Starting phenix.real_space_refine on Fri Jun 20 19:56:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9msd_48575/06_2025/9msd_48575.cif Found real_map, /net/cci-nas-00/data/ceres_data/9msd_48575/06_2025/9msd_48575.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9msd_48575/06_2025/9msd_48575.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9msd_48575/06_2025/9msd_48575.map" model { file = "/net/cci-nas-00/data/ceres_data/9msd_48575/06_2025/9msd_48575.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9msd_48575/06_2025/9msd_48575.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 159 5.16 5 C 15243 2.51 5 N 4113 2.21 5 O 4770 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 24285 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 4399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 558, 4399 Classifications: {'peptide': 558} Link IDs: {'PTRANS': 24, 'TRANS': 533} Chain breaks: 5 Chain: "H" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 961 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "L" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 760 Classifications: {'peptide': 100} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 94} Chain: "D" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "C" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "G" Number of atoms: 4399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 558, 4399 Classifications: {'peptide': 558} Link IDs: {'PTRANS': 24, 'TRANS': 533} Chain breaks: 5 Chain: "I" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 961 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "M" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 760 Classifications: {'peptide': 100} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "E" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "B" Number of atoms: 4399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 558, 4399 Classifications: {'peptide': 558} Link IDs: {'PTRANS': 24, 'TRANS': 533} Chain breaks: 5 Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 961 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "O" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 760 Classifications: {'peptide': 100} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 94} Chain: "K" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "J" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "P" 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: "Q" 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: "R" 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: "S" 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: "T" 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: "U" 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: "V" 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: "W" 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: "X" 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: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "G" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 16.63, per 1000 atoms: 0.68 Number of scatterers: 24285 At special positions: 0 Unit cell: (144.749, 138.718, 150.78, 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 159 16.00 O 4770 8.00 N 4113 7.00 C 15243 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS A 605 " distance=2.02 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.04 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS G 501 " - pdb=" SG CYS G 605 " distance=2.02 Simple disulfide: pdb=" SG CYS G 598 " - pdb=" SG CYS G 604 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.04 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS B 605 " distance=2.02 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 92 " distance=2.03 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " 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 Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " NAG-ASN " NAG A 701 " - " ASN A 88 " " NAG A 702 " - " ASN A 160 " " NAG A 703 " - " ASN A 230 " " NAG A 704 " - " ASN A 234 " " NAG A 705 " - " ASN A 241 " " NAG A 706 " - " ASN A 301 " " NAG A 707 " - " ASN A 332 " " NAG A 708 " - " ASN A 448 " " NAG A 709 " - " ASN A 386 " " NAG B 701 " - " ASN B 88 " " NAG B 702 " - " ASN B 160 " " NAG B 703 " - " ASN B 230 " " NAG B 704 " - " ASN B 234 " " NAG B 705 " - " ASN B 241 " " NAG B 706 " - " ASN B 301 " " NAG B 707 " - " ASN B 332 " " NAG B 708 " - " ASN B 448 " " NAG B 709 " - " ASN B 386 " " NAG G 701 " - " ASN G 88 " " NAG G 702 " - " ASN G 160 " " NAG G 703 " - " ASN G 230 " " NAG G 704 " - " ASN G 234 " " NAG G 705 " - " ASN G 241 " " NAG G 706 " - " ASN G 301 " " NAG G 707 " - " ASN G 332 " " NAG G 708 " - " ASN G 448 " " NAG G 709 " - " ASN G 386 " " NAG P 1 " - " ASN A 156 " " NAG Q 1 " - " ASN A 197 " " NAG R 1 " - " ASN A 262 " " NAG S 1 " - " ASN G 156 " " NAG T 1 " - " ASN G 197 " " NAG U 1 " - " ASN G 262 " " NAG V 1 " - " ASN B 156 " " NAG W 1 " - " ASN B 197 " " NAG X 1 " - " ASN B 262 " Time building additional restraints: 7.43 Conformation dependent library (CDL) restraints added in 2.9 seconds 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5550 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 48 sheets defined 14.5% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.85 Creating SS restraints... Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 99 through 112 Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 335 through 349 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 474 through 479 Processing helix chain 'A' and resid 541 through 545 removed outlier: 3.543A pdb=" N LEU A 544 " --> pdb=" O ALA A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 596 removed outlier: 3.775A pdb=" N THR A 578 " --> pdb=" O LYS A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 623 Processing helix chain 'A' and resid 627 through 635 Processing helix chain 'A' and resid 638 through 661 removed outlier: 4.000A pdb=" N ARG A 644 " --> pdb=" O GLY A 640 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.733A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.633A pdb=" N THR H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.916A pdb=" N ILE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.631A pdb=" N GLU D 83 " --> pdb=" O ALA D 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 64 Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'G' and resid 96 through 98 No H-bonds generated for 'chain 'G' and resid 96 through 98' Processing helix chain 'G' and resid 99 through 112 Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'G' and resid 122 through 126 Processing helix chain 'G' and resid 335 through 349 Processing helix chain 'G' and resid 368 through 373 Processing helix chain 'G' and resid 541 through 545 removed outlier: 3.543A pdb=" N LEU G 544 " --> pdb=" O ALA G 541 " (cutoff:3.500A) Processing helix chain 'G' and resid 573 through 596 removed