Starting phenix.real_space_refine on Wed Jun 25 00:35:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f38_28833/06_2025/8f38_28833_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f38_28833/06_2025/8f38_28833.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f38_28833/06_2025/8f38_28833.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f38_28833/06_2025/8f38_28833.map" model { file = "/net/cci-nas-00/data/ceres_data/8f38_28833/06_2025/8f38_28833_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f38_28833/06_2025/8f38_28833_neut.cif" } resolution = 2.64 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= -0.001 sd= 0.079 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 14871 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 81 5.16 5 C 10644 2.51 5 N 2829 2.21 5 O 3398 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16952 Number of models: 1 Model: "" Number of chains: 21 Chain: "G" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 783 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 100} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 901 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 118, 899 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} Conformer: "B" Number of residues, atoms: 118, 899 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} bond proxies already assigned to first conformer: 917 Chain: "E" Number of atoms: 901 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 118, 899 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} Conformer: "B" Number of residues, atoms: 118, 899 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} bond proxies already assigned to first conformer: 917 Chain: "F" Number of atoms: 901 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 118, 899 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} Conformer: "B" Number of residues, atoms: 118, 899 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} bond proxies already assigned to first conformer: 917 Chain: "A" Number of atoms: 3799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3799 Classifications: {'peptide': 480} Link IDs: {'PTRANS': 21, 'TRANS': 458} Chain breaks: 1 Chain: "B" Number of atoms: 3799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3799 Classifications: {'peptide': 480} Link IDs: {'PTRANS': 21, 'TRANS': 458} Chain breaks: 1 Chain: "C" Number of atoms: 3799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3799 Classifications: {'peptide': 480} Link IDs: {'PTRANS': 21, 'TRANS': 458} Chain breaks: 1 Chain: "H" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 783 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 100} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "I" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 783 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 100} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" 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: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" 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: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" 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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 35 Classifications: {'water': 35} Link IDs: {None: 34} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Time building chain proxies: 11.76, per 1000 atoms: 0.69 Number of scatterers: 16952 At special positions: 0 Unit cell: (135, 127.575, 143.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 81 16.00 O 3398 8.00 N 2829 7.00 C 10644 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.04 Simple disulfide: pdb=" SG CYS A 21 " - pdb=" SG CYS A 480 " distance=2.03 Simple disulfide: pdb=" SG CYS A 72 " - pdb=" SG CYS A 84 " distance=2.03 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 152 " distance=2.03 Simple disulfide: pdb=" SG CYS A 295 " - pdb=" SG CYS A 319 " distance=2.03 Simple disulfide: pdb=" SG CYS A 487 " - pdb=" SG CYS A 491 " distance=2.03 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 480 " distance=2.03 Simple disulfide: pdb=" SG CYS B 72 " - pdb=" SG CYS B 84 " distance=2.03 Simple disulfide: pdb=" SG CYS B 107 " - pdb=" SG CYS B 152 " distance=2.03 Simple disulfide: pdb=" SG CYS B 295 " - pdb=" SG CYS B 319 " distance=2.03 Simple disulfide: pdb=" SG CYS B 487 " - pdb=" SG CYS B 491 " distance=2.03 Simple disulfide: pdb=" SG CYS C 21 " - pdb=" SG CYS C 480 " distance=2.03 Simple disulfide: pdb=" SG CYS C 72 " - pdb=" SG CYS C 84 " distance=2.03 Simple disulfide: pdb=" SG CYS C 107 " - pdb=" SG CYS C 152 " distance=2.03 Simple disulfide: pdb=" SG CYS C 295 " - pdb=" SG CYS C 319 " distance=2.03 Simple disulfide: pdb=" SG CYS C 487 " - pdb=" SG CYS C 491 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM16567 O5 NAG M 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 601 " - " ASN A 28 " " NAG A 602 " - " ASN A 142 " " NAG A 603 " - " ASN A 303 " " NAG A 604 " - " ASN A 497 " " NAG A 605 " - " ASN A 71 " " NAG A 606 " - " ASN A 176 " " NAG B 601 " - " ASN B 28 " " NAG B 602 " - " ASN B 142 " " NAG B 603 " - " ASN B 303 " " NAG B 604 " - " ASN B 497 " " NAG B 605 " - " ASN B 71 " " NAG B 606 " - " ASN B 176 " " NAG C 601 " - " ASN C 142 " " NAG C 602 " - " ASN C 303 " " NAG C 603 " - " ASN C 497 " " NAG C 604 " - " ASN C 71 " " NAG C 605 " - " ASN C 176 " " NAG C 606 " - " ASN C 28 " " NAG J 1 " - " ASN A 40 " " NAG K 1 " - " ASN A 104 " " NAG L 1 " - " ASN B 104 " " NAG M 1 " - " ASN B 40 " " NAG N 1 " - " ASN C 104 " " NAG O 1 " - " ASN C 40 " Time building additional restraints: 4.24 Conformation dependent library (CDL) restraints added in 2.6 seconds 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3864 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 54 sheets defined 18.4% alpha, 33.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.23 Creating SS restraints... Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.754A pdb=" N THR D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.735A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.744A pdb=" N THR F 91 " --> pdb=" O SER F 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 80 Processing helix chain 'A' and resid 84 through 88 Processing helix chain 'A' and resid 114 through 123 Processing helix chain 'A' and resid 200 through 209 Processing helix chain 'A' and resid 380 through 402 removed outlier: 3.676A pdb=" N THR A 384 " --> pdb=" O ASP A 380 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN A 386 " --> pdb=" O LYS A 382 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N MET A 402 " --> pdb=" O VAL A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 470 removed outlier: 3.954A pdb=" N GLU A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG A 449 " --> pdb=" O LEU A 445 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A 451 " --> pdb=" O ASN A 447 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN A 468 " --> pdb=" O LYS A 464 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU A 469 " --> pdb=" O VAL A 465 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS A 470 " --> pdb=" O LYS A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 496 Processing helix chain 'A' and resid 501 through 506 removed outlier: 3.847A pdb=" N TYR A 505 " --> pdb=" O ASP A 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 80 Processing helix chain 'B' and resid 84 through 88 Processing helix chain 'B' and resid 114 through 123 Processing helix chain 'B' and resid 200 through 209 Processing helix chain 'B' and resid 380 through 402 removed outlier: 3.675A pdb=" N THR B 384 " --> pdb=" O ASP B 380 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN B 386 " --> pdb=" O LYS B 382 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N MET B 402 " --> pdb=" O VAL B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 470 removed outlier: 3.954A pdb=" N GLU B 448 " --> pdb=" O LEU B 444 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG B 449 " --> pdb=" O LEU B 445 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU B 451 " --> pdb=" O ASN B 447 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN B 468 " --> pdb=" O LYS B 464 