Starting phenix.real_space_refine on Sun Feb 18 11:20:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yff_33788/02_2024/7yff_33788_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yff_33788/02_2024/7yff_33788.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yff_33788/02_2024/7yff_33788_neut_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yff_33788/02_2024/7yff_33788_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yff_33788/02_2024/7yff_33788_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yff_33788/02_2024/7yff_33788.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yff_33788/02_2024/7yff_33788.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yff_33788/02_2024/7yff_33788_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yff_33788/02_2024/7yff_33788_neut_trim_updated.pdb" } resolution = 3.6 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= 0.009 sd= 0.073 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 106 5.16 5 C 13962 2.51 5 N 3713 2.21 5 O 4037 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 192": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 21820 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 5605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 767, 5605 Classifications: {'peptide': 767} Incomplete info: {'truncation_to_alanine': 129} Link IDs: {'PTRANS': 33, 'TRANS': 733} Chain breaks: 6 Unresolved non-hydrogen bonds: 471 Unresolved non-hydrogen angles: 583 Unresolved non-hydrogen dihedrals: 387 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 11, 'TYR:plan': 2, 'ASN:plan1': 13, 'HIS:plan': 5, 'PHE:plan': 6, 'GLU:plan': 19, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 276 Chain: "B" Number of atoms: 5193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 740, 5193 Classifications: {'peptide': 740} Incomplete info: {'truncation_to_alanine': 156} Link IDs: {'PTRANS': 33, 'TRANS': 706} Chain breaks: 11 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 630 Unresolved non-hydrogen angles: 799 Unresolved non-hydrogen dihedrals: 516 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 5, 'TYR:plan': 7, 'ASN:plan1': 7, 'TRP:plan': 2, 'ASP:plan': 14, 'PHE:plan': 4, 'GLU:plan': 16, 'ARG:plan': 28} Unresolved non-hydrogen planarities: 419 Chain: "C" Number of atoms: 5605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 767, 5605 Classifications: {'peptide': 767} Incomplete info: {'truncation_to_alanine': 129} Link IDs: {'PTRANS': 33, 'TRANS': 733} Chain breaks: 6 Unresolved non-hydrogen bonds: 471 Unresolved non-hydrogen angles: 583 Unresolved non-hydrogen dihedrals: 387 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 11, 'TYR:plan': 2, 'ASN:plan1': 13, 'HIS:plan': 5, 'PHE:plan': 6, 'GLU:plan': 19, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 276 Chain: "D" Number of atoms: 5193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 740, 5193 Classifications: {'peptide': 740} Incomplete info: {'truncation_to_alanine': 156} Link IDs: {'PTRANS': 33, 'TRANS': 706} Chain breaks: 11 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 630 Unresolved non-hydrogen angles: 799 Unresolved non-hydrogen dihedrals: 516 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 5, 'TYR:plan': 7, 'ASN:plan1': 7, 'TRP:plan': 2, 'ASP:plan': 14, 'PHE:plan': 4, 'GLU:plan': 16, 'ARG:plan': 28} Unresolved non-hydrogen planarities: 419 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: "A" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 47 Unusual residues: {'NAG': 3} Inner-chain residues flagged as termini: ['pdbres="GLY A 903 "'] Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'7RC': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'NAG': 4} Inner-chain residues flagged as termini: ['pdbres="GLY C 904 "'] Classifications: {'peptide': 1, 'undetermined': 4} Modifications used: {'COO': 1} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'7RC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.00, per 1000 atoms: 0.55 Number of scatterers: 21820 At special positions: 0 Unit cell: (116.739, 138.159, 180.999, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 106 16.00 P 2 15.00 O 4037 8.00 N 3713 7.00 C 13962 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS A 744 " - pdb=" SG CYS A 798 " distance=2.03 Simple disulfide: pdb=" SG CYS B 104 " - pdb=" SG CYS B 348 " distance=2.03 Simple disulfide: pdb=" SG CYS B 455 " - pdb=" SG CYS B 483 " distance=2.03 Simple disulfide: pdb=" SG CYS B 462 " - pdb=" SG CYS B 484 " distance=2.03 Simple disulfide: pdb=" SG CYS B 773 " - pdb=" SG CYS B 828 " distance=2.03 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 308 " distance=2.03 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 455 " distance=2.03 Simple disulfide: pdb=" SG CYS C 744 " - pdb=" SG CYS C 798 " distance=2.03 Simple disulfide: pdb=" SG CYS D 104 " - pdb=" SG CYS D 348 " distance=2.03 Simple disulfide: pdb=" SG CYS D 455 " - pdb=" SG CYS D 483 " distance=2.03 Simple disulfide: pdb=" SG CYS D 462 " - pdb=" SG CYS D 484 " distance=2.03 Simple disulfide: pdb=" SG CYS D 773 " - pdb=" SG CYS D 828 " 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=2, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " NAG-ASN " NAG A 901 " - " ASN A 471 " " NAG A 902 " - " ASN A 276 " " NAG A 904 " - " ASN A 368 " " NAG C 901 " - " ASN C 471 " " NAG C 902 " - " ASN C 276 " " NAG C 903 " - " ASN C 61 " " NAG C 905 " - " ASN C 368 " " NAG E 1 " - " ASN A 61 " " NAG F 1 " - " ASN A 771 " " NAG G 1 " - " ASN C 771 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.24 Conformation dependent library (CDL) restraints added in 4.6 seconds 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5616 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 101 helices and 25 sheets defined 40.0% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.30 Creating SS restraints... Processing helix chain 'A' and resid 39 through 52 Processing helix chain 'A' and resid 71 through 85 Processing helix chain 'A' and resid 105 through 115 removed outlier: 3.733A pdb=" N PHE A 113 " --> pdb=" O TYR A 109 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N TYR A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG A 115 " --> pdb=" O ALA A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 128 No H-bonds generated for 'chain 'A' and resid 126 through 128' Processing helix chain 'A' and resid 144 through 157 removed outlier: 3.721A pdb=" N SER A 148 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 186 Processing helix chain 'A' and resid 205 through 212 Processing helix chain 'A' and resid 225 through 238 Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 274 through 279 removed outlier: 3.709A pdb=" N ALA A 279 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 294 Processing helix chain 'A' and resid 318 through 327 Processing helix