outlier: 3.775A pdb=" N THR G 578 " --> pdb=" O LYS G 574 " (cutoff:3.500A) Processing helix chain 'G' and resid 618 through 623 Processing helix chain 'G' and resid 627 through 635 Processing helix chain 'G' and resid 638 through 661 removed outlier: 4.000A pdb=" N ARG G 644 " --> pdb=" O GLY G 640 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.734A pdb=" N TYR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.633A pdb=" N THR I 87 " --> pdb=" O SER I 84 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.916A pdb=" N ILE M 83 " --> pdb=" O PRO M 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.631A pdb=" N GLU F 83 " --> pdb=" O ALA F 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 64 Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'B' and resid 96 through 98 No H-bonds generated for 'chain 'B' and resid 96 through 98' Processing helix chain 'B' and resid 99 through 112 Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 122 through 126 Processing helix chain 'B' and resid 335 through 349 Processing helix chain 'B' and resid 368 through 373 Processing helix chain 'B' and resid 474 through 479 Processing helix chain 'B' and resid 541 through 545 removed outlier: 3.543A pdb=" N LEU B 544 " --> pdb=" O ALA B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 596 removed outlier: 3.775A pdb=" N THR B 578 " --> pdb=" O LYS B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 623 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 661 removed outlier: 4.000A pdb=" N ARG B 644 " --> pdb=" O GLY B 640 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.734A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 87 removed outlier: 3.633A pdb=" N THR N 87 " --> pdb=" O SER N 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 83 removed outlier: 3.916A pdb=" N ILE O 83 " --> pdb=" O PRO O 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.631A pdb=" N GLU K 83 " --> pdb=" O ALA K 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 64 Processing helix chain 'J' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.106A pdb=" N VAL A 36 " --> pdb=" O THR A 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.637A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 312 removed outlier: 6.833A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 315 through 323A current: chain 'A' and resid 393 through 395 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 393 through 395 current: chain 'A' and resid 464 through 470 Processing sheet with id=AA8, first strand: chain 'A' and resid 374 through 378 removed outlier: 4.239A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 10 through 12 current: chain 'H' and resid 44 through 52 removed outlier: 3.712A pdb=" N TRP H 50 " --> pdb=" O ASN H 58 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 56 through 59 current: chain 'H' and resid 102 through 103 Processing sheet with id=AB2, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB3, first strand: chain 'L' and resid 34 through 38 removed outlier: 6.745A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 45 through 48 current: chain 'L' and resid 97 through 98 Processing sheet with id=AB4, first strand: chain 'D' and resid 9 through 13 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 9 through 13 current: chain 'D' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 45 through 49 current: chain 'D' and resid 96 through 98 No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'D' and resid 19 through 24 Processing sheet with id=AB6, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AB7, first strand: chain 'C' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 10 through 12 current: chain 'C' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 57 through 59 current: chain 'C' and resid 100H through 103 Processing sheet with id=AB8, first strand: chain 'G' and resid 494 through 499 removed outlier: 5.105A pdb=" N VAL G 36 " --> pdb=" O THR G 606 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 45 through 47 Processing sheet with id=AC1, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AC2, first strand: chain 'G' and resid 91 through 94 Processing sheet with id=AC3, first strand: chain 'G' and resid 169 through 177 Processing sheet with id=AC4, first strand: chain 'G' and resid 201 through 203 removed outlier: 6.637A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 259 through 261 current: chain 'G' and resid 284 through 312 removed outlier: 6.833A pdb=" N ASN G 301 " --> pdb=" O ILE G 323 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ILE G 323 " --> pdb=" O ASN G 301 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N THR G 303 " --> pdb=" O GLY G 321 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 315 through 323A current: chain 'G' and resid 393 through 395 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 393 through 395 current: chain 'G' and resid 464 through 470 Processing sheet with id=AC6, first strand: chain 'G' and resid 374 through 378 removed outlier: 4.239A pdb=" N PHE G 382 " --> pdb=" O LYS G 421 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AC8, first strand: chain 'I' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 10 through 12 current: chain 'I' and resid 44 through 52 removed outlier: 3.712A pdb=" N TRP I 50 " --> pdb=" O ASN I 58 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 56 through 59 current: chain 'I' and resid 102 through 103 Processing sheet with id=AC9, first strand: chain 'M' and resid 4 through 7 Processing sheet with id=AD1, first strand: chain 'M' and resid 34 through 38 removed outlier: 6.746A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 45 through 48 current: chain 'M' and resid 97 through 98 Processing sheet with id=AD2, first strand: chain 'F' and resid 9 through 13 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 9 through 13 current: chain 'F' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 45 through 49 current: chain 'F' and resid 96 through 98 No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'F' and resid 19 through 24 Processing sheet with id=AD4, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AD5, first strand: chain 'E' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 10 through 12 current: chain 'E' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 57 through 59 current: chain 'E' and resid 100H through 103 Processing sheet with id=AD6, first strand: chain 'B' and resid 494 through 499 removed outlier: 5.106A pdb=" N VAL B 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 45 through 47 Processing sheet with id=AD8, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AD9, first strand: chain 'B' and resid 91 through 94 Processing sheet with id=AE1, first strand: chain 'B' and resid 169 through 177 Processing sheet with id=AE2, first strand: chain 'B' and resid 201 through 203 