52 (0.17), residues: 900 sheet: 0.44 (0.38), residues: 170 loop : -2.77 (0.20), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 649 HIS 0.016 0.001 HIS A1048 PHE 0.012 0.001 PHE B 555 TYR 0.013 0.001 TYR B 628 ARG 0.004 0.000 ARG A 622 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 156 time to evaluate : 1.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 873 MET cc_start: 0.7637 (OUTLIER) cc_final: 0.7154 (mtt) REVERT: B 873 MET cc_start: 0.7640 (OUTLIER) cc_final: 0.7153 (mtt) outliers start: 33 outliers final: 14 residues processed: 172 average time/residue: 1.4044 time to fit residues: 263.3929 Evaluate side-chains 145 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 129 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 873 MET Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 873 MET Chi-restraints excluded: chain B residue 1029 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 160 optimal weight: 1.9990 chunk 170 optimal weight: 0.6980 chunk 152 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 141 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1069 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1069 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14302 Z= 0.183 Angle : 0.589 10.298 19422 Z= 0.303 Chirality : 0.043 0.231 2296 Planarity : 0.005 0.066 2390 Dihedral : 6.659 52.525 2284 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.85 % Favored : 91.92 % Rotamer: Outliers : 2.23 % Allowed : 14.61 % Favored : 83.15 % 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: -0.44 (0.20), residues: 1758 helix: 1.21 (0.18), residues: 898 sheet: 0.52 (0.37), residues: 170 loop : -2.68 (0.21), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 649 HIS 0.006 0.001 HIS B1048 PHE 0.011 0.001 PHE A 555 TYR 0.011 0.001 TYR B 628 ARG 0.008 0.001 ARG A 557 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 139 time to evaluate : 1.655 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 873 MET cc_start: 0.7579 (OUTLIER) cc_final: 0.7089 (mtt) REVERT: A 916 LEU cc_start: 0.7010 (mm) cc_final: 0.6263 (mm) REVERT: B 873 MET cc_start: 0.7580 (OUTLIER) cc_final: 0.7084 (mtt) REVERT: B 916 LEU cc_start: 0.7001 (mm) cc_final: 0.6258 (mm) outliers start: 33 outliers final: 18 residues processed: 157 average time/residue: 1.2640 time to fit residues: 218.2218 Evaluate side-chains 144 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 124 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 873 MET Chi-restraints excluded: chain A residue 927 MET Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 873 MET Chi-restraints excluded: chain B residue 927 MET Chi-restraints excluded: chain B residue 1029 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 96 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 126 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 145 optimal weight: 0.0070 chunk 117 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 86 optimal weight: 0.6980 chunk 152 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1056 ASN ** A1069 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 859 ASN B1056 ASN ** B1069 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14302 Z= 0.159 Angle : 0.540 6.557 19422 Z= 0.282 Chirality : 0.042 0.218 2296 Planarity : 0.004 0.067 2390 Dihedral : 5.744 35.949 2284 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.22 % Favored : 92.55 % Rotamer: Outliers : 2.98 % Allowed : 14.34 % Favored : 82.68 % 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: -0.06 (0.20), residues: 1758 helix: 1.59 (0.18), residues: 900 sheet: 0.62 (0.37), residues: 170 loop : -2.59 (0.21), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 649 HIS 0.003 0.000 HIS A1048 PHE 0.011 0.001 PHE A 555 TYR 0.010 0.001 TYR A 628 ARG 0.005 0.000 ARG A 557 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 130 time to evaluate : 1.634 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 873 MET cc_start: 0.7572 (OUTLIER) cc_final: 0.7096 (mtt) REVERT: B 873 MET cc_start: 0.7575 (OUTLIER) cc_final: 0.7091 (mtt) outliers start: 44 outliers final: 22 residues processed: 160 average time/residue: 1.2043 time to fit residues: 212.7106 Evaluate side-chains 149 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 125 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 873 MET Chi-restraints excluded: chain A residue 908 ASP Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 873 MET Chi-restraints excluded: chain B residue 908 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 153 optimal weight: 1.9990 chunk 33 optimal weight: 0.0030 chunk 99 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 170 optimal weight: 0.5980 chunk 141 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 164 optimal weight: 4.9990 overall best weight: 0.8192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1069 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 859 ASN ** B1069 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14302 