chain 'A' and resid 357 through 359 No H-bonds generated for 'chain 'A' and resid 357 through 359' Processing helix chain 'A' and resid 458 through 470 Processing helix chain 'A' and resid 500 through 507 removed outlier: 3.658A pdb=" N SER A 507 " --> pdb=" O GLU A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 526 removed outlier: 3.811A pdb=" N TYR A 526 " --> pdb=" O GLU A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 583 Processing helix chain 'A' and resid 603 through 615 Processing helix chain 'A' and resid 627 through 657 Processing helix chain 'A' and resid 670 through 673 No H-bonds generated for 'chain 'A' and resid 670 through 673' Processing helix chain 'A' and resid 688 through 695 Processing helix chain 'A' and resid 700 through 709 removed outlier: 3.753A pdb=" N ARG A 704 " --> pdb=" O SER A 700 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS A 708 " --> pdb=" O ARG A 704 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N HIS A 709 " --> pdb=" O HIS A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 723 removed outlier: 3.867A pdb=" N ILE A 718 " --> pdb=" O ALA A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 742 removed outlier: 4.166A pdb=" N PHE A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 778 removed outlier: 3.669A pdb=" N SER A 775 " --> pdb=" O ASN A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 792 Processing helix chain 'A' and resid 812 through 839 Processing helix chain 'B' and resid 61 through 69 Processing helix chain 'B' and resid 71 through 74 No H-bonds generated for 'chain 'B' and resid 71 through 74' Processing helix chain 'B' and resid 96 through 109 Processing helix chain 'B' and resid 125 through 137 removed outlier: 3.819A pdb=" N ILE B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 181 Processing helix chain 'B' and resid 198 through 208 Processing helix chain 'B' and resid 230 through 238 Processing helix chain 'B' and resid 250 through 263 Proline residue: B 255 - end of helix Processing helix chain 'B' and resid 316 through 336 removed outlier: 3.741A pdb=" N ARG B 336 " --> pdb=" O GLN B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 499 Processing helix chain 'B' and resid 524 through 528 Processing helix chain 'B' and resid 544 through 549 Processing helix chain 'B' and resid 575 through 578 removed outlier: 4.066A pdb=" N LEU B 578 " --> pdb=" O SER B 575 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 575 through 578' Processing helix chain 'B' and resid 583 through 606 Processing helix chain 'B' and resid 631 through 640 removed outlier: 3.723A pdb=" N VAL B 640 " --> pdb=" O LEU B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 680 Processing helix chain 'B' and resid 718 through 725 Processing helix chain 'B' and resid 727 through 733 removed outlier: 3.582A pdb=" N TYR B 732 " --> pdb=" O ASP B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 747 removed outlier: 5.510A pdb=" N THR B 746 " --> pdb=" O GLU B 743 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN B 747 " --> pdb=" O ALA B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 769 removed outlier: 3.656A pdb=" N TYR B 765 " --> pdb=" O ALA B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 813 removed outlier: 3.753A pdb=" N ARG B 801 " --> pdb=" O ARG B 798 " (cutoff:3.500A) Proline residue: B 802 - end of helix removed outlier: 3.689A pdb=" N LEU B 805 " --> pdb=" O PRO B 802 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU B 811 " --> pdb=" O LEU B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 842 through 868 Processing helix chain 'C' and resid 39 through 52 Processing helix chain 'C' and resid 71 through 85 Processing helix chain 'C' and resid 105 through 115 removed outlier: 3.739A pdb=" N PHE C 113 " --> pdb=" O TYR C 109 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N TYR C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG C 115 " --> pdb=" O ALA C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 128 No H-bonds generated for 'chain 'C' and resid 126 through 128' Processing helix chain 'C' and resid 144 through 157 removed outlier: 3.726A pdb=" N SER C 148 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 186 Processing helix chain 'C' and resid 205 through 212 Processing helix chain 'C' and resid 225 through 238 Processing helix chain 'C' and resid 251 through 260 Processing helix chain 'C' and resid 274 through 279 removed outlier: 3.708A pdb=" N ALA C 279 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 294 Processing helix chain 'C' and resid 318 through 327 Processing helix chain 'C' and resid 357 through 359 No H-bonds generated for 'chain 'C' and resid 357 through 359' Processing helix chain 'C' and resid 458 through 470 Processing helix chain 'C' and resid 500 through 507 removed outlier: 3.664A pdb=" N SER C 507 " --> pdb=" O GLU C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 526 removed outlier: 3.815A pdb=" N TYR C 526 " --> pdb=" O GLU C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 554 through 557 Proline residue: C 557 - end of helix No H-bonds generated for 'chain 'C' and resid 554 through 557' Processing helix chain 'C' and resid 560 through 583 Processing helix chain 'C' and resid 603 through 615 Processing helix chain 'C' and resid 627 through 657 Processing helix chain 'C' and resid 670 through 673 No H-bonds generated for 'chain 'C' and resid 670 through 673' Processing helix chain 'C' and resid 688 through 695 Processing helix chain 'C' and resid 700 through 709 removed outlier: 3.753A pdb=" N ARG C 704 " --> pdb=" O SER C 700 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS C 708 " --> pdb=" O ARG C 704 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N HIS C 709 " --> pdb=" O HIS C 705 " (cutoff:3.500A) Processing helix chain 'C' and resid 714 through 723 removed outlier: 3.872A pdb=" N ILE C 718 " --> pdb=" O ALA C 714 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 742 removed outlier: 4.166A pdb=" N PHE C 738 " --> pdb=" O ALA C 734 " (cutoff:3.500A) Processing helix chain 'C' and resid 769 through 778 Processing helix chain 'C' and resid 785 through 792 Processing helix chain 'C' and resid 812 through 839 Processing helix chain 'D' and resid 61 through 69 Processing helix chain 'D' and resid 71 through 74 No H-bonds generated for 'chain 'D' and resid 71 through 74' Processing helix chain 'D' and resid 96 through 109 Processing helix chain 'D' and resid 125 through 137 removed outlier: 3.818A pdb=" N ILE D 129 " --> pdb=" O ALA D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 181 Processing helix chain 'D' and resid 198 through 208 Processing helix chain 'D' and resid 230 through 238 Processing helix chain 'D' and resid 250 through 263 Proline residue: D 255 - end of helix Processing helix chain 'D' and resid 316 through 336 