removed outlier: 6.637A pdb=" N THR B 202 " --> pdb=" O TYR B 435 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 259 through 261 current: chain 'B' and resid 284 through 312 removed outlier: 6.833A pdb=" N ASN B 301 " --> pdb=" O ILE B 323 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ILE B 323 " --> pdb=" O ASN B 301 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N THR B 303 " --> pdb=" O GLY B 321 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N GLN B 315 " --> pdb=" O ILE B 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 315 through 323A current: chain 'B' and resid 393 through 395 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 393 through 395 current: chain 'B' and resid 464 through 470 Processing sheet with id=AE4, first strand: chain 'B' and resid 374 through 378 removed outlier: 4.239A pdb=" N PHE B 382 " --> pdb=" O LYS B 421 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'N' and resid 3 through 6 Processing sheet with id=AE6, first strand: chain 'N' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 10 through 12 current: chain 'N' and resid 44 through 52 removed outlier: 3.712A pdb=" N TRP N 50 " --> pdb=" O ASN N 58 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 56 through 59 current: chain 'N' and resid 102 through 103 Processing sheet with id=AE7, first strand: chain 'O' and resid 4 through 7 Processing sheet with id=AE8, first strand: chain 'O' and resid 34 through 38 removed outlier: 6.746A pdb=" N TRP O 35 " --> pdb=" O LEU O 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 45 through 48 current: chain 'O' and resid 97 through 98 Processing sheet with id=AE9, first strand: chain 'K' and resid 9 through 13 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 9 through 13 current: chain 'K' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 45 through 49 current: chain 'K' and resid 96 through 98 No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'K' and resid 19 through 24 Processing sheet with id=AF2, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AF3, first strand: chain 'J' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 10 through 12 current: chain 'J' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 57 through 59 current: chain 'J' and resid 100H through 103 630 hydrogen bonds defined for protein. 1584 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.87 Time building geometry restraints manager: 7.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7688 1.34 - 1.47: 6322 1.47 - 1.59: 10551 1.59 - 1.71: 0 1.71 - 1.84: 228 Bond restraints: 24789 Sorted by residual: bond pdb=" N ARG I 71 " pdb=" CA ARG I 71 " ideal model delta sigma weight residual 1.455 1.484 -0.029 1.21e-02 6.83e+03 5.59e+00 bond pdb=" N ARG H 71 " pdb=" CA ARG H 71 " ideal model delta sigma weight residual 1.455 1.484 -0.029 1.21e-02 6.83e+03 5.57e+00 bond pdb=" N ARG N 71 " pdb=" CA ARG N 71 " ideal model delta sigma weight residual 1.455 1.484 -0.028 1.21e-02 6.83e+03 5.52e+00 bond pdb=" C GLN E 13 " pdb=" N PRO E 14 " ideal model delta sigma weight residual 1.334 1.378 -0.045 2.34e-02 1.83e+03 3.63e+00 bond pdb=" C GLN C 13 " pdb=" N PRO C 14 " ideal model delta sigma weight residual 1.334 1.378 -0.044 2.34e-02 1.83e+03 3.56e+00 ... (remaining 24784 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 30898 1.51 - 3.03: 2182 3.03 - 4.54: 411 4.54 - 6.06: 82 6.06 - 7.57: 36 Bond angle restraints: 33609 Sorted by residual: angle pdb=" CA TRP I 50 " pdb=" CB TRP I 50 " pdb=" CG TRP I 50 " ideal model delta sigma weight residual 113.60 120.99 -7.39 1.90e+00 2.77e-01 1.51e+01 angle pdb=" CA TRP N 50 " pdb=" CB TRP N 50 " pdb=" CG TRP N 50 " ideal model delta sigma weight residual 113.60 120.95 -7.35 1.90e+00 2.77e-01 1.50e+01 angle pdb=" CA TRP H 50 " pdb=" CB TRP H 50 " pdb=" CG TRP H 50 " ideal model delta sigma weight residual 113.60 120.95 -7.35 1.90e+00 2.77e-01 1.50e+01 angle pdb=" C LEU G 663 " pdb=" N ASP G 664 " pdb=" CA ASP G 664 " ideal model delta sigma weight residual 121.70 128.39 -6.69 1.80e+00 3.09e-01 1.38e+01 angle pdb=" C LEU B 663 " pdb=" N ASP B 664 " pdb=" CA ASP B 664 " ideal model delta sigma weight residual 121.70 128.37 -6.67 1.80e+00 3.09e-01 1.37e+01 ... (remaining 33604 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.48: 14373 20.48 - 40.96: 801 40.96 - 61.44: 165 61.44 - 81.92: 48 81.92 - 102.40: 18 Dihedral angle restraints: 15405 sinusoidal: 6717 harmonic: 8688 Sorted by residual: dihedral pdb=" CD ARG I 71 " pdb=" NE ARG I 71 " pdb=" CZ ARG I 71 " pdb=" NH1 ARG I 71 " ideal model delta sinusoidal sigma weight residual 0.00 -58.34 58.34 1 1.00e+01 1.00e-02 4.56e+01 dihedral pdb=" CD ARG N 71 " pdb=" NE ARG N 71 " pdb=" CZ ARG N 71 " pdb=" NH1 ARG N 71 " ideal model delta sinusoidal sigma weight residual 0.00 -58.33 58.33 1 1.00e+01 1.00e-02 4.56e+01 dihedral pdb=" CD ARG H 71 " pdb=" NE ARG H 71 " pdb=" CZ ARG H 71 " pdb=" NH1 ARG H 71 " ideal model delta sinusoidal sigma weight residual 0.00 -58.30 58.30 1 1.00e+01 1.00e-02 4.56e+01 ... (remaining 15402 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2629 0.049 - 0.097: 866 0.097 - 0.146: 317 0.146 - 0.194: 34 0.194 - 0.243: 9 Chirality restraints: 3855 Sorted by residual: chirality pdb=" C1 NAG A 704 " pdb=" ND2 ASN A 234 " pdb=" C2 NAG A 704 " pdb=" O5 NAG A 704 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" C1 NAG G 704 " pdb=" ND2 ASN G 234 " pdb=" C2 NAG G 704 " pdb=" O5 NAG G 704 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" C1 NAG B 704 " pdb=" ND2 ASN B 234 " pdb=" C2 NAG B 704 " pdb=" O5 NAG B 704 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 3852 not shown) Planarity restraints: 4275 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG I 71 " 0.946 9.50e-02 1.11e+02 4.24e-01 1.09e+02 pdb=" NE ARG I 71 " -0.056 2.00e-02 2.50e+03 pdb=" CZ ARG I 71 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG I 71 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG I 71 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 71 " 0.946 9.50e-02 1.11e+02 4.24e-01 1.09e+02 pdb=" NE ARG H 71 " -0.056 2.00e-02 2.50e+03 pdb=" CZ ARG H 71 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG H 71 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG H 71 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG N 71 " -0.946 9.50e-02 1.11e+02 4.24e-01 1.09e+02 pdb=" NE ARG N 71 " 0.056 2.00e-02 2.50e+03 pdb=" CZ ARG N 71 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG N 71 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG N 71 " -0.025 2.00e-02 2.50e+03 ... (remaining 4272 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 6730 2.82 - 3.34: 20511 3.34 - 3.86: 39381 3.86 - 4.38: 46848 4.38 - 4.90: 82767 Nonbonded interactions: 196237 Sorted by model distance: nonbonded pdb=" NH1 ARG H 96 " pdb=" OE1 GLU L 55 " model vdw 2.298 3.120 nonbonded pdb=" NH1 ARG I 96 " pdb=" OE1 GLU M 55 " model vdw 2.298 3.120 nonbonded pdb=" NH1 ARG N 96 " pdb=" OE1 GLU O 55 " model vdw 2.299 3.120 nonbonded pdb=" OD2 ASP B 289 " pdb=" NH2 ARG B 344 " model vdw 2.306 3.120 nonbonded pdb=" OD2 ASP A 289 " pdb=" NH2 ARG A 344 " model vdw 2.306 3.120 ... (remaining 196232 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: 0.16 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'G' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'J' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'N' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' } ncs_group { reference = chain 'R' selection = chain 'U' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 1.080 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 57.450 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 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 0.056 24882 Z= 0.227 Angle : 0.922 7.570 33843 Z= 0.490 Chirality : 0.055 0.243 3855 Planarity : 0.016 0.424 4239 Dihedral : 13.627 102.400 9720 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 0.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.57 % Allowed : 8.73 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.15), residues: 2976 helix: -1.64 (0.23), residues: 390 sheet: -0.31 (0.16), residues: 984 loop : -0.68 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 479 HIS 0.006 0.002 HIS G 339 PHE 0.051 0.003 PHE I 97 TYR 0.042 0.002 TYR F 96 ARG 0.032 0.004 ARG H 53 Details of bonding type rmsd link_NAG-ASN : bond 0.00324 ( 36) link_NAG-ASN : angle 2.19123 ( 108) link_BETA1-4 : bond 0.00405 ( 12) link_BETA1-4 : angle 1.74333 ( 36) hydrogen bonds : bond 0.18979 ( 630) hydrogen bonds : angle 7.55716 ( 1584) SS BOND : bond 0.00401 ( 45) SS BOND : angle 1.89589 ( 90) covalent geometry : bond 0.00529 (24789) covalent geometry : angle 0.90940 (33609) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 482 time to evaluate : 3.467 Fit side-chains revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8143 (tp40) cc_final: 0.7260 (tt0) REVERT: A 405 ASN cc_start: 0.7106 (p0) cc_final: 0.6601 (p0) REVERT: H 28 SER cc_start: 0.8360 (t) cc_final: 0.8041 (p) REVERT: L 45 LYS cc_start: 0.8286 (tttt) cc_final: 0.8060 (tttp) REVERT: D 11 VAL cc_start: 0.7994 (p) cc_final: 0.7755 (m) REVERT: D 31 ASN cc_start: 0.8291 (p0) cc_final: 0.8081 (p0) REVERT: C 70 SER cc_start: 0.8864 (t) cc_final: 0.8469 (m) REVERT: C 91 TYR cc_start: 0.8737 (m-80) cc_final: 0.8143 (m-10) REVERT: C 108 LEU cc_start: 0.8477 (tt) cc_final: 0.8007 (mm) REVERT: G 35 TRP cc_start: 0.9079 (m100) cc_final: 0.8472 (m-90) REVERT: G 49 ARG cc_start: 0.7838 (ptt-90) cc_final: 0.7481 (ptp90) REVERT: G 99 ASP cc_start: 0.7390 (OUTLIER) cc_final: 0.7090 (m-30) REVERT: G 100 MET cc_start: 0.8770 (mtp) cc_final: 0.8553 (mtm) REVERT: G 114 GLN cc_start: 0.8427 (tp40) cc_final: 0.7581 (tt0) REVERT: G 405 ASN cc_start: 0.7047 (p0) cc_final: 0.6330 (p0) REVERT: G 657 GLU cc_start: 0.8071 (tt0) cc_final: 0.7693 (tt0) REVERT: I 28 SER cc_start: 0.8219 (t) cc_final: 0.7851 (p) REVERT: F 31 ASN cc_start: 0.8173 (p0) cc_final: 0.7908 (p0) REVERT: F 79 GLN cc_start: 0.7230 (mp10) cc_final: 0.6821 (mp10) REVERT: E 70 SER cc_start: 0.8813 (t) cc_final: 0.8452 (m) REVERT: E 91 TYR cc_start: 0.8739 (m-80) cc_final: 0.8159 (m-10) REVERT: E 108 LEU cc_start: 0.8479 (tt) cc_final: 0.8119 (mm) REVERT: B 99 ASP cc_start: 0.7327 (OUTLIER) cc_final: 0.7119 (m-30) REVERT: B 114 GLN cc_start: 0.8147 (tp40) cc_final: 0.7230 (tt0) REVERT: B 293 GLU cc_start: 0.8344 (tt0) cc_final: 0.8084 (mt-10) REVERT: B 371 ILE cc_start: 0.8693 (pt) cc_final: 0.8472 (pt) REVERT: N 28 SER cc_start: 0.8204 (t) cc_final: 0.7693 (p) REVERT: N 69 MET cc_start: 0.8750 (mtt) cc_final: 0.8407 (mtt) REVERT: N 96 ARG cc_start: 0.7785 (ptm160) cc_final: 0.7471 (ptm160) REVERT: N 100 SER cc_start: 0.8397 (t) cc_final: 0.8179 (m) REVERT: K 31 ASN cc_start: 0.8269 (p0) cc_final: 0.7964 (p0) REVERT: K 74 THR cc_start: 0.8134 (m) cc_final: 0.7902 (p) REVERT: K 96 TYR cc_start: 0.8997 (m-80) cc_final: 0.8778 (m-80) REVERT: J 3 GLN cc_start: 0.7868 (tp40) cc_final: 0.7645 (tp-100) REVERT: J 70 SER cc_start: 0.8731 (t) cc_final: 0.8384 (m) REVERT: J 91 TYR cc_start: 0.8637 (m-80) cc_final: 0.8087 (m-10) outliers start: 15 outliers final: 6 residues processed: 494 average time/residue: 0.4148 time to fit residues: 315.0569 Evaluate side-chains 368 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 360 time to evaluate : 2.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain G residue 99 ASP Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain M residue 49 TYR Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain O residue 49 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 250 optimal weight: 0.9990 chunk 225 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 232 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 141 optimal weight: 0.8980 chunk 173 optimal weight: 0.8980 chunk 269 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 61 GLN L 34 ASN ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 61 GLN E 81 GLN ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 61 GLN J 76 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.163885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.132338 restraints weight = 28614.241| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.63 r_work: 0.3379 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 24882 Z= 0.182 Angle : 0.631 12.534 33843 Z= 0.328 Chirality : 0.047 0.183 3855 Planarity : 0.004 0.035 4239 Dihedral : 7.085 73.580 4288 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.84 % Allowed : 10.68 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.81 (0.15), residues: 2976 helix: -0.80 (0.25), residues: 408 sheet: -0.16 (0.15), residues: 1044 loop : -0.64 (0.15), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP G 479 HIS 0.004 0.001 HIS A 287 PHE 0.022 0.002 PHE I 97 TYR 0.019 0.002 TYR A 402 ARG 0.006 0.001 ARG A 327 Details of bonding type rmsd link_NAG-ASN : bond 0.00387 ( 36) link_NAG-ASN : angle 2.00328 ( 108) link_BETA1-4 : bond 0.00573 ( 12) link_BETA1-4 : angle 1.91044 ( 36) hydrogen bonds : bond 0.04774 ( 630) hydrogen bonds : angle 5.47770 ( 1584) SS BOND : bond 0.00586 ( 45) SS BOND : angle 1.72914 ( 90) covalent geometry : bond 0.00433 (24789) covalent geometry : angle 0.61321 (33609) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 401 time to evaluate : 2.