Z= 0.181 Angle : 0.558 6.715 19422 Z= 0.290 Chirality : 0.043 0.201 2296 Planarity : 0.004 0.063 2390 Dihedral : 5.569 36.740 2284 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.51 % Favored : 92.15 % Rotamer: Outliers : 3.52 % Allowed : 14.48 % Favored : 82.00 % 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: 0.02 (0.21), residues: 1758 helix: 1.70 (0.18), residues: 902 sheet: 0.66 (0.37), residues: 170 loop : -2.64 (0.21), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 649 HIS 0.003 0.001 HIS B1048 PHE 0.011 0.001 PHE A 555 TYR 0.011 0.001 TYR A 628 ARG 0.006 0.000 ARG B 622 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 128 time to evaluate : 1.608 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 573 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8322 (tt) REVERT: A 873 MET cc_start: 0.7607 (OUTLIER) cc_final: 0.7119 (mtt) REVERT: B 573 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8322 (tt) REVERT: B 873 MET cc_start: 0.7610 (OUTLIER) cc_final: 0.7117 (mtt) outliers start: 52 outliers final: 27 residues processed: 161 average time/residue: 1.1808 time to fit residues: 210.2067 Evaluate side-chains 154 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 123 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 873 MET Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 743 SER Chi-restraints excluded: chain B residue 873 MET Chi-restraints excluded: chain B residue 1029 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 19 optimal weight: 0.0670 chunk 97 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 169 optimal weight: 5.9990 chunk 106 optimal weight: 0.5980 chunk 103 optimal weight: 0.6980 chunk 78 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 overall best weight: 0.8520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1069 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1069 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14302 Z= 0.187 Angle : 0.574 8.599 19422 Z= 0.297 Chirality : 0.044 0.372 2296 Planarity : 0.004 0.064 2390 Dihedral : 5.714 50.418 2284 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.51 % Favored : 92.26 % Rotamer: Outliers : 2.98 % Allowed : 14.61 % Favored : 82.41 % Cbeta Deviations : 0.12 % 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: 0.17 (0.21), residues: 1758 helix: 1.81 (0.18), residues: 902 sheet: 0.72 (0.38), residues: 170 loop : -2.54 (0.21), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 649 HIS 0.003 0.001 HIS B1048 PHE 0.011 0.001 PHE A 555 TYR 0.010 0.001 TYR A 628 ARG 0.004 0.000 ARG A 557 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 123 time to evaluate : 1.683 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 573 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8316 (tt) REVERT: A 873 MET cc_start: 0.7617 (OUTLIER) cc_final: 0.7127 (mtt) REVERT: B 573 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8314 (tt) REVERT: B 873 MET cc_start: 0.7615 (OUTLIER) cc_final: 0.7116 (mtt) outliers start: 44 outliers final: 27 residues processed: 156 average time/residue: 1.2981 time to fit residues: 223.1407 Evaluate side-chains 152 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 121 time to evaluate : 1.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 873 MET Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 743 SER Chi-restraints excluded: chain B residue 873 MET Chi-restraints excluded: chain B residue 1029 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 4.9990 chunk 101 optimal weight: 10.0000 chunk 51 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 115 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 133 optimal weight: 0.6980 chunk 154 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1069 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1069 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14302 Z= 0.190 Angle : 0.557 6.913 19422 Z= 0.290 Chirality : 0.043 0.321 2296 Planarity : 0.004 0.064 2390 Dihedral : 5.465 43.365 2284 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.79 % Favored : 91.98 % Rotamer: Outliers : 2.91 % Allowed : 14.95 % Favored : 82.14 % 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: 0.23 (0.21), residues: 1758 helix: 1.86 (0.18), residues: 904 sheet: 0.74 (0.38), residues: 170 loop : -2.53 (0.21), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 649 HIS 0.004 0.001 HIS A 700 PHE 0.011 0.001 PHE B 555 TYR 0.012 0.001 TYR A 628 ARG 0.005 0.000 ARG A 622 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 123 time to evaluate : 1.725 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 573 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8317 (tt) REVERT: A 873 MET cc_start: 0.7557 (OUTLIER) cc_final: 0.7327 (mpt) REVERT: B 573 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8317 (tt) REVERT: B 873 MET cc_start: 0.7553 (OUTLIER) cc_final: 0.6997 (mtt) outliers start: 43 outliers final: 27 residues processed: 152 average time/residue: 