removed outlier: 3.740A pdb=" N ARG D 336 " --> pdb=" O GLN D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 499 Processing helix chain 'D' and resid 524 through 528 Processing helix chain 'D' and resid 544 through 549 Processing helix chain 'D' and resid 575 through 578 removed outlier: 4.072A pdb=" N LEU D 578 " --> pdb=" O SER D 575 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 575 through 578' Processing helix chain 'D' and resid 583 through 606 Processing helix chain 'D' and resid 631 through 640 removed outlier: 3.723A pdb=" N VAL D 640 " --> pdb=" O LEU D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 680 Processing helix chain 'D' and resid 718 through 725 Processing helix chain 'D' and resid 727 through 734 removed outlier: 3.579A pdb=" N TYR D 732 " --> pdb=" O ASP D 728 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 747 removed outlier: 5.507A pdb=" N THR D 746 " --> pdb=" O GLU D 743 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN D 747 " --> pdb=" O ALA D 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 760 through 769 removed outlier: 3.655A pdb=" N TYR D 765 " --> pdb=" O ALA D 761 " (cutoff:3.500A) Processing helix chain 'D' and resid 798 through 813 removed outlier: 3.754A pdb=" N ARG D 801 " --> pdb=" O ARG D 798 " (cutoff:3.500A) Proline residue: D 802 - end of helix removed outlier: 3.682A pdb=" N LEU D 805 " --> pdb=" O PRO D 802 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU D 811 " --> pdb=" O LEU D 808 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 823 Processing helix chain 'D' and resid 842 through 868 Processing sheet with id= A, first strand: chain 'A' and resid 90 through 92 Processing sheet with id= B, first strand: chain 'A' and resid 219 through 221 Processing sheet with id= C, first strand: chain 'A' and resid 399 through 402 removed outlier: 6.278A pdb=" N GLU A 475 " --> pdb=" O ILE A 400 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N THR A 402 " --> pdb=" O GLU A 475 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N HIS A 477 " --> pdb=" O THR A 402 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 409 through 413 removed outlier: 3.565A pdb=" N GLY A 438 " --> pdb=" O VAL A 451 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 486 through 488 removed outlier: 3.785A pdb=" N GLU A 497 " --> pdb=" O GLU A 488 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 729 through 732 Processing sheet with id= G, first strand: chain 'B' and resid 244 through 246 removed outlier: 6.708A pdb=" N GLY B 303 " --> pdb=" O TRP B 272 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N MET B 274 " --> pdb=" O GLY B 303 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N PHE B 305 " --> pdb=" O MET B 274 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LEU B 304 " --> pdb=" O LEU B 392 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY B 402 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N SER B 391 " --> pdb=" O VAL B 400 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N VAL B 400 " --> pdb=" O SER B 391 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 431 through 436 removed outlier: 6.365A pdb=" N SER B 502 " --> pdb=" O LEU B 432 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL B 434 " --> pdb=" O SER B 502 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N ASP B 504 " --> pdb=" O VAL B 434 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N THR B 436 " --> pdb=" O ASP B 504 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N TYR B 506 " --> pdb=" O THR B 436 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 443 through 447 Processing sheet with id= J, first strand: chain 'B' and resid 515 through 517 Processing sheet with id= K, first strand: chain 'B' and resid 557 through 559 removed outlier: 4.083A pdb=" N VAL B 557 " --> pdb=" O TYR B 789 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 561 through 565 Processing sheet with id= M, first strand: chain 'B' and resid 682 through 684 Processing sheet with id= N, first strand: chain 'C' and resid 90 through 92 Processing sheet with id= O, first strand: chain 'C' and resid 164 through 167 Processing sheet with id= P, first strand: chain 'C' and resid 399 through 402 removed outlier: 6.278A pdb=" N GLU C 475 " --> pdb=" O ILE C 400 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N THR C 402 " --> pdb=" O GLU C 475 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N HIS C 477 " --> pdb=" O THR C 402 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'C' and resid 409 through 413 removed outlier: 3.570A pdb=" N GLY C 438 " --> pdb=" O VAL C 451 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 486 through 488 removed outlier: 3.789A pdb=" N GLU C 497 " --> pdb=" O GLU C 488 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 729 through 732 Processing sheet with id= T, first strand: chain 'D' and resid 244 through 246 removed outlier: 6.709A pdb=" N GLY D 303 " --> pdb=" O TRP D 272 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N MET D 274 " --> pdb=" O GLY D 303 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N PHE D 305 " --> pdb=" O MET D 274 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LEU D 304 " --> pdb=" O LEU D 392 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY D 402 " --> pdb=" O VAL D 389 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N SER D 391 " --> pdb=" O VAL D 400 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N VAL D 400 " --> pdb=" O SER D 391 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 431 through 436 removed outlier: 6.368A pdb=" N SER D 502 " --> pdb=" O LEU D 432 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL D 434 " --> pdb=" O SER D 502 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N ASP D 504 " --> pdb=" O VAL D 434 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N THR D 436 " --> pdb=" O ASP D 504 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N TYR D 506 " --> pdb=" O THR D 436 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'D' and resid 443 through 447 Processing sheet with id= W, first strand: chain 'D' and resid 515 through 517 Processing sheet with id= X, first strand: chain 'D' and resid 557 through 559 removed outlier: 4.087A pdb=" N VAL D 557 " --> pdb=" O TYR D 789 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 561 through 565 893 hydrogen bonds defined for protein. 2538 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: 7.67 Time building geometry restraints manager: 9.