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU B 469 " --> pdb=" O VAL B 465 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS B 470 " --> pdb=" O LYS B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 496 Processing helix chain 'B' and resid 501 through 506 removed outlier: 3.847A pdb=" N TYR B 505 " --> pdb=" O ASP B 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 80 Processing helix chain 'C' and resid 84 through 88 Processing helix chain 'C' and resid 114 through 123 Processing helix chain 'C' and resid 200 through 209 Processing helix chain 'C' and resid 380 through 402 removed outlier: 3.675A pdb=" N THR C 384 " --> pdb=" O ASP C 380 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN C 386 " --> pdb=" O LYS C 382 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N MET C 402 " --> pdb=" O VAL C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 470 removed outlier: 3.954A pdb=" N GLU C 448 " --> pdb=" O LEU C 444 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG C 449 " --> pdb=" O LEU C 445 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU C 451 " --> pdb=" O ASN C 447 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN C 468 " --> pdb=" O LYS C 464 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU C 469 " --> pdb=" O VAL C 465 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS C 470 " --> pdb=" O LYS C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 496 Processing helix chain 'C' and resid 501 through 506 removed outlier: 3.847A pdb=" N TYR C 505 " --> pdb=" O ASP C 501 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 9 through 12 removed outlier: 6.438A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 9 through 12 Processing sheet with id=AA3, first strand: chain 'G' and resid 17 through 20 Processing sheet with id=AA4, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AA5, first strand: chain 'D' and resid 10 through 11 removed outlier: 6.627A pdb=" N ILE D 34 " --> pdb=" O GLY D 50 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLY D 50 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N TRP D 36 " --> pdb=" O MET D 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 10 through 11 removed outlier: 3.825A pdb=" N VAL D 110 " --> pdb=" O LYS D 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AA8, first strand: chain 'E' and resid 10 through 11 removed outlier: 6.620A pdb=" N ILE E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLY E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.820A pdb=" N VAL E 110 " --> pdb=" O LYS E 98 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 4 through 6 Processing sheet with id=AB2, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.613A pdb=" N ILE F 34 " --> pdb=" O GLY F 50 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N GLY F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N TRP F 36 " --> pdb=" O MET F 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 10 through 11 removed outlier: 3.816A pdb=" N VAL F 110 " --> pdb=" O LYS F 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 374 through 379 Processing sheet with id=AB5, first strand: chain 'A' and resid 32 through 33 Processing sheet with id=AB6, first strand: chain 'A' and resid 46 through 48 Processing sheet with id=AB7, first strand: chain 'A' and resid 50 through 51 Processing sheet with id=AB8, first strand: chain 'A' and resid 58 through 61 removed outlier: 6.436A pdb=" N LEU A 58 " --> pdb=" O ASP A 289 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N CYS A 291 " --> pdb=" O LEU A 58 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 67 through 68 removed outlier: 6.539A pdb=" N LEU A 67 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ILE A 96 " --> pdb=" O ILE A 282 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 125 through 132 removed outlier: 3.605A pdb=" N SER A 127 " --> pdb=" O SER A 274 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TYR A 269 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LEU A 192 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE A 271 " --> pdb=" O LEU A 190 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N LEU A 192 " --> pdb=" O PRO A 267 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 125 through 132 removed outlier: 3.605A pdb=" N SER A 127 " --> pdb=" O SER A 274 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TYR A 269 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LEU A 192 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE A 271 " --> pdb=" O LEU A 190 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 143 through 144 Processing sheet with id=AC4, first strand: chain 'A' and resid 149 through 154 removed outlier: 4.721A pdb=" N CYS A 152 " --> pdb=" O SER A 159 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 177 through 182 Processing sheet with id=AC6, first strand: chain 'A' and resid 301 through 302 removed outlier: 3.895A pdb=" N CYS A 295 " --> pdb=" O ILE A 302 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 374 through 379 Processing sheet with id=AC8, first strand: chain 'B' and resid 32 through 33 Processing sheet with id=AC9, first strand: chain 'B' and resid 46 through 48 Processing sheet with id=AD1, first strand: chain 'B' and resid 50 through 51 Processing sheet with id=AD2, first strand: chain 'B' and resid 58 through 61 removed outlier: 6.436A pdb=" N LEU B 58 " --> pdb=" O ASP B 289 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N CYS B 291 " --> pdb=" O LEU B 58 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 67 through 68 removed outlier: 6.539A pdb=" N LEU B 67 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ILE B 96 " --> pdb=" O ILE B 282 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 125 through 132 removed outlier: 3.605A pdb=" N SER B 127 " --> pdb=" O SER B 274 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TYR B 269 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LEU B 192 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE B 271 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N LEU B 192 " --> pdb=" O PRO B 267 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 125 through 132 removed outlier: 3.605A pdb=" N SER B 127 " --> pdb=" O SER B 274 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TYR B 269 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LEU B 192 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE B 271 " --> pdb=" O LEU B 190 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 143 through 144 Processing sheet with id=AD7, first strand: chain 'B' and resid 149 through 154 removed outlier: 4.721A pdb=" N CYS B 152 " --> pdb=" O SER B 159 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 177 through 182 Processing sheet with id=AD9, first strand: chain 'B' and resid 301 through 302 removed outlier: 3.895A pdb=" N CYS B 295 " --> pdb=" O ILE B 302 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 374 through 379 Processing sheet with id=AE2, first strand: chain 'C' and resid 32 through 33 Processing sheet with id=AE3, first strand: chain 'C' and resid 46 through 48 Processing sheet with id=AE4, first strand: chain 'C' and resid 50 through 51 Processing sheet with id=AE5, first strand: chain 'C' and resid 58 through 61 removed outlier: 6.435A pdb=" N LEU C 58 " --> pdb=" O ASP C 289 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N CYS C 291 " --> pdb=" O LEU C 58 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 67 through 68 removed outlier: 6.539A pdb=" N LEU C 67 " --> pdb=" O VAL C 97 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ILE C 96 " --> pdb=" O ILE C 282 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'C' and resid 125 through 132 removed outlier: 3.605A pdb=" N SER C 127 " --> pdb=" O SER C 274 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TYR C 269 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LEU C 192 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE C 271 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N LEU C 192 " --> pdb=" O PRO C 267 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 125 through 132 removed outlier: 3.605A pdb=" N SER C 127 " --> pdb=" O SER C 274 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TYR C 269 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LEU C 192 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE C 271 " --> pdb=" O LEU C 190 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 143 through 144 Processing sheet with id=AF1, first strand: chain 'C' and resid 149 through 154 removed outlier: 4.720A pdb=" N CYS C 152 " --> pdb=" O SER C 159 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 177 through 182 Processing sheet with id=AF3, first strand: chain 'C' and resid 301 through 302 removed outlier: 3.895A pdb=" N CYS C 295 " --> pdb=" O ILE C 302 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 9 through 12 removed outlier: 6.438A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 9 through 12 Processing sheet with id=AF6, first strand: chain 'H' and resid 17 through 20 Processing sheet with id=AF7, first strand: chain 'I' and resid 9 through 12 removed outlier: 6.438A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 9 through 12 Processing sheet with id=AF9, first strand: chain 'I' and resid 17 through 20 684 hydrogen bonds defined for protein. 