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8419 (tp40) cc_final: 0.7856 (tt0) REVERT: L 45 LYS cc_start: 0.8206 (tttt) cc_final: 0.7651 (ttmt) REVERT: L 53 ASN cc_start: 0.7818 (t0) cc_final: 0.7526 (t0) REVERT: D 31 ASN cc_start: 0.8434 (p0) cc_final: 0.8033 (p0) REVERT: C 70 SER cc_start: 0.8854 (t) cc_final: 0.8512 (m) REVERT: C 91 TYR cc_start: 0.8966 (m-80) cc_final: 0.8522 (m-10) REVERT: G 35 TRP cc_start: 0.8990 (m100) cc_final: 0.8579 (m-90) REVERT: G 114 GLN cc_start: 0.8604 (tp40) cc_final: 0.8114 (tt0) REVERT: G 278 MET cc_start: 0.8346 (OUTLIER) cc_final: 0.8107 (ttp) REVERT: F 31 ASN cc_start: 0.8289 (p0) cc_final: 0.7882 (p0) REVERT: F 36 TYR cc_start: 0.8633 (m-80) cc_final: 0.8238 (m-80) REVERT: E 70 SER cc_start: 0.8839 (t) cc_final: 0.8503 (m) REVERT: E 91 TYR cc_start: 0.8907 (m-80) cc_final: 0.8506 (m-10) REVERT: E 108 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8164 (mm) REVERT: B 114 GLN cc_start: 0.8364 (tp40) cc_final: 0.7840 (tt0) REVERT: N 69 MET cc_start: 0.8573 (mtt) cc_final: 0.8367 (mtt) REVERT: O 61 ARG cc_start: 0.5541 (ptt-90) cc_final: 0.5290 (ptt-90) REVERT: K 74 THR cc_start: 0.8005 (m) cc_final: 0.7595 (p) REVERT: J 70 SER cc_start: 0.8666 (t) cc_final: 0.8248 (m) REVERT: J 91 TYR cc_start: 0.8808 (m-80) cc_final: 0.8450 (m-10) outliers start: 48 outliers final: 31 residues processed: 426 average time/residue: 0.5131 time to fit residues: 333.9430 Evaluate side-chains 392 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 359 time to evaluate : 3.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 94 ARG Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 278 MET Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 97 MET Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 68 THR Chi-restraints excluded: chain N residue 83 ILE Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain K residue 72 SER Chi-restraints excluded: chain K residue 104 LEU Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain J residue 94 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 123 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 174 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 34 ASN D 69 ASN C 76 ASN F 37 GLN F 39 HIS J 81 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.163439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.131376 restraints weight = 28425.315| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.64 r_work: 0.3364 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 24882 Z= 0.152 Angle : 0.574 11.291 33843 Z= 0.297 Chirality : 0.045 0.192 3855 Planarity : 0.004 0.038 4239 Dihedral : 6.221 61.936 4278 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.60 % Allowed : 11.25 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.15), residues: 2976 helix: -0.41 (0.26), residues: 408 sheet: -0.06 (0.16), residues: 1002 loop : -0.51 (0.15), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 50 HIS 0.003 0.001 HIS G 287 PHE 0.014 0.001 PHE I 97 TYR 0.020 0.001 TYR A 402 ARG 0.006 0.000 ARG A 327 Details of bonding type rmsd link_NAG-ASN : bond 0.00249 ( 36) link_NAG-ASN : angle 1.76976 ( 108) link_BETA1-4 : bond 0.00488 ( 12) link_BETA1-4 : angle 1.93012 ( 36) hydrogen bonds : bond 0.04143 ( 630) hydrogen bonds : angle 5.01644 ( 1584) SS BOND : bond 0.00593 ( 45) SS BOND : angle 1.66415 ( 90) covalent geometry : bond 0.00360 (24789) covalent geometry : angle 0.55658 (33609) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 374 time to evaluate : 2.831 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8404 (tp40) cc_final: 0.7821 (tt0) REVERT: A 370 GLU cc_start: 0.7610 (mp0) cc_final: 0.7320 (mp0) REVERT: L 21 ILE cc_start: 0.7821 (mt) cc_final: 0.7331 (mt) REVERT: L 45 LYS cc_start: 0.8184 (tttt) cc_final: 0.7572 (ttmt) REVERT: D 31 ASN cc_start: 0.8467 (p0) cc_final: 0.8180 (p0) REVERT: C 70 SER cc_start: 0.8803 (t) cc_final: 0.8500 (m) REVERT: C 82 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7867 (mp) REVERT: C 91 TYR cc_start: 0.8990 (m-80) cc_final: 0.8573 (m-80) REVERT: G 35 TRP cc_start: 0.9031 (m100) cc_final: 0.8632 (m-90) REVERT: G 114 GLN cc_start: 0.8548 (tp40) cc_final: 0.8031 (tt0) REVERT: G 241 ASN cc_start: 0.8416 (t0) cc_final: 0.8106 (t0) REVERT: G 278 MET cc_start: 0.8330 (OUTLIER) cc_final: 0.8105 (ttp) REVERT: G 664 ASP cc_start: 0.7119 (OUTLIER) cc_final: 0.6860 (t0) REVERT: M 21 ILE cc_start: 0.8206 (mt) cc_final: 0.7744 (mt) REVERT: M 53 ASN cc_start: 0.7693 (t0) cc_final: 0.7216 (t0) REVERT: F 31 ASN cc_start: 0.8316 (p0) cc_final: 0.8032 (p0) REVERT: F 73 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7532 (tp) REVERT: E 70 SER cc_start: 0.8873 (t) cc_final: 0.8544 (m) REVERT: E 91 TYR cc_start: 0.8923 (m-80) cc_final: 0.8459 (m-10) REVERT: E 108 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8180 (mm) REVERT: B 114 GLN cc_start: 0.8380 (tp40) cc_final: 0.7861 (tt0) REVERT: B 341 MET cc_start: 0.8136 (ttp) cc_final: 0.7697 (tmm) REVERT: B 657 GLU cc_start: 0.8292 (tt0) cc_final: 0.7892 (tt0) REVERT: N 76 ARG cc_start: 0.7968 (mtm-85) cc_final: 0.7681 (mtm-85) REVERT: J 70 SER cc_start: 0.8660 (t) cc_final: 0.8286 (m) REVERT: J 91 TYR cc_start: 0.8869 (m-80) cc_final: 0.8503 (m-10) outliers start: 68 outliers final: 42 residues processed: 412 average time/residue: 0.3838 time to fit residues: 243.6757 Evaluate side-chains 398 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 351 time to evaluate : 2.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 94 ARG Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 76 ASN Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 278 MET Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain G residue 664 ASP Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 97 MET Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 83 ILE Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain K residue 72 SER Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 108 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 114 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 283 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 233 optimal weight: 0.7980 chunk 231 optimal weight: 0.2980 chunk 170 optimal weight: 7.9990 chunk 85 optimal weight: 1.9990 chunk 296 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 99 optimal weight: 0.5980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN ** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 34 ASN L 53 ASN D 79 GLN ** G 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 34 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.161333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.128552 restraints weight = 28887.589| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.68 r_work: 0.3334 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 24882 Z= 0.175 Angle : 0.577 10.821 33843 Z= 0.297 Chirality : 0.046 0.193 3855 Planarity : 0.004 0.038 4239 Dihedral : 5.909 56.153 4278 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.95 % Allowed : 11.86 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 (0.15), residues: 2976 helix: -0.42 (0.26), residues: 426 sheet: 0.03 (0.16), residues: 1044 loop : -0.63 (0.15), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 50 HIS 0.004 0.001 HIS B 287 PHE 0.012 0.001 PHE N 97 TYR 0.020 0.001 TYR B 402 ARG 0.007 0.000 ARG A 327 Details of bonding type rmsd link_NAG-ASN : bond 0.00249 ( 36) link_NAG-ASN : angle 1.76321 ( 108) link_BETA1-4 : bond 0.00391 ( 12) link_BETA1-4 : angle 2.00133 ( 36) hydrogen bonds : bond 0.04058 ( 630) hydrogen bonds : angle 4.83367 ( 1584) SS BOND : bond 0.00665 ( 45) SS BOND : angle 1.71982 ( 90) covalent geometry : bond 0.00420 (24789) covalent geometry : angle 0.56000 (33609) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 364 time to evaluate : 3.