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.35: 7153 1.35 - 1.52: 7105 1.52 - 1.68: 7836 1.68 - 1.84: 176 1.84 - 2.00: 2 Bond restraints: 22272 Sorted by residual: bond pdb=" CA VAL C 514 " pdb=" C VAL C 514 " ideal model delta sigma weight residual 1.523 1.432 0.091 1.27e-02 6.20e+03 5.17e+01 bond pdb=" C07 7RC D 901 " pdb=" P01 7RC D 901 " ideal model delta sigma weight residual 1.861 2.003 -0.142 2.00e-02 2.50e+03 5.07e+01 bond pdb=" C07 7RC B 901 " pdb=" P01 7RC B 901 " ideal model delta sigma weight residual 1.861 2.002 -0.141 2.00e-02 2.50e+03 4.96e+01 bond pdb=" C08 7RC B 901 " pdb=" O05 7RC B 901 " ideal model delta sigma weight residual 1.259 1.390 -0.131 2.00e-02 2.50e+03 4.30e+01 bond pdb=" C08 7RC D 901 " pdb=" O05 7RC D 901 " ideal model delta sigma weight residual 1.259 1.390 -0.131 2.00e-02 2.50e+03 4.27e+01 ... (remaining 22267 not shown) Histogram of bond angle deviations from ideal: 99.56 - 106.45: 684 106.45 - 113.34: 12382 113.34 - 120.22: 7160 120.22 - 127.11: 9919 127.11 - 134.00: 256 Bond angle restraints: 30401 Sorted by residual: angle pdb=" C GLU A 192 " pdb=" CA GLU A 192 " pdb=" CB GLU A 192 " ideal model delta sigma weight residual 117.23 107.19 10.04 1.36e+00 5.41e-01 5.45e+01 angle pdb=" C GLU D 815 " pdb=" N ILE D 816 " pdb=" CA ILE D 816 " ideal model delta sigma weight residual 120.46 113.12 7.34 1.37e+00 5.33e-01 2.87e+01 angle pdb=" C GLU B 815 " pdb=" N ILE B 816 " pdb=" CA ILE B 816 " ideal model delta sigma weight residual 120.46 113.13 7.33 1.37e+00 5.33e-01 2.86e+01 angle pdb=" C VAL C 514 " pdb=" CA VAL C 514 " pdb=" CB VAL C 514 " ideal model delta sigma weight residual 111.29 102.78 8.51 1.64e+00 3.72e-01 2.69e+01 angle pdb=" C01 7RC B 901 " pdb=" C08 7RC B 901 " pdb=" O05 7RC B 901 " ideal model delta sigma weight residual 120.00 106.58 13.42 3.00e+00 1.11e-01 2.00e+01 ... (remaining 30396 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.68: 11986 22.68 - 45.36: 1076 45.36 - 68.04: 157 68.04 - 90.73: 30 90.73 - 113.41: 12 Dihedral angle restraints: 13261 sinusoidal: 4587 harmonic: 8674 Sorted by residual: dihedral pdb=" CB CYS B 104 " pdb=" SG CYS B 104 " pdb=" SG CYS B 348 " pdb=" CB CYS B 348 " ideal model delta sinusoidal sigma weight residual 93.00 151.76 -58.76 1 1.00e+01 1.00e-02 4.62e+01 dihedral pdb=" CB CYS D 104 " pdb=" SG CYS D 104 " pdb=" SG CYS D 348 " pdb=" CB CYS D 348 " ideal model delta sinusoidal sigma weight residual 93.00 151.76 -58.76 1 1.00e+01 1.00e-02 4.62e+01 dihedral pdb=" CB CYS B 773 " pdb=" SG CYS B 773 " pdb=" SG CYS B 828 " pdb=" CB CYS B 828 " ideal model delta sinusoidal sigma weight residual -86.00 -141.27 55.27 1 1.00e+01 1.00e-02 4.13e+01 ... (remaining 13258 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.246: 3616 0.246 - 0.493: 3 0.493 - 0.739: 0 0.739 - 0.986: 1 0.986 - 1.232: 1 Chirality restraints: 3621 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 771 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.17 -1.23 2.00e-01 2.50e+01 3.80e+01 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.54 -0.86 2.00e-01 2.50e+01 1.86e+01 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 -2.47 0.07 2.00e-02 2.50e+03 1.32e+01 ... (remaining 3618 not shown) Planarity restraints: 3881 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 901 " -0.329 2.00e-02 2.50e+03 2.87e-01 1.03e+03 pdb=" C7 NAG A 901 " 0.075 2.00e-02 2.50e+03 pdb=" C8 NAG A 901 " -0.075 2.00e-02 2.50e+03 pdb=" N2 NAG A 901 " 0.509 2.00e-02 2.50e+03 pdb=" O7 NAG A 901 " -0.180 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 902 " 0.229 2.00e-02 2.50e+03 1.91e-01 4.54e+02 pdb=" C7 NAG A 902 " -0.063 2.00e-02 2.50e+03 pdb=" C8 NAG A 902 " 0.160 2.00e-02 2.50e+03 pdb=" N2 NAG A 902 " -0.316 2.00e-02 2.50e+03 pdb=" O7 NAG A 902 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C01 7RC B 901 " 0.102 2.00e-02 2.50e+03 2.08e-01 4.32e+02 pdb=" C08 7RC B 901 " -0.359 2.00e-02 2.50e+03 pdb=" O01 7RC B 901 " 0.132 2.00e-02 2.50e+03 pdb=" O05 7RC B 901 " 0.126 2.00e-02 2.50e+03 ... (remaining 3878 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 216 2.61 - 3.18: 20591 3.18 - 3.75: 32997 3.75 - 4.33: 41898 4.33 - 4.90: 70740 Nonbonded interactions: 166442 Sorted by model distance: nonbonded pdb=" OG1 THR D 541 " pdb=" O01 7RC D 901 " model vdw 2.036 2.440 nonbonded pdb=" OG1 THR B 541 " pdb=" O01 7RC B 901 " model vdw 2.045 2.440 nonbonded pdb=" N GLU D 558 " pdb=" OE1 GLU D 558 " model vdw 2.174 2.520 nonbonded pdb=" N GLU B 558 " pdb=" OE1 GLU B 558 " model vdw 2.174 2.520 nonbonded pdb=" O HIS A 780 " pdb=" N MET A 785 " model vdw 2.177 2.520 ... (remaining 166437 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 'C' and (resid 38 through 840 or resid 901 through 902 or resid 904 throu \ gh 905)) } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.450 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: 0.020 Extract box with map and model: 6.000 Check model and map are aligned: 0.360 Set scattering table: 0.210 Process input model: 61.550 Find NCS groups from input model: 1.980 Set up NCS constraints: 0.180 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:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 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 0.142 22272 Z= 0.284 Angle : 0.554 13.417 30401 Z= 0.291 Chirality : 0.047 1.232 3621 Planarity : 0.008 0.287 3871 Dihedral : 17.114 113.408 7597 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 22.78 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.81 % Favored : 92.92 % Rotamer: Outliers : 0.30 % Allowed : 32.33 % Favored : 67.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.17), residues: 2938 helix: 2.77 (0.16), residues: 1256 sheet: -1.29 (0.33), residues: 284 loop : -2.04 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.000 TRP A 768 HIS 0.004 0.001 HIS A 404 PHE 0.009 0.001 PHE D 422 TYR 0.005 0.000 TYR A 647 ARG 0.001 0.000 ARG A 448 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 176 time to evaluate : 2.547 Fit side-chains REVERT: D 830 ASN cc_start: 0.7436 (p0) cc_final: 0.7021 (p0) outliers start: 6 outliers final: 3 residues processed: 181 average time/residue: 0.2707 time to fit residues: 84.6047 Evaluate side-chains 174 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 171 time to evaluate : 2.