1809 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: 7.11 Time building geometry restraints manager: 5.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3209 1.33 - 1.45: 4698 1.45 - 1.58: 9286 1.58 - 1.70: 0 1.70 - 1.83: 114 Bond restraints: 17307 Sorted by residual: bond pdb=" C CYS C 291 " pdb=" O CYS C 291 " ideal model delta sigma weight residual 1.233 1.201 0.032 1.28e-02 6.10e+03 6.38e+00 bond pdb=" C CYS A 291 " pdb=" O CYS A 291 " ideal model delta sigma weight residual 1.233 1.201 0.032 1.28e-02 6.10e+03 6.26e+00 bond pdb=" C CYS B 291 " pdb=" O CYS B 291 " ideal model delta sigma weight residual 1.233 1.201 0.032 1.28e-02 6.10e+03 6.22e+00 bond pdb=" N CYS H 22 " pdb=" CA CYS H 22 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.29e-02 6.01e+03 4.67e+00 bond pdb=" N SER H 23 " pdb=" CA SER H 23 " ideal model delta sigma weight residual 1.460 1.486 -0.026 1.20e-02 6.94e+03 4.64e+00 ... (remaining 17302 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 22327 1.24 - 2.47: 940 2.47 - 3.71: 204 3.71 - 4.95: 28 4.95 - 6.18: 15 Bond angle restraints: 23514 Sorted by residual: angle pdb=" C GLU C 290 " pdb=" N CYS C 291 " pdb=" CA CYS C 291 " ideal model delta sigma weight residual 122.02 116.04 5.98 1.89e+00 2.80e-01 1.00e+01 angle pdb=" C GLU A 290 " pdb=" N CYS A 291 " pdb=" CA CYS A 291 " ideal model delta sigma weight residual 122.02 116.05 5.97 1.89e+00 2.80e-01 9.96e+00 angle pdb=" C GLU B 290 " pdb=" N CYS B 291 " pdb=" CA CYS B 291 " ideal model delta sigma weight residual 122.02 116.06 5.96 1.89e+00 2.80e-01 9.93e+00 angle pdb=" O GLU C 290 " pdb=" C GLU C 290 " pdb=" N CYS C 291 " ideal model delta sigma weight residual 122.19 118.21 3.98 1.29e+00 6.01e-01 9.54e+00 angle pdb=" O GLU A 290 " pdb=" C GLU A 290 " pdb=" N CYS A 291 " ideal model delta sigma weight residual 122.19 118.21 3.98 1.29e+00 6.01e-01 9.53e+00 ... (remaining 23509 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.58: 9451 21.58 - 43.15: 912 43.15 - 64.73: 229 64.73 - 86.30: 70 86.30 - 107.88: 30 Dihedral angle restraints: 10692 sinusoidal: 4605 harmonic: 6087 Sorted by residual: dihedral pdb=" CB CYS B 487 " pdb=" SG CYS B 487 " pdb=" SG CYS B 491 " pdb=" CB CYS B 491 " ideal model delta sinusoidal sigma weight residual -86.00 -33.91 -52.09 1 1.00e+01 1.00e-02 3.70e+01 dihedral pdb=" CB CYS A 487 " pdb=" SG CYS A 487 " pdb=" SG CYS A 491 " pdb=" CB CYS A 491 " ideal model delta sinusoidal sigma weight residual -86.00 -33.95 -52.05 1 1.00e+01 1.00e-02 3.70e+01 dihedral pdb=" CB CYS C 487 " pdb=" SG CYS C 487 " pdb=" SG CYS C 491 " pdb=" CB CYS C 491 " ideal model delta sinusoidal sigma weight residual -86.00 -33.97 -52.03 1 1.00e+01 1.00e-02 3.69e+01 ... (remaining 10689 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 2559 0.106 - 0.211: 68 0.211 - 0.317: 8 0.317 - 0.423: 3 0.423 - 0.528: 2 Chirality restraints: 2640 Sorted by residual: chirality pdb=" C1 NAG B 606 " pdb=" ND2 ASN B 176 " pdb=" C2 NAG B 606 " pdb=" O5 NAG B 606 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 6.98e+00 chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN C 40 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.90 0.50 2.00e-01 2.50e+01 6.13e+00 chirality pdb=" C1 NAG C 601 " pdb=" ND2 ASN C 142 " pdb=" C2 NAG C 601 " pdb=" O5 NAG C 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.16e+00 ... (remaining 2637 not shown) Planarity restraints: 3027 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 176 " -0.160 2.00e-02 2.50e+03 1.57e-01 3.09e+02 pdb=" CG ASN B 176 " 0.066 2.00e-02 2.50e+03 pdb=" OD1 ASN B 176 " 0.072 2.00e-02 2.50e+03 pdb=" ND2 ASN B 176 " 0.221 2.00e-02 2.50e+03 pdb=" C1 NAG B 606 " -0.199 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 40 " 0.156 2.00e-02 2.50e+03 1.45e-01 2.61e+02 pdb=" CG ASN B 40 " -0.078 2.00e-02 2.50e+03 pdb=" OD1 ASN B 40 " -0.093 2.00e-02 2.50e+03 pdb=" ND2 ASN B 40 " -0.174 2.00e-02 2.50e+03 pdb=" C1 NAG M 1 " 0.188 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 40 " -0.095 2.00e-02 2.50e+03 8.45e-02 8.93e+01 pdb=" CG ASN C 40 " 0.054 2.00e-02 2.50e+03 pdb=" OD1 ASN C 40 " 0.043 2.00e-02 2.50e+03 pdb=" ND2 ASN C 40 " 0.104 2.00e-02 2.50e+03 pdb=" C1 NAG O 1 " -0.106 2.00e-02 2.50e+03 ... (remaining 3024 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 499 2.70 - 3.25: 14295 3.25 - 3.80: 24846 3.80 - 4.35: 34185 4.35 - 4.90: 59293 Nonbonded interactions: 133118 Sorted by model distance: nonbonded pdb=" OD1 ASN C 176 " pdb=" C1 NAG C 605 " model vdw 2.148 2.776 nonbonded pdb=" OD1 ASN B 40 " pdb=" C1 NAG M 1 " model vdw 2.225 2.776 nonbonded pdb=" O GLY C 355 " pdb=" O HOH C 701 " model vdw 2.240 3.040 nonbonded pdb=" ND2 ASN B 176 " pdb=" N2 NAG B 606 " model vdw 2.257 2.560 nonbonded pdb=" O GLY A 355 " pdb=" O HOH A 701 " model vdw 2.262 3.040 ... (remaining 133113 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and (resid 2 through 29 or resid 31 through 119)) selection = (chain 'E' and (resid 2 through 29 or resid 31 through 119)) selection = (chain 'F' and (resid 2 through 29 or resid 31 through 119)) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'N' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.180 Construct map_model_manager: 0.010 Extract box with map and model: 0.710 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 48.100 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:15.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 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 : 0.005 0.240 17358 Z= 0.240 Angle : 0.797 33.261 23649 Z= 0.362 Chirality : 0.049 0.528 2640 Planarity : 0.005 0.078 3003 Dihedral : 19.167 107.878 6774 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.29 % Allowed : 2.29 % Favored : 97.42 % Rotamer: Outliers : 4.08 % Allowed : 24.85 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.18), residues: 2100 helix: 2.55 (0.29), residues: 318 sheet: 0.73 (0.21), residues: 615 loop : -0.94 (0.16), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 435 HIS 0.005 0.001 HIS A 369 PHE 0.013 0.001 PHE A 453 TYR 0.012 0.001 TYR I 99 ARG 0.003 0.000 ARG C 162 Details of bonding type rmsd link_NAG-ASN : bond 0.08691 ( 24) link_NAG-ASN : angle 9.41458 ( 72) link_BETA1-4 : bond 0.00509 ( 9) link_BETA1-4 : angle 1.66727 ( 27) hydrogen bonds : bond 0.14811 ( 633) hydrogen bonds : angle 6.77406 ( 1809) SS BOND : bond 0.00305 ( 18) SS BOND : angle 0.84495 ( 36) covalent geometry : bond 0.00350 (17307) covalent geometry : angle 0.60285 (23514) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 202 time to evaluate : 1.745 Fit side-chains REVERT: G 5 THR cc_start: 0.6825 (OUTLIER) cc_final: 0.6409 (p) REVERT: D 74 ASP cc_start: 0.8252 (m-30) cc_final: 0.8017 (m-30) REVERT: A 162 ARG cc_start: 0.8278 (mpt180) cc_final: 0.8053 (mpt90) REVERT: A 400 GLU cc_start: 0.7969 (tt0) cc_final: 0.7665 (tt0) REVERT: A 459 LYS cc_start: 0.8181 (tttm) cc_final: 0.7730 (tttt) REVERT: B 162 ARG cc_start: 0.8310 (mpt180) cc_final: 0.8067 (mpt90) REVERT: B 400 GLU cc_start: 0.8070 (tt0) cc_final: 0.7808 (tt0) REVERT: B 403 ASN cc_start: 0.7258 (m-40) cc_final: 0.6965 (m-40) REVERT: B 420 MET cc_start: 0.7958 (ttm) cc_final: 0.7585 (mmm) REVERT: B 459 LYS cc_start: 0.8071 (tttm) cc_final: 0.7630 (tttt) REVERT: C 64 ILE cc_start: 0.8550 (mt) cc_final: 0.8173 (mt) REVERT: C 162 ARG cc_start: 0.8297 (mpt180) cc_final: 0.8059 (mpt90) REVERT: C 370 GLN cc_start: 0.7780 (OUTLIER) cc_final: 0.7339 (tp-100) REVERT: C 381 GLN cc_start: 0.7715 (tm-30) cc_final: 0.7361 (tm-30) REVERT: C 400 GLU cc_start: 0.8047 (tt0) cc_final: 0.7755 (tt0) REVERT: C 459 LYS cc_start: 0.8143 (tttm) cc_final: 0.7714 (tttt) REVERT: H 5 THR cc_start: 0.6892 (OUTLIER) cc_final: 0.6610 (p) REVERT: I 5 THR cc_start: 0.6572 (OUTLIER) cc_final: 0.6115 (p) outliers start: 67 outliers final: 46 residues processed: 262 average time/residue: 1.1907 time to fit residues: 350.5127 Evaluate side-chains 225 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 175 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 370 GLN Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 52 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 2.9990 chunk 156 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 105 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 162 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 187 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 39 GLN D 39 GLN E 39 GLN F 39 GLN H 39 GLN I 39 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.154141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.118112 restraints weight = 19128.217| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.32 r_work: 0.3154 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3011 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3011 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 17358 Z= 0.268 Angle : 0.794 9.085 23649 Z= 0.407 Chirality : 0.054 0.456 2640 Planarity : 0.006 0.065 3003 Dihedral : 11.364 67.040 3050 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.29 % Favored : 96.57 % Rotamer: Outliers : 6.14 % Allowed : 21.11 % Favored : 72.75 % 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: 0.09 (0.18), residues: 2100 helix: 2.10 (0.28), residues: 330 sheet: 0.91 (0.20), residues: 648 loop : -1.14 (0.17), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 93 HIS 0.006 0.002 HIS A 25 PHE 0.021 0.003 PHE B 128 TYR 0.016 0.003 TYR I 99 ARG 0.006 0.001 ARG E 30 Details of bonding type rmsd link_NAG-ASN : bond 0.00448 ( 24) link_NAG-ASN : angle 2.95446 ( 72) link_BETA1-4 : bond 0.00700 ( 9) link_BETA1-4 : angle 2.50161 ( 27) hydrogen bonds : bond 0.08579 ( 633) hydrogen bonds : angle 5.31761 ( 1809) SS BOND : bond 0.00779 ( 18) SS BOND : angle 1.89774 ( 36) covalent geometry : bond 0.00645 (17307) covalent geometry : angle 0.77066 (23514) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 190 time to evaluate : 1.663 Fit side-chains REVERT: G 9 SER cc_start: 0.6814 (p) cc_final: 0.6587 (t) REVERT: G 19 THR cc_start: 0.5902 (OUTLIER) cc_final: 0.5604 (t) REVERT: D 74 ASP cc_start: 0.8584 (m-30) cc_final: 0.8375 (m-30) REVERT: F 63 LYS cc_start: 0.7735 (ttpt) cc_final: 0.7392 (ttmm) REVERT: A 162 ARG cc_start: 0.8867 (mpt180) cc_final: 0.8559 (mpt90) REVERT: A 232 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7505 (tptm) REVERT: A 381 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.8021 (tm-30) REVERT: A 400 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8229 (tt0) REVERT: A 459 LYS cc_start: 0.8777 (tttm) cc_final: 0.8446 (tttt) REVERT: B 162 ARG cc_start: 0.8886 (mpt180) cc_final: 0.8593 (mpt90) REVERT: B 400 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8317 (tt0) REVERT: B 459 LYS cc_start: 0.8666 (tttm) cc_final: 0.8327 (tttt) REVERT: C 64 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8394 (mt) REVERT: C 162 ARG cc_start: 0.8854 (mpt180) cc_final: 0.8647 (mpt90) REVERT: C 232 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7467 (tptm) REVERT: C 381 GLN cc_start: 0.8239 (tm-30) cc_final: 0.7976 (tm-30) REVERT: C 400 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8296 (tt0) REVERT: C 459 LYS cc_start: 0.8671 (tttm) cc_final: 0.8337 (tttt) REVERT: H 19 THR cc_start: 0.5857 (OUTLIER) cc_final: 0.5542 (t) REVERT: I 9 SER cc_start: 0.6623 (p) cc_final: 0.6394 (t) REVERT: I 19 THR cc_start: 0.5759 (OUTLIER) cc_final: 0.5461 (t) outliers start: 104 outliers final: 55 residues processed: 265 average time/residue: 1.4088 time to fit residues: 422.9273 Evaluate side-chains 240 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 175 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 381 GLN Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 382 LYS Chi-restraints excluded: chain B residue 400 GLU Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 400 GLU Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 476 ILE Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 32 ASP Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 52 ASN Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 52 ASN Chi-restraints excluded: chain I residue 70 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 65 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 136 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 103 optimal weight: 0.1980 chunk 58 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 ASN C 403 ASN H 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.156392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.120719 restraints weight = 18967.126| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.15 r_work: 0.3209 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3057 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3057 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 17358 Z= 0.155 Angle : 0.638 8.907 23649 Z= 0.327 Chirality : 0.047 0.415 2640 Planarity : 0.005 0.055 3003 Dihedral : 8.682 55.102 3016 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.48 % Favored : 97.38 % Rotamer: Outliers : 4.97 % Allowed : 22.11 % Favored : 72.92 % 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: 0.32 (0.18), residues: 2100 helix: 2.45 (0.28), residues: 330 sheet: 1.02 (0.21), residues: 606 loop : -0.95 (0.16), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 435 HIS 0.005 0.001 HIS B 25 PHE 0.018 0.002 PHE A 453 TYR 0.014 0.002 TYR I 99 ARG 0.003 0.000 ARG E 30 Details of bonding type rmsd link_NAG-ASN : bond 0.00405 ( 24) link_NAG-ASN : angle 2.55393 ( 72) link_BETA1-4 : bond 0.00547 ( 9) link_BETA1-4 : angle 2.28454 ( 27) hydrogen bonds : bond 0.06965 ( 633) hydrogen bonds : angle 4.94804 ( 1809) SS BOND : bond 0.00504 ( 18) SS BOND : angle 1.49127 ( 36) covalent geometry : bond 0.00352 (17307) covalent geometry : angle 0.61687 (23514) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 184 time to evaluate : 1.744 Fit side-chains REVERT: G 9 SER cc_start: 0.6846 (p) cc_final: 0.6630 (t) REVERT: G 52 ASN cc_start: 0.6610 (OUTLIER) cc_final: 0.6175 (t160) REVERT: D 74 ASP cc_start: 0.8587 (m-30) cc_final: 0.8365 (m-30) REVERT: F 63 LYS cc_start: 0.7730 (ttpt) cc_final: 0.7396 (ttmm) REVERT: A 162 ARG cc_start: 0.8844 (mpt180) cc_final: 0.8563 (mpt90) REVERT: A 400 GLU cc_start: 0.8333 (tm-30) cc_final: 0.8085 (tt0) REVERT: A 459 LYS cc_start: 0.8694 (tttm) cc_final: 0.8362 (tttt) REVERT: B 90 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.8050 (tttm) REVERT: B 162 ARG cc_start: 0.8847 (mpt180) cc_final: 0.8585 (mpt90) REVERT: B 232 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7551 (tptm) REVERT: B 400 GLU cc_start: 0.8443 (tm-30) cc_final: 0.8221 (tt0) REVERT: B 420 MET cc_start: 0.8737 (ttm) cc_final: 0.8397 (mmm) REVERT: B 459 LYS cc_start: 0.8609 (tttm) cc_final: 0.8283 (tttt) REVERT: C 64 ILE cc_start: 0.8685 (OUTLIER) cc_final: 0.8331 (mt) REVERT: C 400 GLU cc_start: 0.8391 (tm-30) cc_final: 0.8145 (tt0) REVERT: C 459 LYS cc_start: 0.8599 (tttm) cc_final: 0.8266 (tttt) REVERT: I 9 SER cc_start: 0.6611 (p) cc_final: 0.6348 (t) outliers start: 83 outliers final: 46 residues processed: 250 average time/residue: 1.2046 time to fit residues: 337.3182 Evaluate side-chains 234 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 184 time to evaluate : 1.