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8419 (tp40) cc_final: 0.7856 (tt0) REVERT: A 370 GLU cc_start: 0.7609 (mp0) cc_final: 0.7345 (mp0) REVERT: L 21 ILE cc_start: 0.7882 (mt) cc_final: 0.7395 (mt) REVERT: L 45 LYS cc_start: 0.8158 (tttt) cc_final: 0.7551 (ttmt) REVERT: L 53 ASN cc_start: 0.7660 (OUTLIER) cc_final: 0.7336 (t0) REVERT: D 31 ASN cc_start: 0.8568 (p0) cc_final: 0.8249 (p0) REVERT: C 70 SER cc_start: 0.8826 (t) cc_final: 0.8528 (m) REVERT: C 82 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7885 (mp) REVERT: C 91 TYR cc_start: 0.9022 (m-80) cc_final: 0.8626 (m-80) REVERT: G 114 GLN cc_start: 0.8577 (tp40) cc_final: 0.8039 (tt0) REVERT: G 664 ASP cc_start: 0.7144 (OUTLIER) cc_final: 0.6796 (t0) REVERT: M 5 THR cc_start: 0.8134 (m) cc_final: 0.7921 (m) REVERT: M 21 ILE cc_start: 0.8208 (mt) cc_final: 0.7708 (mt) REVERT: M 53 ASN cc_start: 0.7784 (t0) cc_final: 0.7295 (t0) REVERT: F 73 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7626 (tp) REVERT: E 70 SER cc_start: 0.8864 (t) cc_final: 0.8535 (m) REVERT: E 91 TYR cc_start: 0.8956 (m-80) cc_final: 0.8465 (m-10) REVERT: E 108 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8380 (tt) REVERT: B 114 GLN cc_start: 0.8405 (tp40) cc_final: 0.7886 (tt0) REVERT: B 341 MET cc_start: 0.8168 (ttp) cc_final: 0.7908 (tmm) REVERT: B 657 GLU cc_start: 0.8299 (tt0) cc_final: 0.7899 (tt0) REVERT: K 61 ARG cc_start: 0.7339 (ttp80) cc_final: 0.6969 (ttp80) REVERT: J 70 SER cc_start: 0.8687 (t) cc_final: 0.8330 (m) REVERT: J 91 TYR cc_start: 0.8940 (m-80) cc_final: 0.8529 (m-10) outliers start: 77 outliers final: 53 residues processed: 407 average time/residue: 0.5338 time to fit residues: 341.8860 Evaluate side-chains 398 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 340 time to evaluate : 4.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 401 THR Chi-restraints excluded: chain G residue 418 CYS Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain G residue 664 ASP Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 97 MET Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 418 CYS Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 664 ASP Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 83 ILE Chi-restraints excluded: chain O residue 72 THR Chi-restraints excluded: chain K residue 72 SER Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain K residue 104 LEU Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 108 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 168 optimal weight: 0.0170 chunk 210 optimal weight: 0.7980 chunk 120 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 29 optimal weight: 0.4980 chunk 67 optimal weight: 7.9990 chunk 245 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN ** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 HIS L 34 ASN ** G 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.162903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.131936 restraints weight = 28652.985| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.60 r_work: 0.3369 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24882 Z= 0.116 Angle : 0.535 9.812 33843 Z= 0.274 Chirality : 0.044 0.185 3855 Planarity : 0.003 0.035 4239 Dihedral : 5.397 48.127 4278 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.60 % Allowed : 12.90 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 (0.15), residues: 2976 helix: -0.18 (0.26), residues: 426 sheet: 0.10 (0.16), residues: 960 loop : -0.51 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 50 HIS 0.002 0.001 HIS A 249 PHE 0.011 0.001 PHE B 383 TYR 0.018 0.001 TYR G 402 ARG 0.007 0.000 ARG A 327 Details of bonding type rmsd link_NAG-ASN : bond 0.00232 ( 36) link_NAG-ASN : angle 1.66342 ( 108) link_BETA1-4 : bond 0.00416 ( 12) link_BETA1-4 : angle 1.97769 ( 36) hydrogen bonds : bond 0.03608 ( 630) hydrogen bonds : angle 4.61435 ( 1584) SS BOND : bond 0.00518 ( 45) SS BOND : angle 1.47387 ( 90) covalent geometry : bond 0.00269 (24789) covalent geometry : angle 0.51852 (33609) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 362 time to evaluate : 2.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8399 (tp40) cc_final: 0.7908 (tt0) REVERT: A 370 GLU cc_start: 0.7466 (mp0) cc_final: 0.7213 (mp0) REVERT: A 632 ASP cc_start: 0.8552 (t0) cc_final: 0.8275 (t0) REVERT: L 45 LYS cc_start: 0.8172 (tttt) cc_final: 0.7547 (ttmt) REVERT: L 53 ASN cc_start: 0.7915 (t0) cc_final: 0.7674 (t0) REVERT: D 31 ASN cc_start: 0.8588 (p0) cc_final: 0.8294 (p0) REVERT: C 70 SER cc_start: 0.8781 (t) cc_final: 0.8536 (m) REVERT: C 82 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7872 (mp) REVERT: C 91 TYR cc_start: 0.9012 (m-80) cc_final: 0.8616 (m-80) REVERT: G 114 GLN cc_start: 0.8544 (tp40) cc_final: 0.8038 (tt0) REVERT: G 241 ASN cc_start: 0.8422 (t0) cc_final: 0.8131 (t0) REVERT: G 621 ASP cc_start: 0.8056 (m-30) cc_final: 0.7767 (t0) REVERT: G 664 ASP cc_start: 0.7102 (OUTLIER) cc_final: 0.6876 (t0) REVERT: M 21 ILE cc_start: 0.8194 (mt) cc_final: 0.7703 (mt) REVERT: M 53 ASN cc_start: 0.7747 (t0) cc_final: 0.7279 (t0) REVERT: F 73 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7583 (tp) REVERT: E 70 SER cc_start: 0.8787 (t) cc_final: 0.8500 (m) REVERT: E 91 TYR cc_start: 0.8928 (m-80) cc_final: 0.8430 (m-10) REVERT: E 108 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8439 (tt) REVERT: B 114 GLN cc_start: 0.8386 (tp40) cc_final: 0.7924 (tt0) REVERT: B 341 MET cc_start: 0.8095 (ttp) cc_final: 0.7777 (tmm) REVERT: B 657 GLU cc_start: 0.8270 (tt0) cc_final: 0.7882 (tt0) REVERT: K 31 ASN cc_start: 0.8429 (p0) cc_final: 0.8098 (p0) REVERT: K 61 ARG cc_start: 0.7403 (ttp80) cc_final: 0.7004 (ttp80) REVERT: J 70 SER cc_start: 0.8608 (t) cc_final: 0.8290 (m) REVERT: J 91 TYR cc_start: 0.8918 (m-80) cc_final: 0.8498 (m-10) outliers start: 68 outliers final: 46 residues processed: 402 average time/residue: 0.3858 time to fit residues: 238.3611 Evaluate side-chains 392 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 342 time to evaluate : 2.