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 815 GLU Chi-restraints excluded: chain D residue 590 PHE Chi-restraints excluded: chain D residue 815 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 253 optimal weight: 6.9990 chunk 227 optimal weight: 7.9990 chunk 126 optimal weight: 0.9990 chunk 77 optimal weight: 0.0070 chunk 153 optimal weight: 8.9990 chunk 121 optimal weight: 3.9990 chunk 235 optimal weight: 9.9990 chunk 90 optimal weight: 0.5980 chunk 142 optimal weight: 4.9990 chunk 175 optimal weight: 0.3980 chunk 272 optimal weight: 0.0040 overall best weight: 0.4012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 HIS A 177 GLN A 196 GLN ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 649 ASN B 764 ASN C 134 HIS C 177 GLN C 196 GLN D 649 ASN D 764 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.0957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 22272 Z= 0.157 Angle : 0.548 11.255 30401 Z= 0.273 Chirality : 0.042 0.356 3621 Planarity : 0.004 0.051 3871 Dihedral : 7.880 100.558 3463 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.22 % Favored : 92.61 % Rotamer: Outliers : 3.71 % Allowed : 29.27 % Favored : 67.02 % 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: -0.10 (0.16), residues: 2938 helix: 2.18 (0.15), residues: 1250 sheet: -1.00 (0.33), residues: 276 loop : -2.09 (0.16), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 634 HIS 0.005 0.001 HIS D 197 PHE 0.014 0.001 PHE D 710 TYR 0.019 0.001 TYR C 647 ARG 0.002 0.000 ARG D 482 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 171 time to evaluate : 2.483 Fit side-chains revert: symmetry clash REVERT: B 544 GLU cc_start: 0.6787 (OUTLIER) cc_final: 0.6517 (tt0) REVERT: D 830 ASN cc_start: 0.7413 (p0) cc_final: 0.7056 (p0) outliers start: 74 outliers final: 27 residues processed: 232 average time/residue: 0.2777 time to fit residues: 109.1326 Evaluate side-chains 192 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 164 time to evaluate : 2.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 718 THR Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 815 GLU Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 477 HIS Chi-restraints excluded: chain C residue 511 ASP Chi-restraints excluded: chain C residue 781 GLU Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 422 PHE Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain D residue 462 CYS Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 718 THR Chi-restraints excluded: chain D residue 746 THR Chi-restraints excluded: chain D residue 815 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 151 optimal weight: 30.0000 chunk 84 optimal weight: 30.0000 chunk 226 optimal weight: 40.0000 chunk 185 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 272 optimal weight: 3.9990 chunk 294 optimal weight: 0.9990 chunk 243 optimal weight: 20.0000 chunk 270 optimal weight: 0.2980 chunk 93 optimal weight: 10.0000 chunk 218 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN A 196 GLN A 521 ASN ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 GLN C 196 GLN C 521 ASN ** D 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 22272 Z= 0.237 Angle : 0.549 9.777 30401 Z= 0.274 Chirality : 0.042 0.320 3621 Planarity : 0.004 0.058 3871 Dihedral : 7.629 103.178 3461 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.83 % Favored : 91.97 % Rotamer: Outliers : 3.71 % Allowed : 29.37 % Favored : 66.92 % 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: -0.33 (0.16), residues: 2938 helix: 1.98 (0.15), residues: 1240 sheet: -1.49 (0.31), residues: 308 loop : -2.08 (0.16), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 586 HIS 0.005 0.001 HIS B 829 PHE 0.014 0.001 PHE C 533 TYR 0.012 0.001 TYR A 410 ARG 0.001 0.000 ARG D 532 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 169 time to evaluate : 2.690 Fit side-chains revert: symmetry clash REVERT: D 733 MET cc_start: 0.8313 (OUTLIER) cc_final: 0.8110 (ttp) outliers start: 74 outliers final: 44 residues processed: 228 average time/residue: 0.2649 time to fit residues: 104.2774 Evaluate side-chains 208 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 163 time to evaluate : 2.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 590 PHE Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 718 THR Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 815 GLU Chi-restraints excluded: chain B residue 830 ASN Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 477 HIS Chi-restraints excluded: chain C residue 511 ASP Chi-restraints excluded: chain C residue 781 GLU Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 422 PHE Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 462 CYS Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 541 THR Chi-restraints excluded: chain D residue 543 ASN Chi-restraints excluded: chain D residue 590 PHE Chi-restraints excluded: chain D residue 687 VAL Chi-restraints excluded: chain D residue 718 THR Chi-restraints excluded: chain D residue 733 MET Chi-restraints excluded: chain D residue 746 THR Chi-restraints excluded: chain D residue 815 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 269 optimal weight: 2.9990 chunk 205 optimal weight: 20.0000 chunk 141 optimal weight: 0.8980 chunk 30 optimal weight: 0.4980 chunk 130 optimal weight: 0.9990 chunk 183 optimal weight: 0.9980 chunk 273 optimal weight: 2.9990 chunk 289 optimal weight: 0.8980 chunk 143 optimal weight: 0.9990 chunk 259 optimal weight: 1.9990 chunk 78 optimal weight: 30.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN A 196 GLN A 521 ASN ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 GLN C 196 GLN ** D 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 22272 Z= 0.158 Angle : 0.520 9.716 30401 Z= 0.259 Chirality : 0.041 0.278 3621 Planarity : 0.003 0.056 3871 Dihedral : 6.621 99.005 3461 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.52 % Favored : 92.27 % Rotamer: Outliers : 3.61 % Allowed : 30.07 % Favored : 66.32 % 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: -0.38 (0.16), residues: 2938 helix: 1.92 (0.15), residues: 1246 sheet: -1.45 (0.31), residues: 320 loop : -2.13 (0.16), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 662 HIS 0.004 0.001 HIS C 404 PHE 0.013 0.001 PHE B 422 TYR 0.013 0.001 TYR C 392 ARG 0.001 0.000 ARG B 463 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 168 time to evaluate : 2.544 Fit side-chains revert: symmetry clash REVERT: A 541 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.9053 (tp) REVERT: A 818 MET cc_start: 0.5204 (ptt) cc_final: 0.4899 (mmp) REVERT: C 818 MET cc_start: 0.5200 (ptt) cc_final: 0.4890 (mmp) outliers start: 72 outliers final: 45 residues processed: 222 average time/residue: 0.2570 time to fit residues: 98.9905 Evaluate side-chains 207 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 161 time to evaluate : 2.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 590 PHE Chi-restraints excluded: chain B residue 718 THR Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 815 GLU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 477 HIS Chi-restraints excluded: chain C residue 511 ASP Chi-restraints excluded: chain C residue 781 GLU Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 422 PHE Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 462 CYS Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 541 THR Chi-restraints excluded: chain D residue 543 ASN Chi-restraints excluded: chain D residue 590 PHE Chi-restraints excluded: chain D residue 718 THR Chi-restraints excluded: chain D residue 729 MET Chi-restraints excluded: chain D residue 745 LEU Chi-restraints excluded: chain D residue 746 THR Chi-restraints excluded: chain D residue 815 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 241 optimal weight: 50.0000 chunk 164 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 215 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 247 optimal weight: 0.0970 chunk 200 optimal weight: 0.0070 chunk 0 optimal weight: 60.0000 chunk 148 optimal weight: 1.9990 chunk 260 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 overall best weight: 1.