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 382 LYS Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 294 LYS Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 476 ILE Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 52 ASN Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain I residue 32 ASP Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 52 ASN Chi-restraints excluded: chain I residue 110 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 146 optimal weight: 0.9990 chunk 64 optimal weight: 0.0770 chunk 135 optimal weight: 6.9990 chunk 100 optimal weight: 0.0770 chunk 37 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 125 optimal weight: 6.9990 chunk 153 optimal weight: 0.0470 chunk 27 optimal weight: 10.0000 overall best weight: 1.0398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 ASN C 403 ASN H 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.157776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.121986 restraints weight = 19105.972| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.36 r_work: 0.3229 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3076 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3076 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17358 Z= 0.125 Angle : 0.573 8.737 23649 Z= 0.295 Chirality : 0.045 0.382 2640 Planarity : 0.005 0.053 3003 Dihedral : 7.543 56.909 3011 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.43 % Favored : 97.42 % Rotamer: Outliers : 4.52 % Allowed : 22.67 % Favored : 72.81 % 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 (0.18), residues: 2100 helix: 2.67 (0.28), residues: 330 sheet: 1.17 (0.21), residues: 606 loop : -0.87 (0.17), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 435 HIS 0.004 0.001 HIS A 369 PHE 0.017 0.002 PHE A 128 TYR 0.013 0.001 TYR I 99 ARG 0.002 0.000 ARG E 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00425 ( 24) link_NAG-ASN : angle 2.30241 ( 72) link_BETA1-4 : bond 0.00546 ( 9) link_BETA1-4 : angle 2.05211 ( 27) hydrogen bonds : bond 0.06276 ( 633) hydrogen bonds : angle 4.72929 ( 1809) SS BOND : bond 0.00408 ( 18) SS BOND : angle 1.31452 ( 36) covalent geometry : bond 0.00267 (17307) covalent geometry : angle 0.55349 (23514) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 194 time to evaluate : 1.967 Fit side-chains REVERT: G 9 SER cc_start: 0.6906 (p) cc_final: 0.6645 (t) REVERT: G 19 THR cc_start: 0.5868 (OUTLIER) cc_final: 0.5572 (t) REVERT: G 52 ASN cc_start: 0.6443 (OUTLIER) cc_final: 0.6152 (t0) REVERT: D 74 ASP cc_start: 0.8587 (m-30) cc_final: 0.8349 (m-30) REVERT: F 63 LYS cc_start: 0.7705 (ttpt) cc_final: 0.7370 (ttmm) REVERT: A 162 ARG cc_start: 0.8838 (mpt180) cc_final: 0.8569 (mpt90) REVERT: A 232 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7496 (tptm) REVERT: A 400 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.8067 (tt0) REVERT: A 459 LYS cc_start: 0.8617 (tttm) cc_final: 0.8282 (tttt) REVERT: A 486 LYS cc_start: 0.6764 (mmpt) cc_final: 0.6436 (pptt) REVERT: B 90 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8082 (tttm) REVERT: B 162 ARG cc_start: 0.8844 (mpt180) cc_final: 0.8593 (mpt90) REVERT: B 232 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7536 (tptm) REVERT: B 400 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8168 (tt0) REVERT: B 420 MET cc_start: 0.8682 (ttm) cc_final: 0.8379 (mmm) REVERT: B 459 LYS cc_start: 0.8530 (tttm) cc_final: 0.8199 (tttt) REVERT: B 486 LYS cc_start: 0.6813 (mmpt) cc_final: 0.6480 (pptt) REVERT: C 22 ILE cc_start: 0.9146 (OUTLIER) cc_final: 0.8777 (mm) REVERT: C 64 ILE cc_start: 0.8681 (mt) cc_final: 0.8321 (mt) REVERT: C 400 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8114 (tt0) REVERT: C 459 LYS cc_start: 0.8553 (tttm) cc_final: 0.8214 (tttt) REVERT: C 486 LYS cc_start: 0.6852 (mmpt) cc_final: 0.6471 (pptt) REVERT: I 9 SER cc_start: 0.6635 (p) cc_final: 0.6359 (t) REVERT: I 19 THR cc_start: 0.5778 (OUTLIER) cc_final: 0.5522 (t) REVERT: I 52 ASN cc_start: 0.6305 (OUTLIER) cc_final: 0.6096 (t0) outliers start: 75 outliers final: 42 residues processed: 250 average time/residue: 1.2267 time to fit residues: 341.9871 Evaluate side-chains 249 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 196 time to evaluate : 1.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 382 LYS Chi-restraints excluded: chain B residue 400 GLU Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 294 LYS Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 400 GLU Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 476 ILE Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain H residue 32 ASP Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 32 ASP Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 52 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 60 optimal weight: 7.9990 chunk 169 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 19 optimal weight: 7.9990 chunk 156 optimal weight: 6.9990 chunk 189 optimal weight: 0.2980 chunk 70 optimal weight: 6.9990 chunk 108 optimal weight: 5.9990 chunk 164 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 overall best weight: 3.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 6 GLN A 403 ASN C 403 ASN H 6 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.153719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.117858 restraints weight = 19242.699| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.31 r_work: 0.3164 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3009 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3009 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 17358 Z= 0.269 Angle : 0.773 9.705 23649 Z= 0.400 Chirality : 0.054 0.511 2640 Planarity : 0.006 0.061 3003 Dihedral : 7.785 59.471 3009 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.20 % Favored : 96.66 % Rotamer: Outliers : 6.20 % Allowed : 20.88 % Favored : 72.92 % 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: 0.23 (0.17), residues: 2100 helix: 2.41 (0.28), residues: 330 sheet: 1.17 (0.20), residues: 612 loop : -1.17 (0.16), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 93 HIS 0.007 0.002 HIS A 25 PHE 0.018 0.003 PHE C 128 TYR 0.016 0.002 TYR I 99 ARG 0.007 0.001 ARG F 30 Details of bonding type rmsd link_NAG-ASN : bond 0.00497 ( 24) link_NAG-ASN : angle 2.89951 ( 72) link_BETA1-4 : bond 0.00620 ( 9) link_BETA1-4 : angle 2.52858 ( 27) hydrogen bonds : bond 0.08480 ( 633) hydrogen bonds : angle 5.14419 ( 1809) SS BOND : bond 0.00757 ( 18) SS BOND : angle 1.80952 ( 36) covalent geometry : bond 0.00651 (17307) covalent geometry : angle 0.75002 (23514) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 192 time to evaluate : 1.985 Fit side-chains REVERT: G 9 SER cc_start: 0.6711 (p) cc_final: 0.6437 (t) REVERT: G 19 THR cc_start: 0.5943 (OUTLIER) cc_final: 0.5657 (t) REVERT: D 74 ASP cc_start: 0.8622 (m-30) cc_final: 0.8420 (m-30) REVERT: A 162 ARG cc_start: 0.8862 (mpt180) cc_final: 0.8554 (mpt90) REVERT: A 232 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.7507 (tptm) REVERT: A 400 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8267 (tt0) REVERT: A 459 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8486 (tttt) REVERT: A 486 LYS cc_start: 0.6836 (mmpt) cc_final: 0.6522 (pptt) REVERT: B 90 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8084 (tttm) REVERT: B 162 ARG cc_start: 0.8887 (mpt180) cc_final: 0.8661 (mpt90) REVERT: B 381 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.8131 (mt0) REVERT: B 400 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8322 (tt0) REVERT: B 459 LYS cc_start: 0.8700 (tttm) cc_final: 0.8383 (tttt) REVERT: B 486 LYS cc_start: 0.6956 (mmpt) cc_final: 0.6589 (pptt) REVERT: C 232 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7513 (tptm) REVERT: C 370 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.7384 (tp-100) REVERT: C 381 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.8043 (mt0) REVERT: C 400 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8244 (tt0) REVERT: C 459 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8424 (tttt) REVERT: C 486 LYS cc_start: 0.6803 (mmpt) cc_final: 0.6496 (pptt) REVERT: H 19 THR cc_start: 0.5862 (OUTLIER) cc_final: 0.5567 (t) REVERT: I 9 SER cc_start: 0.6499 (p) cc_final: 0.6217 (t) REVERT: I 19 THR cc_start: 0.5834 (OUTLIER) cc_final: 0.5554 (t) REVERT: I 52 ASN cc_start: 0.6589 (OUTLIER) cc_final: 0.6277 (t0) outliers start: 105 outliers final: 60 residues processed: 270 average time/residue: 1.1777 time to fit residues: 356.8416 Evaluate side-chains 259 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 184 time to evaluate : 1.