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 239 CYS Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain G residue 664 ASP Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 83 ILE Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 97 MET Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 418 CYS Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 664 ASP Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 83 ILE Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 72 THR Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain K residue 104 LEU Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 108 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 163 optimal weight: 6.9990 chunk 196 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 292 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 283 optimal weight: 6.9990 chunk 129 optimal weight: 2.9990 chunk 230 optimal weight: 0.8980 chunk 267 optimal weight: 10.0000 chunk 18 optimal weight: 0.3980 chunk 105 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 276 ASN O 34 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.161247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.129013 restraints weight = 28443.276| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.64 r_work: 0.3353 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 24882 Z= 0.132 Angle : 0.542 9.574 33843 Z= 0.277 Chirality : 0.044 0.186 3855 Planarity : 0.003 0.035 4239 Dihedral : 5.096 41.742 4278 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.37 % Allowed : 13.39 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.39 (0.15), residues: 2976 helix: 0.05 (0.27), residues: 408 sheet: 0.11 (0.16), residues: 1008 loop : -0.51 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 50 HIS 0.003 0.001 HIS G 339 PHE 0.033 0.001 PHE E 67 TYR 0.017 0.001 TYR B 402 ARG 0.008 0.000 ARG A 327 Details of bonding type rmsd link_NAG-ASN : bond 0.00250 ( 36) link_NAG-ASN : angle 1.65483 ( 108) link_BETA1-4 : bond 0.00403 ( 12) link_BETA1-4 : angle 2.01059 ( 36) hydrogen bonds : bond 0.03641 ( 630) hydrogen bonds : angle 4.52946 ( 1584) SS BOND : bond 0.00585 ( 45) SS BOND : angle 1.48299 ( 90) covalent geometry : bond 0.00315 (24789) covalent geometry : angle 0.52584 (33609) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 353 time to evaluate : 2.646 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8414 (tp40) cc_final: 0.7904 (tt0) REVERT: A 370 GLU cc_start: 0.7492 (mp0) cc_final: 0.7247 (mp0) REVERT: A 632 ASP cc_start: 0.8606 (t0) cc_final: 0.8328 (t0) REVERT: L 45 LYS cc_start: 0.8104 (tttt) cc_final: 0.7467 (ttmt) REVERT: L 53 ASN cc_start: 0.7850 (t0) cc_final: 0.7582 (t0) REVERT: D 31 ASN cc_start: 0.8631 (p0) cc_final: 0.8338 (p0) REVERT: D 73 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7597 (tp) REVERT: C 70 SER cc_start: 0.8830 (t) cc_final: 0.8591 (m) REVERT: C 82 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7842 (mp) REVERT: C 91 TYR cc_start: 0.9008 (m-80) cc_final: 0.8597 (m-80) REVERT: G 114 GLN cc_start: 0.8544 (tp40) cc_final: 0.8019 (tt0) REVERT: G 621 ASP cc_start: 0.8061 (m-30) cc_final: 0.7770 (t0) REVERT: G 664 ASP cc_start: 0.7063 (OUTLIER) cc_final: 0.6861 (t0) REVERT: I 82 ARG cc_start: 0.8374 (mpp80) cc_final: 0.8171 (mpp80) REVERT: F 73 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7631 (tp) REVERT: E 7 THR cc_start: 0.8502 (m) cc_final: 0.8284 (p) REVERT: E 70 SER cc_start: 0.8793 (t) cc_final: 0.8510 (m) REVERT: E 108 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8468 (tt) REVERT: B 114 GLN cc_start: 0.8384 (tp40) cc_final: 0.7905 (tt0) REVERT: B 341 MET cc_start: 0.8149 (ttp) cc_final: 0.7843 (tmm) REVERT: B 461 ASN cc_start: 0.8452 (p0) cc_final: 0.8240 (p0) REVERT: B 657 GLU cc_start: 0.8285 (tt0) cc_final: 0.7933 (tt0) REVERT: K 31 ASN cc_start: 0.8450 (p0) cc_final: 0.8116 (p0) REVERT: J 70 SER cc_start: 0.8649 (t) cc_final: 0.8354 (m) REVERT: J 91 TYR cc_start: 0.8922 (m-80) cc_final: 0.8469 (m-10) outliers start: 62 outliers final: 49 residues processed: 385 average time/residue: 0.3824 time to fit residues: 227.2684 Evaluate side-chains 393 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 339 time to evaluate : 2.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 239 CYS Chi-restraints excluded: chain A residue 328 GLU Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain G residue 664 ASP Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 83 ILE Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain E residue 97 MET Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 664 ASP Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 83 ILE Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 72 THR Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain K residue 104 LEU Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 108 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 280 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 168 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 28 optimal weight: 0.0470 chunk 31 optimal weight: 0.8980 chunk 139 optimal weight: 3.9990 chunk 195 optimal weight: 1.9990 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 ASN ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 34 ASN D 79 GLN ** G 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 GLN B 339 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.163449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.133914 restraints weight = 28632.500| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 1.58 r_work: 0.3370 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24882 Z= 0.121 Angle : 0.528 9.758 33843 Z= 0.271 Chirality : 0.044 0.186 3855 Planarity : 0.003 0.036 4239 Dihedral : 4.836 35.411 4278 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.60 % Allowed : 13.24 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.15), residues: 2976 helix: -0.02 (0.27), residues: 426 sheet: 0.13 (0.16), residues: 1008 loop : -0.54 (0.16), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP I 50 HIS 0.002 0.001 HIS G 339 PHE 0.024 0.001 PHE E 67 TYR 0.016 0.001 TYR B 402 ARG 0.009 0.000 ARG A 327 Details of bonding type rmsd link_NAG-ASN : bond 0.00218 ( 36) link_NAG-ASN : angle 1.61812 ( 108) link_BETA1-4 : bond 0.00438 ( 12) link_BETA1-4 : angle 1.98713 ( 36) hydrogen bonds : bond 0.03534 ( 630) hydrogen bonds : angle 4.43259 ( 1584) SS BOND : bond 0.00507 ( 45) SS BOND : angle 1.52831 ( 90) covalent geometry : bond 0.00284 (24789) covalent geometry : angle 0.51209 (33609) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 348 time to evaluate : 2.