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 GLN C 196 GLN C 521 ASN ** D 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 676 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 22272 Z= 0.165 Angle : 0.517 9.652 30401 Z= 0.257 Chirality : 0.041 0.273 3621 Planarity : 0.003 0.058 3871 Dihedral : 6.353 89.847 3461 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.62 % Favored : 92.17 % Rotamer: Outliers : 4.02 % Allowed : 29.77 % Favored : 66.21 % 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 (0.16), residues: 2938 helix: 1.86 (0.15), residues: 1250 sheet: -1.72 (0.29), residues: 344 loop : -2.08 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 662 HIS 0.003 0.001 HIS C 404 PHE 0.012 0.001 PHE B 422 TYR 0.016 0.001 TYR A 392 ARG 0.001 0.000 ARG D 463 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 167 time to evaluate : 2.494 Fit side-chains revert: symmetry clash REVERT: A 541 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.9052 (tp) REVERT: A 810 PHE cc_start: 0.7895 (OUTLIER) cc_final: 0.7060 (m-80) REVERT: A 818 MET cc_start: 0.5155 (ptt) cc_final: 0.4793 (mmp) REVERT: C 818 MET cc_start: 0.5191 (ptt) cc_final: 0.4812 (mmp) outliers start: 80 outliers final: 57 residues processed: 227 average time/residue: 0.2626 time to fit residues: 103.6701 Evaluate side-chains 223 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 164 time to evaluate : 2.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 810 PHE Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 590 PHE Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 718 THR Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 815 GLU Chi-restraints excluded: chain B residue 830 ASN Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 477 HIS Chi-restraints excluded: chain C residue 511 ASP Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 781 GLU Chi-restraints excluded: chain C residue 786 GLU Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 422 PHE Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 462 CYS Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 541 THR Chi-restraints excluded: chain D residue 543 ASN Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 590 PHE Chi-restraints excluded: chain D residue 647 VAL Chi-restraints excluded: chain D residue 676 ASN Chi-restraints excluded: chain D residue 687 VAL Chi-restraints excluded: chain D residue 718 THR Chi-restraints excluded: chain D residue 746 THR Chi-restraints excluded: chain D residue 776 VAL Chi-restraints excluded: chain D residue 815 GLU Chi-restraints excluded: chain D residue 833 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 97 optimal weight: 4.9990 chunk 261 optimal weight: 9.9990 chunk 57 optimal weight: 0.9980 chunk 170 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 290 optimal weight: 3.9990 chunk 240 optimal weight: 0.2980 chunk 134 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 96 optimal weight: 9.9990 chunk 152 optimal weight: 40.0000 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN A 196 GLN A 780 HIS A 812 ASN ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 GLN C 196 GLN C 491 ASN C 780 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 22272 Z= 0.327 Angle : 0.572 9.655 30401 Z= 0.289 Chirality : 0.043 0.301 3621 Planarity : 0.004 0.057 3871 Dihedral : 6.529 89.852 3461 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.82 % Favored : 90.98 % Rotamer: Outliers : 4.77 % Allowed : 29.57 % Favored : 65.66 % 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: -0.54 (0.16), residues: 2938 helix: 1.70 (0.15), residues: 1248 sheet: -1.50 (0.31), residues: 320 loop : -2.13 (0.16), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 586 HIS 0.004 0.001 HIS C 709 PHE 0.022 0.002 PHE A 533 TYR 0.015 0.001 TYR A 392 ARG 0.003 0.000 ARG C 523 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 160 time to evaluate : 2.766 Fit side-chains revert: symmetry clash REVERT: A 810 PHE cc_start: 0.8171 (OUTLIER) cc_final: 0.7236 (m-80) REVERT: A 813 MET cc_start: 0.5712 (mmm) cc_final: 0.5473 (mtp) REVERT: C 818 MET cc_start: 0.5231 (ptt) cc_final: 0.4821 (mmp) outliers start: 95 outliers final: 65 residues processed: 238 average time/residue: 0.2563 time to fit residues: 106.3485 Evaluate side-chains 225 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 159 time to evaluate : 2.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 810 PHE Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 590 PHE Chi-restraints excluded: chain B residue 647 VAL Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 718 THR Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 815 GLU Chi-restraints excluded: chain B residue 830 ASN Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 477 HIS Chi-restraints excluded: chain C residue 511 ASP Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 781 GLU Chi-restraints excluded: chain C residue 786 GLU Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 422 PHE Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain D residue 462 CYS Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 541 THR Chi-restraints excluded: chain D residue 543 ASN Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 590 PHE Chi-restraints excluded: chain D residue 647 VAL Chi-restraints excluded: chain D residue 654 THR Chi-restraints excluded: chain D residue 687 VAL Chi-restraints excluded: chain D residue 718 THR Chi-restraints excluded: chain D residue 745 LEU Chi-restraints excluded: chain D residue 746 THR Chi-restraints excluded: chain D residue 763 LEU Chi-restraints excluded: chain D residue 815 GLU Chi-restraints excluded: chain D residue 833 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 279 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 chunk 165 optimal weight: 9.9990 chunk 211 optimal weight: 3.9990 chunk 164 optimal weight: 5.9990 chunk 244 optimal weight: 0.0470 chunk 162 optimal weight: 10.0000 chunk 289 optimal weight: 0.8980 chunk 180 optimal weight: 20.0000 chunk 176 optimal weight: 20.0000 chunk 133 optimal weight: 1.9990 overall best weight: 1.0682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN A 196 GLN A 780 HIS ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 676 ASN C 177 GLN C 196 GLN C 780 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22272 Z= 0.169 Angle : 0.529 9.623 30401 Z= 0.263 Chirality : 0.041 0.256 3621 Planarity : 0.003 0.058 3871 Dihedral : 6.224 89.949 3461 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.93 % Favored : 91.87 % Rotamer: Outliers : 3.82 % Allowed : 30.57 % Favored : 65.61 % 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: -0.49 (0.16), residues: 2938 helix: 1.79 (0.15), residues: 1244 sheet: -1.51 (0.30), residues: 320 loop : -2.14 (0.16), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 247 HIS 0.003 0.001 HIS A 404 PHE 0.013 0.001 PHE B 422 TYR 0.021 0.001 TYR C 392 ARG 0.002 0.000 ARG B 735 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 160 time to evaluate : 2.601 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 810 PHE cc_start: 0.8059 (OUTLIER) cc_final: 0.7167 (m-80) REVERT: A 818 MET cc_start: 0.5145 (ptt) cc_final: 0.4797 (mmp) REVERT: B 733 MET cc_start: 0.7903 (ttt) cc_final: 0.7684 (ttt) REVERT: C 818 MET cc_start: 0.5140 (ptt) cc_final: 0.4707 (mmp) outliers start: 76 outliers final: 58 residues processed: 224 average time/residue: 0.2553 time to fit residues: 99.0403 Evaluate side-chains 215 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 156 time to evaluate : 2.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 810 PHE Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 590 PHE Chi-restraints excluded: chain B residue 647 VAL Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 676 ASN Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 718 THR Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 815 GLU Chi-restraints excluded: chain B residue 828 CYS Chi-restraints excluded: chain B residue 830 ASN Chi-restraints excluded: chain B residue 833 ILE Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 477 HIS Chi-restraints excluded: chain C residue 511 ASP Chi-restraints excluded: chain C residue 781 GLU Chi-restraints excluded: chain C residue 786 GLU Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 422 PHE Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain D residue 462 CYS Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 541 THR Chi-restraints excluded: chain D residue 543 ASN Chi-restraints excluded: chain D residue 590 PHE Chi-restraints excluded: chain D residue 647 VAL Chi-restraints excluded: chain D residue 687 VAL Chi-restraints excluded: chain D residue 718 THR Chi-restraints excluded: chain D residue 745 LEU Chi-restraints excluded: chain D residue 746 THR Chi-restraints excluded: chain D residue 763 LEU Chi-restraints excluded: chain D residue 776 VAL Chi-restraints excluded: chain D residue 815 GLU Chi-restraints excluded: chain D residue 833 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 178 optimal weight: 8.9990 chunk 115 optimal weight: 2.9990 chunk 172 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 183 optimal weight: 2.9990 chunk 196 optimal weight: 0.6980 chunk 142 optimal weight: 4.9990 chunk 26 optimal weight: 20.0000 chunk 227 optimal weight: 10.0000 chunk 263 optimal weight: 0.9980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN A 196 GLN A 780 HIS ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 GLN C 196 GLN C 780 HIS ** D 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22272 Z= 0.188 Angle : 0.536 9.607 30401 Z= 0.265 Chirality : 0.041 0.262 3621 Planarity : 0.003 0.057 3871 Dihedral : 6.081 88.432 3461 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.30 % Favored : 91.49 % Rotamer: Outliers : 3.82 % Allowed : 30.52 % Favored : 65.66 % 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: -0.51 (0.16), residues: 2938 helix: 1.81 (0.15), residues: 1238 sheet: -1.51 (0.30), residues: 320 loop : -2.18 (0.16), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 608 HIS 0.004 0.001 HIS C 404 PHE 0.013 0.001 PHE B 422 TYR 0.020 0.001 TYR C 392 ARG 0.001 0.000 ARG B 463 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 161 time to evaluate : 2.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 810 PHE cc_start: 0.8110 (OUTLIER) cc_final: 0.7148 (m-80) REVERT: A 818 MET cc_start: 0.5107 (ptt) cc_final: 0.4783 (mmp) REVERT: C 818 MET cc_start: 0.5169 (ptt) cc_final: 0.4755 (mmp) outliers start: 76 outliers final: 67 residues processed: 220 average time/residue: 0.2587 time to fit residues: 99.2739 Evaluate side-chains 226 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 158 time to evaluate : 2.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 810 PHE Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 197 HIS Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 590 PHE Chi-restraints excluded: chain B residue 647 VAL Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 718 THR Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 815 GLU Chi-restraints excluded: chain B residue 828 CYS Chi-restraints excluded: chain B residue 830 ASN Chi-restraints excluded: chain B residue 833 ILE Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 477 HIS Chi-restraints excluded: chain C residue 511 ASP Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 781 GLU Chi-restraints excluded: chain C residue 786 GLU Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 197 HIS Chi-restraints excluded: chain D residue 422 PHE Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 462 CYS Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 541 THR Chi-restraints excluded: chain D residue 543 ASN Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 590 PHE Chi-restraints excluded: chain D residue 647 VAL Chi-restraints excluded: chain D residue 687 VAL Chi-restraints excluded: chain D residue 718 THR Chi-restraints excluded: chain D residue 745 LEU Chi-restraints excluded: chain D residue 746 THR Chi-restraints excluded: chain D residue 763 LEU Chi-restraints excluded: chain D residue 776 VAL Chi-restraints excluded: chain D residue 815 GLU Chi-restraints excluded: chain D residue 828 CYS Chi-restraints excluded: chain D residue 833 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 277 optimal weight: 7.9990 chunk 252 optimal weight: 50.0000 chunk 269 optimal weight: 2.9990 chunk 276 optimal weight: 0.9990 chunk 162 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 211 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 243 optimal weight: 20.0000 chunk 254 optimal weight: 0.0970 chunk 268 optimal weight: 0.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN A 196 GLN ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 GLN C 196 GLN C 812 ASN ** D 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22272 Z= 0.180 Angle : 0.536 9.606 30401 Z= 0.264 Chirality : 0.041 0.259 3621 Planarity : 0.003 0.058 3871 Dihedral : 5.913 86.512 3461 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.07 % Favored : 91.73 % Rotamer: Outliers : 3.92 % Allowed : 30.37 % Favored : 65.