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 381 GLN Chi-restraints excluded: chain B residue 382 LYS Chi-restraints excluded: chain B residue 400 GLU Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 220 SER Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 294 LYS Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 370 GLN Chi-restraints excluded: chain C residue 381 GLN Chi-restraints excluded: chain C residue 400 GLU Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 459 LYS Chi-restraints excluded: chain C residue 476 ILE Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 32 ASP Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 52 ASN Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 32 ASP Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 52 ASN Chi-restraints excluded: chain I residue 110 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 25 optimal weight: 4.9990 chunk 5 optimal weight: 0.4980 chunk 92 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 185 optimal weight: 0.8980 chunk 166 optimal weight: 6.9990 chunk 171 optimal weight: 0.5980 chunk 63 optimal weight: 0.0970 chunk 96 optimal weight: 4.9990 chunk 143 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.0180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 6 GLN G 52 ASN A 403 ASN C 403 ASN H 6 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.157610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.122183 restraints weight = 19242.383| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.12 r_work: 0.3237 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3080 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3080 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17358 Z= 0.124 Angle : 0.574 8.563 23649 Z= 0.297 Chirality : 0.045 0.408 2640 Planarity : 0.005 0.052 3003 Dihedral : 7.170 59.285 3007 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.48 % Favored : 97.38 % Rotamer: Outliers : 4.58 % Allowed : 22.78 % Favored : 72.64 % 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 (0.18), residues: 2100 helix: 2.70 (0.28), residues: 330 sheet: 1.20 (0.21), residues: 576 loop : -0.90 (0.16), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 435 HIS 0.004 0.001 HIS A 369 PHE 0.017 0.002 PHE A 128 TYR 0.013 0.001 TYR I 99 ARG 0.002 0.000 ARG D 30 Details of bonding type rmsd link_NAG-ASN : bond 0.00433 ( 24) link_NAG-ASN : angle 2.40441 ( 72) link_BETA1-4 : bond 0.00530 ( 9) link_BETA1-4 : angle 1.89956 ( 27) hydrogen bonds : bond 0.06300 ( 633) hydrogen bonds : angle 4.72540 ( 1809) SS BOND : bond 0.00350 ( 18) SS BOND : angle 1.44439 ( 36) covalent geometry : bond 0.00262 (17307) covalent geometry : angle 0.55392 (23514) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 195 time to evaluate : 1.678 Fit side-chains REVERT: G 9 SER cc_start: 0.6780 (p) cc_final: 0.6525 (t) REVERT: G 19 THR cc_start: 0.5895 (OUTLIER) cc_final: 0.5601 (t) REVERT: D 74 ASP cc_start: 0.8600 (m-30) cc_final: 0.8380 (m-30) REVERT: A 162 ARG cc_start: 0.8806 (mpt180) cc_final: 0.8529 (mpt90) REVERT: A 400 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.8059 (tt0) REVERT: A 459 LYS cc_start: 0.8659 (tttm) cc_final: 0.8331 (tttt) REVERT: A 486 LYS cc_start: 0.6830 (mmpt) cc_final: 0.6554 (pptt) REVERT: B 90 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8109 (tttm) REVERT: B 162 ARG cc_start: 0.8828 (mpt180) cc_final: 0.8570 (mpt90) REVERT: B 420 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.8323 (mmm) REVERT: B 459 LYS cc_start: 0.8539 (tttm) cc_final: 0.8219 (tttt) REVERT: B 486 LYS cc_start: 0.6900 (mmpt) cc_final: 0.6589 (pptt) REVERT: C 232 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7461 (tptm) REVERT: C 370 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.7382 (tp-100) REVERT: C 400 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.8002 (tt0) REVERT: C 459 LYS cc_start: 0.8568 (tttm) cc_final: 0.8249 (tttt) REVERT: C 486 LYS cc_start: 0.6826 (mmpt) cc_final: 0.6550 (pptt) REVERT: H 19 THR cc_start: 0.5850 (OUTLIER) cc_final: 0.5559 (t) REVERT: I 9 SER cc_start: 0.6608 (p) cc_final: 0.6338 (t) REVERT: I 19 THR cc_start: 0.5846 (OUTLIER) cc_final: 0.5604 (t) outliers start: 76 outliers final: 44 residues processed: 252 average time/residue: 1.2678 time to fit residues: 356.8717 Evaluate side-chains 245 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 192 time to evaluate : 1.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 294 LYS Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 370 GLN Chi-restraints excluded: chain C residue 400 GLU Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 476 ILE Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 32 ASP Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 52 ASN Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 32 ASP Chi-restraints excluded: chain I residue 49 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 24 optimal weight: 3.9990 chunk 41 optimal weight: 0.3980 chunk 99 optimal weight: 5.9990 chunk 94 optimal weight: 0.0970 chunk 146 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 199 optimal weight: 20.0000 chunk 4 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 69 optimal weight: 9.9990 overall best weight: 1.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 6 GLN A 403 ASN C 403 ASN I 52 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.156497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.120796 restraints weight = 19121.428| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.35 r_work: 0.3211 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3059 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3059 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17358 Z= 0.156 Angle : 0.618 9.145 23649 Z= 0.319 Chirality : 0.047 0.426 2640 Planarity : 0.005 0.053 3003 Dihedral : 7.007 58.871 3005 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.15 % Favored : 97.71 % Rotamer: Outliers : 4.58 % Allowed : 23.06 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.18), residues: 2100 helix: 2.70 (0.28), residues: 330 sheet: 1.23 (0.21), residues: 576 loop : -0.89 (0.16), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 435 HIS 0.005 0.001 HIS B 25 PHE 0.019 0.002 PHE C 453 TYR 0.014 0.002 TYR I 99 ARG 0.003 0.000 ARG E 30 Details of bonding type rmsd link_NAG-ASN : bond 0.00421 ( 24) link_NAG-ASN : angle 2.43102 ( 72) link_BETA1-4 : bond 0.00535 ( 9) link_BETA1-4 : angle 1.97811 ( 27) hydrogen bonds : bond 0.06835 ( 633) hydrogen bonds : angle 4.78265 ( 1809) SS BOND : bond 0.00490 ( 18) SS BOND : angle 1.48593 ( 36) covalent geometry : bond 0.00357 (17307) covalent geometry : angle 0.59861 (23514) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 189 time to evaluate : 1.713 Fit side-chains REVERT: G 9 SER cc_start: 0.6717 (p) cc_final: 0.6455 (t) REVERT: G 19 THR cc_start: 0.5889 (OUTLIER) cc_final: 0.5607 (t) REVERT: D 74 ASP cc_start: 0.8602 (m-30) cc_final: 0.8380 (m-30) REVERT: A 162 ARG cc_start: 0.8829 (mpt180) cc_final: 0.8543 (mpt90) REVERT: A 232 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7473 (tptm) REVERT: A 400 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8101 (tt0) REVERT: A 459 LYS cc_start: 0.8679 (tttm) cc_final: 0.8355 (tttt) REVERT: A 486 LYS cc_start: 0.6869 (mmpt) cc_final: 0.6547 (pptt) REVERT: B 90 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.8094 (tttm) REVERT: B 162 ARG cc_start: 0.8850 (mpt180) cc_final: 0.8585 (mpt90) REVERT: B 459 LYS cc_start: 0.8582 (tttm) cc_final: 0.8255 (tttt) REVERT: B 486 LYS cc_start: 0.6945 (mmpt) cc_final: 0.6606 (pptt) REVERT: C 232 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7455 (tptm) REVERT: C 259 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8161 (mt-10) REVERT: C 370 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7365 (tp-100) REVERT: C 400 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8121 (tt0) REVERT: C 459 LYS cc_start: 0.8572 (tttm) cc_final: 0.8240 (tttt) REVERT: C 486 LYS cc_start: 0.6826 (mmpt) cc_final: 0.6528 (pptt) REVERT: H 19 THR cc_start: 0.5835 (OUTLIER) cc_final: 0.5546 (t) REVERT: I 9 SER cc_start: 0.6589 (p) cc_final: 0.6317 (t) REVERT: I 19 THR cc_start: 0.5860 (OUTLIER) cc_final: 0.5618 (t) outliers start: 76 outliers final: 51 residues processed: 247 average time/residue: 1.2426 time to fit residues: 343.2846 Evaluate side-chains 250 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 189 time to evaluate : 1.