1.2427 time to fit residues: 208.3049 Evaluate side-chains 154 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 123 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 873 MET Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 743 SER Chi-restraints excluded: chain B residue 873 MET Chi-restraints excluded: chain B residue 1029 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 162 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 124 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 142 optimal weight: 0.5980 chunk 149 optimal weight: 0.6980 chunk 157 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1069 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1069 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14302 Z= 0.174 Angle : 0.553 8.753 19422 Z= 0.287 Chirality : 0.042 0.300 2296 Planarity : 0.004 0.063 2390 Dihedral : 5.395 45.156 2284 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.62 % Favored : 92.15 % Rotamer: Outliers : 2.57 % Allowed : 15.29 % Favored : 82.14 % 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 (0.21), residues: 1758 helix: 1.96 (0.18), residues: 902 sheet: 0.78 (0.38), residues: 170 loop : -2.47 (0.21), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 649 HIS 0.002 0.001 HIS B1048 PHE 0.011 0.001 PHE A 555 TYR 0.010 0.001 TYR A 628 ARG 0.006 0.000 ARG A 622 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 122 time to evaluate : 1.591 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 573 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8301 (tt) REVERT: B 573 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8300 (tt) REVERT: B 873 MET cc_start: 0.7576 (OUTLIER) cc_final: 0.7064 (mtt) outliers start: 38 outliers final: 29 residues processed: 154 average time/residue: 1.2550 time to fit residues: 213.1427 Evaluate side-chains 153 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 121 time to evaluate : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 743 SER Chi-restraints excluded: chain B residue 873 MET Chi-restraints excluded: chain B residue 1029 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 167 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 79 optimal weight: 0.0000 chunk 116 optimal weight: 0.9990 chunk 175 optimal weight: 4.9990 chunk 161 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 107 optimal weight: 0.4980 chunk 85 optimal weight: 0.9980 chunk 110 optimal weight: 10.0000 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1069 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1069 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14302 Z= 0.167 Angle : 0.540 6.740 19422 Z= 0.281 Chirality : 0.042 0.288 2296 Planarity : 0.004 0.064 2390 Dihedral : 5.201 38.964 2284 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.74 % Favored : 92.15 % Rotamer: Outliers : 2.50 % Allowed : 15.22 % Favored : 82.27 % 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: 0.43 (0.21), residues: 1758 helix: 2.03 (0.18), residues: 902 sheet: 0.83 (0.39), residues: 170 loop : -2.43 (0.21), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 864 HIS 0.002 0.001 HIS B1048 PHE 0.011 0.001 PHE B 555 TYR 0.010 0.001 TYR A 628 ARG 0.007 0.000 ARG A 622 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 123 time to evaluate : 1.515 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 28 residues processed: 151 average time/residue: 1.2065 time to fit residues: 200.9801 Evaluate side-chains 147 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 119 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 743 SER Chi-restraints excluded: chain B residue 1029 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 128 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 38 optimal weight: 0.3980 chunk 139 optimal weight: 0.7980 chunk 58 optimal weight: 0.1980 chunk 143 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1069 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1069 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.128708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.093851 restraints weight = 19314.472| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.30 r_work: 0.2931 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14302 Z= 0.154 Angle : 0.528 6.816 19422 Z= 0.275 Chirality : 0.042 0.279 2296 Planarity : 0.004 0.063 2390 Dihedral : 5.018 40.075 2284 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.62 % Favored : 92.26 % Rotamer: Outliers : 2.03 % Allowed : 15.70 % Favored : 82.27 % 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: 0.52 (0.21), residues: 1758 helix: 2.10 (0.18), residues: 902 sheet: 0.87 (0.39), residues: 170 loop : -2.39 (0.21), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 649 HIS 0.002 0.001 HIS B1048 PHE 0.011 0.001 PHE B 555 TYR 0.010 0.001 TYR A 650 ARG 0.007 0.000 ARG A 622 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4772.71 seconds wall clock time: 85 minutes 40.10 seconds (5140.10 seconds total)