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.16), residues: 2938 helix: 1.82 (0.15), residues: 1240 sheet: -1.50 (0.30), residues: 320 loop : -2.17 (0.16), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 608 HIS 0.004 0.001 HIS C 404 PHE 0.013 0.001 PHE B 422 TYR 0.022 0.001 TYR C 392 ARG 0.001 0.000 ARG B 463 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 163 time to evaluate : 2.732 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 818 MET cc_start: 0.5088 (ptt) cc_final: 0.4716 (mmp) REVERT: C 818 MET cc_start: 0.5127 (ptt) cc_final: 0.4666 (mmp) outliers start: 78 outliers final: 69 residues processed: 224 average time/residue: 0.2546 time to fit residues: 99.4209 Evaluate side-chains 227 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 158 time to evaluate : 2.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 197 HIS Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 590 PHE Chi-restraints excluded: chain B residue 647 VAL Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 718 THR Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 815 GLU Chi-restraints excluded: chain B residue 828 CYS Chi-restraints excluded: chain B residue 830 ASN Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 477 HIS Chi-restraints excluded: chain C residue 511 ASP Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 781 GLU Chi-restraints excluded: chain C residue 786 GLU Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 197 HIS Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 422 PHE Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain D residue 462 CYS Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 541 THR Chi-restraints excluded: chain D residue 543 ASN Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 590 PHE Chi-restraints excluded: chain D residue 647 VAL Chi-restraints excluded: chain D residue 687 VAL Chi-restraints excluded: chain D residue 718 THR Chi-restraints excluded: chain D residue 746 THR Chi-restraints excluded: chain D residue 763 LEU Chi-restraints excluded: chain D residue 776 VAL Chi-restraints excluded: chain D residue 815 GLU Chi-restraints excluded: chain D residue 828 CYS Chi-restraints excluded: chain D residue 833 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 176 optimal weight: 7.9990 chunk 284 optimal weight: 0.4980 chunk 173 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 chunk 198 optimal weight: 0.9980 chunk 298 optimal weight: 0.9980 chunk 275 optimal weight: 6.9990 chunk 237 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 183 optimal weight: 1.9990 chunk 145 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 491 ASN ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 GLN C 196 GLN ** D 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22272 Z= 0.170 Angle : 0.537 9.581 30401 Z= 0.263 Chirality : 0.041 0.256 3621 Planarity : 0.003 0.057 3871 Dihedral : 5.650 83.664 3461 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.17 % Favored : 91.63 % Rotamer: Outliers : 3.41 % Allowed : 31.17 % Favored : 65.41 % 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: -0.46 (0.16), residues: 2938 helix: 1.91 (0.15), residues: 1226 sheet: -1.49 (0.30), residues: 320 loop : -2.19 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 608 HIS 0.004 0.001 HIS D 197 PHE 0.013 0.001 PHE B 422 TYR 0.021 0.001 TYR A 392 ARG 0.001 0.000 ARG C 673 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 161 time to evaluate : 2.474 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 818 MET cc_start: 0.5052 (ptt) cc_final: 0.4707 (mmp) REVERT: C 818 MET cc_start: 0.5070 (ptt) cc_final: 0.4624 (mmp) outliers start: 68 outliers final: 68 residues processed: 214 average time/residue: 0.2567 time to fit residues: 95.4089 Evaluate side-chains 226 residues out of total 2562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 158 time to evaluate : 2.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 197 HIS Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 590 PHE Chi-restraints excluded: chain B residue 647 VAL Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 718 THR Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 815 GLU Chi-restraints excluded: chain B residue 828 CYS Chi-restraints excluded: chain B residue 830 ASN Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 477 HIS Chi-restraints excluded: chain C residue 511 ASP Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 781 GLU Chi-restraints excluded: chain C residue 786 GLU Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 197 HIS Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 422 PHE Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain D residue 462 CYS Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 541 THR Chi-restraints excluded: chain D residue 543 ASN Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 590 PHE Chi-restraints excluded: chain D residue 647 VAL Chi-restraints excluded: chain D residue 687 VAL Chi-restraints excluded: chain D residue 718 THR Chi-restraints excluded: chain D residue 746 THR Chi-restraints excluded: chain D residue 763 LEU Chi-restraints excluded: chain D residue 776 VAL Chi-restraints excluded: chain D residue 815 GLU Chi-restraints excluded: chain D residue 828 CYS Chi-restraints excluded: chain D residue 833 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 189 optimal weight: 3.9990 chunk 253 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 chunk 219 optimal weight: 0.9990 chunk 35 optimal weight: 0.0470 chunk 66 optimal weight: 4.9990 chunk 238 optimal weight: 5.9990 chunk 99 optimal weight: 9.9990 chunk 244 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 overall best weight: 3.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN A 196 GLN ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 GLN C 196 GLN ** D 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.133590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.091759 restraints weight = 44219.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.091907 restraints weight = 32184.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.090966 restraints weight = 27562.995| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 22272 Z= 0.340 Angle : 0.590 9.574 30401 Z= 0.297 Chirality : 0.044 0.284 3621 Planarity : 0.004 0.059 3871 Dihedral : 5.820 77.123 3461 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.39 % Favored : 90.40 % Rotamer: Outliers : 3.82 % Allowed : 30.57 % Favored : 65.61 % 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: -0.57 (0.16), residues: 2938 helix: 1.69 (0.15), residues: 1246 sheet: -1.15 (0.33), residues: 290 loop : -2.26 (0.16), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 608 HIS 0.005 0.001 HIS D 197 PHE 0.021 0.002 PHE C 533 TYR 0.021 0.001 TYR A 392 ARG 0.004 0.000 ARG C 523 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3580.43 seconds wall clock time: 66 minutes 16.34 seconds (3976.34 seconds total)