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 382 LYS Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 259 GLU Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 294 LYS Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 370 GLN Chi-restraints excluded: chain C residue 400 GLU Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 476 ILE Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 32 ASP Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 52 ASN Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 32 ASP Chi-restraints excluded: chain I residue 49 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 178 optimal weight: 0.8980 chunk 30 optimal weight: 9.9990 chunk 156 optimal weight: 5.9990 chunk 145 optimal weight: 0.9990 chunk 168 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 166 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 142 optimal weight: 0.4980 chunk 107 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 ASN C 403 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.156802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.120928 restraints weight = 19011.934| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.24 r_work: 0.3212 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3059 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3059 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17358 Z= 0.146 Angle : 0.605 9.278 23649 Z= 0.313 Chirality : 0.046 0.415 2640 Planarity : 0.005 0.052 3003 Dihedral : 6.840 59.713 3004 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.15 % Favored : 97.71 % Rotamer: Outliers : 4.75 % Allowed : 22.95 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.18), residues: 2100 helix: 2.70 (0.28), residues: 330 sheet: 1.32 (0.21), residues: 603 loop : -0.89 (0.16), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 435 HIS 0.005 0.001 HIS B 25 PHE 0.018 0.002 PHE C 453 TYR 0.015 0.001 TYR I 99 ARG 0.003 0.000 ARG E 30 Details of bonding type rmsd link_NAG-ASN : bond 0.00423 ( 24) link_NAG-ASN : angle 2.38863 ( 72) link_BETA1-4 : bond 0.00527 ( 9) link_BETA1-4 : angle 1.92878 ( 27) hydrogen bonds : bond 0.06681 ( 633) hydrogen bonds : angle 4.75103 ( 1809) SS BOND : bond 0.00478 ( 18) SS BOND : angle 1.43840 ( 36) covalent geometry : bond 0.00330 (17307) covalent geometry : angle 0.58619 (23514) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 193 time to evaluate : 1.874 Fit side-chains REVERT: G 9 SER cc_start: 0.6707 (p) cc_final: 0.6445 (t) REVERT: G 19 THR cc_start: 0.5856 (OUTLIER) cc_final: 0.5579 (t) REVERT: D 74 ASP cc_start: 0.8572 (m-30) cc_final: 0.8348 (m-30) REVERT: A 162 ARG cc_start: 0.8840 (mpt180) cc_final: 0.8557 (mpt90) REVERT: A 232 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7481 (tptm) REVERT: A 400 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.8086 (tt0) REVERT: A 459 LYS cc_start: 0.8659 (tttm) cc_final: 0.8330 (tttt) REVERT: A 486 LYS cc_start: 0.6874 (mmpt) cc_final: 0.6553 (pptt) REVERT: B 90 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.8053 (tttm) REVERT: B 162 ARG cc_start: 0.8857 (mpt180) cc_final: 0.8594 (mpt90) REVERT: B 459 LYS cc_start: 0.8556 (tttm) cc_final: 0.8223 (tttt) REVERT: B 486 LYS cc_start: 0.6963 (mmpt) cc_final: 0.6591 (pptt) REVERT: C 22 ILE cc_start: 0.9166 (OUTLIER) cc_final: 0.8945 (mt) REVERT: C 232 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7448 (tptm) REVERT: C 259 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8186 (mt-10) REVERT: C 370 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7333 (tp-100) REVERT: C 381 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.7977 (mt0) REVERT: C 400 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.8102 (tt0) REVERT: C 459 LYS cc_start: 0.8567 (tttm) cc_final: 0.8231 (tttt) REVERT: C 486 LYS cc_start: 0.6823 (mmpt) cc_final: 0.6536 (pptt) REVERT: H 19 THR cc_start: 0.5817 (OUTLIER) cc_final: 0.5534 (t) REVERT: I 9 SER cc_start: 0.6607 (p) cc_final: 0.6343 (t) REVERT: I 19 THR cc_start: 0.5847 (OUTLIER) cc_final: 0.5606 (t) outliers start: 79 outliers final: 54 residues processed: 252 average time/residue: 1.2505 time to fit residues: 353.7105 Evaluate side-chains 256 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 190 time to evaluate : 1.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 382 LYS Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 220 SER Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 259 GLU Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 294 LYS Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 370 GLN Chi-restraints excluded: chain C residue 381 GLN Chi-restraints excluded: chain C residue 400 GLU Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 476 ILE Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 32 ASP Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 52 ASN Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 32 ASP Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 110 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 150 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 110 optimal weight: 7.9990 chunk 152 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 ASN C 403 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.155799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.119929 restraints weight = 19168.315| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.28 r_work: 0.3201 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3045 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3045 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17358 Z= 0.174 Angle : 0.647 9.514 23649 Z= 0.334 Chirality : 0.048 0.438 2640 Planarity : 0.005 0.053 3003 Dihedral : 6.842 59.139 3004 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.24 % Favored : 97.62 % Rotamer: Outliers : 4.47 % Allowed : 23.06 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.18), residues: 2100 helix: 2.75 (0.28), residues: 324 sheet: 1.31 (0.21), residues: 603 loop : -0.94 (0.16), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 47 HIS 0.006 0.001 HIS B 25 PHE 0.019 0.002 PHE C 453 TYR 0.016 0.002 TYR I 99 ARG 0.004 0.000 ARG E 30 Details of bonding type rmsd link_NAG-ASN : bond 0.00439 ( 24) link_NAG-ASN : angle 2.50650 ( 72) link_BETA1-4 : bond 0.00557 ( 9) link_BETA1-4 : angle 2.02695 ( 27) hydrogen bonds : bond 0.07152 ( 633) hydrogen bonds : angle 4.83527 ( 1809) SS BOND : bond 0.00558 ( 18) SS BOND : angle 1.52970 ( 36) covalent geometry : bond 0.00404 (17307) covalent geometry : angle 0.62696 (23514) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 190 time to evaluate : 1.985 Fit side-chains REVERT: G 9 SER cc_start: 0.6696 (p) cc_final: 0.6428 (t) REVERT: G 19 THR cc_start: 0.5874 (OUTLIER) cc_final: 0.5598 (t) REVERT: D 74 ASP cc_start: 0.8584 (m-30) cc_final: 0.8366 (m-30) REVERT: A 162 ARG cc_start: 0.8839 (mpt180) cc_final: 0.8553 (mpt90) REVERT: A 232 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7503 (tptm) REVERT: A 400 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8130 (tt0) REVERT: A 459 LYS cc_start: 0.8688 (tttm) cc_final: 0.8367 (tttt) REVERT: A 486 LYS cc_start: 0.6883 (mmpt) cc_final: 0.6567 (pptt) REVERT: B 90 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.8058 (tttm) REVERT: B 162 ARG cc_start: 0.8859 (mpt180) cc_final: 0.8585 (mpt90) REVERT: B 232 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7498 (tptm) REVERT: B 459 LYS cc_start: 0.8622 (tttm) cc_final: 0.8297 (tttt) REVERT: B 486 LYS cc_start: 0.6984 (mmpt) cc_final: 0.6628 (pptt) REVERT: C 22 ILE cc_start: 0.9183 (OUTLIER) cc_final: 0.8940 (mt) REVERT: C 232 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7466 (tptm) REVERT: C 259 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8214 (mt-10) REVERT: C 370 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7388 (tp-100) REVERT: C 381 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.7982 (mt0) REVERT: C 400 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8148 (tt0) REVERT: C 459 LYS cc_start: 0.8596 (tttm) cc_final: 0.8264 (tttt) REVERT: C 486 LYS cc_start: 0.6823 (mmpt) cc_final: 0.6560 (pptt) REVERT: H 19 THR cc_start: 0.5837 (OUTLIER) cc_final: 0.5550 (t) REVERT: I 9 SER cc_start: 0.6599 (p) cc_final: 0.6329 (t) REVERT: I 19 THR cc_start: 0.5892 (OUTLIER) cc_final: 0.5655 (t) outliers start: 74 outliers final: 53 residues processed: 247 average time/residue: 1.1498 time to fit residues: 319.5933 Evaluate side-chains 253 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 187 time to evaluate : 1.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 382 LYS Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 220 SER Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 259 GLU Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 294 LYS Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 370 GLN Chi-restraints excluded: chain C residue 381 GLN Chi-restraints excluded: chain C residue 400 GLU Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 476 ILE Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 32 ASP Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 52 ASN Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 32 ASP Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 110 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 153 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 147 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 55 optimal weight: 0.6980 chunk 157 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 ASN C 403 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.157131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.121381 restraints weight = 19199.681| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.34 r_work: 0.3221 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3065 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3065 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17358 Z= 0.138 Angle : 0.591 9.217 23649 Z= 0.305 Chirality : 0.046 0.404 2640 Planarity : 0.005 0.052 3003 Dihedral : 6.600 59.589 3004 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.15 % Favored : 97.71 % Rotamer: Outliers : 4.24 % Allowed : 23.45 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.18), residues: 2100 helix: 2.85 (0.28), residues: 324 sheet: 1.35 (0.21), residues: 603 loop : -0.89 (0.16), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 435 HIS 0.005 0.001 HIS B 25 PHE 0.017 0.002 PHE C 128 TYR 0.015 0.001 TYR I 99 ARG 0.003 0.000 ARG E 30 Details of bonding type rmsd link_NAG-ASN : bond 0.00424 ( 24) link_NAG-ASN : angle 2.35824 ( 72) link_BETA1-4 : bond 0.00524 ( 9) link_BETA1-4 : angle 1.84152 ( 27) hydrogen bonds : bond 0.06501 ( 633) hydrogen bonds : angle 4.70882 ( 1809) SS BOND : bond 0.00470 ( 18) SS BOND : angle 1.41330 ( 36) covalent geometry : bond 0.00307 (17307) covalent geometry : angle 0.57216 (23514) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 193 time to evaluate : 2.471 Fit side-chains REVERT: G 9 SER cc_start: 0.6692 (p) cc_final: 0.6426 (t) REVERT: G 19 THR cc_start: 0.5859 (OUTLIER) cc_final: 0.5585 (t) REVERT: D 74 ASP cc_start: 0.8556 (m-30) cc_final: 0.8325 (m-30) REVERT: A 162 ARG cc_start: 0.8831 (mpt180) cc_final: 0.8551 (mpt90) REVERT: A 232 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7502 (tptm) REVERT: A 400 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.8066 (tt0) REVERT: A 459 LYS cc_start: 0.8633 (tttm) cc_final: 0.8299 (tttt) REVERT: A 486 LYS cc_start: 0.6845 (mmpt) cc_final: 0.6572 (pptt) REVERT: B 90 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.8067 (tttm) REVERT: B 162 ARG cc_start: 0.8853 (mpt180) cc_final: 0.8596 (mpt90) REVERT: B 232 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7509 (tptm) REVERT: B 403 ASN cc_start: 0.7442 (m110) cc_final: 0.7158 (m-40) REVERT: B 459 LYS cc_start: 0.8544 (tttm) cc_final: 0.8217 (tttt) REVERT: B 486 LYS cc_start: 0.6888 (mmpt) cc_final: 0.6562 (pptt) REVERT: C 22 ILE cc_start: 0.9165 (OUTLIER) cc_final: 0.8908 (mt) REVERT: C 232 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7450 (tptm) REVERT: C 259 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8134 (mt-10) REVERT: C 370 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7338 (tp-100) REVERT: C 381 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.7963 (mt0) REVERT: C 400 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8106 (tt0) REVERT: C 459 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8208 (tttt) REVERT: C 486 LYS cc_start: 0.6761 (mmpt) cc_final: 0.6531 (pptt) REVERT: H 19 THR cc_start: 0.5822 (OUTLIER) cc_final: 0.5542 (t) REVERT: I 9 SER cc_start: 0.6676 (p) cc_final: 0.6356 (t) REVERT: I 19 THR cc_start: 0.5859 (OUTLIER) cc_final: 0.5625 (t) outliers start: 70 outliers final: 54 residues processed: 245 average time/residue: 1.7042 time to fit residues: 470.8818 Evaluate side-chains 259 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 191 time to evaluate : 1.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 382 LYS Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 220 SER Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 259 GLU Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 294 LYS Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 370 GLN Chi-restraints excluded: chain C residue 381 GLN Chi-restraints excluded: chain C residue 400 GLU Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 459 LYS Chi-restraints excluded: chain C residue 476 ILE Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 32 ASP Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 52 ASN Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 32 ASP Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 110 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 164 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 chunk 61 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 206 optimal weight: 0.6980 chunk 159 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 117 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 ASN C 403 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.158930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.123939 restraints weight = 19190.068| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.21 r_work: 0.3262 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3095 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3095 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 17358 Z= 0.114 Angle : 0.543 8.689 23649 Z= 0.281 Chirality : 0.044 0.356 2640 Planarity : 0.005 0.052 3003 Dihedral : 6.248 56.282 3004 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.34 % Favored : 97.52 % Rotamer: Outliers : 3.69 % Allowed : 24.01 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.18), residues: 2100 helix: 3.04 (0.28), residues: 324 sheet: 1.37 (0.21), residues: 606 loop : -0.78 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 435 HIS 0.004 0.001 HIS A 369 PHE 0.017 0.001 PHE A 128 TYR 0.013 0.001 TYR I 99 ARG 0.002 0.000 ARG E 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00412 ( 24) link_NAG-ASN : angle 2.12497 ( 72) link_BETA1-4 : bond 0.00518 ( 9) link_BETA1-4 : angle 1.65117 ( 27) hydrogen bonds : bond 0.05803 ( 633) hydrogen bonds : angle 4.54528 ( 1809) SS BOND : bond 0.00377 ( 18) SS BOND : angle 1.27402 ( 36) covalent geometry : bond 0.00240 (17307) covalent geometry : angle 0.52675 (23514) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15609.35 seconds wall clock time: 270 minutes 6.72 seconds (16206.72 seconds total)