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8409 (tp40) cc_final: 0.7905 (tt0) REVERT: A 370 GLU cc_start: 0.7462 (mp0) cc_final: 0.7225 (mp0) REVERT: A 632 ASP cc_start: 0.8590 (t0) cc_final: 0.8305 (t0) REVERT: L 45 LYS cc_start: 0.8064 (tttt) cc_final: 0.7415 (ttmt) REVERT: L 53 ASN cc_start: 0.7776 (t0) cc_final: 0.7490 (t0) REVERT: D 31 ASN cc_start: 0.8626 (p0) cc_final: 0.8349 (p0) REVERT: C 70 SER cc_start: 0.8802 (t) cc_final: 0.8516 (m) REVERT: C 82 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7825 (mp) REVERT: C 91 TYR cc_start: 0.8974 (m-80) cc_final: 0.8622 (m-80) REVERT: G 114 GLN cc_start: 0.8504 (tp40) cc_final: 0.7942 (tt0) REVERT: G 241 ASN cc_start: 0.8400 (t0) cc_final: 0.8180 (t0) REVERT: G 621 ASP cc_start: 0.8060 (m-30) cc_final: 0.7788 (t0) REVERT: M 53 ASN cc_start: 0.7678 (t0) cc_final: 0.7290 (t0) REVERT: F 62 PHE cc_start: 0.8590 (m-80) cc_final: 0.8211 (m-80) REVERT: E 70 SER cc_start: 0.8778 (t) cc_final: 0.8503 (m) REVERT: B 114 GLN cc_start: 0.8398 (tp40) cc_final: 0.7907 (tt0) REVERT: B 341 MET cc_start: 0.8164 (ttp) cc_final: 0.7854 (tmm) REVERT: B 461 ASN cc_start: 0.8455 (p0) cc_final: 0.8236 (p0) REVERT: B 657 GLU cc_start: 0.8271 (tt0) cc_final: 0.7932 (tt0) REVERT: K 31 ASN cc_start: 0.8451 (p0) cc_final: 0.8131 (p0) REVERT: J 70 SER cc_start: 0.8657 (t) cc_final: 0.8375 (m) REVERT: J 91 TYR cc_start: 0.8880 (m-80) cc_final: 0.8387 (m-10) outliers start: 68 outliers final: 55 residues processed: 386 average time/residue: 0.3758 time to fit residues: 226.2130 Evaluate side-chains 391 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 335 time to evaluate : 2.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 239 CYS Chi-restraints excluded: chain A residue 328 GLU Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 328 GLU Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 371 ILE Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain E residue 97 MET Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 83 ILE Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 72 THR Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain K residue 72 SER Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 108 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 191 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 255 optimal weight: 2.9990 chunk 262 optimal weight: 3.9990 chunk 236 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 292 optimal weight: 0.2980 chunk 125 optimal weight: 1.9990 chunk 187 optimal weight: 5.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 216 HIS ** G 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.159568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.127396 restraints weight = 28641.033| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.65 r_work: 0.3325 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 24882 Z= 0.158 Angle : 0.570 12.952 33843 Z= 0.290 Chirality : 0.045 0.206 3855 Planarity : 0.004 0.036 4239 Dihedral : 4.867 33.467 4278 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.41 % Allowed : 13.66 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.15), residues: 2976 helix: 0.25 (0.27), residues: 399 sheet: 0.14 (0.16), residues: 1008 loop : -0.63 (0.15), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 50 HIS 0.003 0.001 HIS G 339 PHE 0.027 0.001 PHE E 67 TYR 0.016 0.001 TYR B 402 ARG 0.009 0.000 ARG A 327 Details of bonding type rmsd link_NAG-ASN : bond 0.00246 ( 36) link_NAG-ASN : angle 1.70836 ( 108) link_BETA1-4 : bond 0.00407 ( 12) link_BETA1-4 : angle 2.01064 ( 36) hydrogen bonds : bond 0.03754 ( 630) hydrogen bonds : angle 4.48145 ( 1584) SS BOND : bond 0.00554 ( 45) SS BOND : angle 1.88777 ( 90) covalent geometry : bond 0.00379 (24789) covalent geometry : angle 0.55133 (33609) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 340 time to evaluate : 2.719 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8474 (tp40) cc_final: 0.7995 (tt0) REVERT: A 370 GLU cc_start: 0.7487 (mp0) cc_final: 0.7238 (mp0) REVERT: A 632 ASP cc_start: 0.8658 (t0) cc_final: 0.8373 (t0) REVERT: L 45 LYS cc_start: 0.8116 (tttt) cc_final: 0.7473 (ttmt) REVERT: L 53 ASN cc_start: 0.7729 (t0) cc_final: 0.7424 (t0) REVERT: D 31 ASN cc_start: 0.8628 (p0) cc_final: 0.8397 (p0) REVERT: D 52 THR cc_start: 0.8838 (p) cc_final: 0.8417 (t) REVERT: C 70 SER cc_start: 0.8821 (t) cc_final: 0.8570 (m) REVERT: C 82 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7874 (mp) REVERT: G 114 GLN cc_start: 0.8549 (tp40) cc_final: 0.8026 (tt0) REVERT: G 621 ASP cc_start: 0.8151 (m-30) cc_final: 0.7860 (t0) REVERT: M 53 ASN cc_start: 0.7702 (t0) cc_final: 0.7289 (t0) REVERT: F 45 LYS cc_start: 0.8617 (tttt) cc_final: 0.8312 (tttt) REVERT: F 61 ARG cc_start: 0.7675 (ttp80) cc_final: 0.7387 (ttp80) REVERT: E 70 SER cc_start: 0.8811 (t) cc_final: 0.8545 (m) REVERT: B 95 MET cc_start: 0.8935 (OUTLIER) cc_final: 0.8666 (ptt) REVERT: B 114 GLN cc_start: 0.8413 (tp40) cc_final: 0.7966 (tt0) REVERT: B 341 MET cc_start: 0.8226 (ttp) cc_final: 0.7940 (tmm) REVERT: B 657 GLU cc_start: 0.8294 (tt0) cc_final: 0.7971 (tt0) REVERT: K 31 ASN cc_start: 0.8533 (p0) cc_final: 0.8234 (p0) REVERT: K 52 THR cc_start: 0.8756 (p) cc_final: 0.8373 (t) REVERT: J 43 LYS cc_start: 0.7791 (mmtt) cc_final: 0.7404 (mttm) REVERT: J 70 SER cc_start: 0.8700 (t) cc_final: 0.8428 (m) REVERT: J 91 TYR cc_start: 0.8901 (m-80) cc_final: 0.8385 (m-10) REVERT: J 97 MET cc_start: 0.8572 (mtp) cc_final: 0.8349 (mtp) outliers start: 63 outliers final: 55 residues processed: 375 average time/residue: 0.3575 time to fit residues: 208.6103 Evaluate side-chains 392 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 335 time to evaluate : 2.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 328 GLU Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 328 GLU Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 371 ILE Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 83 ILE Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain E residue 97 MET Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 385 CYS Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 83 ILE Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 72 THR Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain K residue 72 SER Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 108 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 242 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 208 optimal weight: 3.9990 chunk 170 optimal weight: 6.9990 chunk 221 optimal weight: 1.9990 chunk 289 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 256 optimal weight: 1.9990 chunk 51 optimal weight: 0.0770 overall best weight: 0.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 34 ASN ** G 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.159616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.126789 restraints weight = 28708.133| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.73 r_work: 0.3328 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24882 Z= 0.152 Angle : 0.562 11.038 33843 Z= 0.287 Chirality : 0.045 0.198 3855 Planarity : 0.004 0.034 4239 Dihedral : 4.854 31.471 4278 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.56 % Allowed : 13.70 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.15), residues: 2976 helix: 0.05 (0.27), residues: 417 sheet: 0.12 (0.16), residues: 1008 loop : -0.59 (0.16), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP I 50 HIS 0.003 0.001 HIS G 339 PHE 0.016 0.001 PHE E 67 TYR 0.017 0.001 TYR G 402 ARG 0.009 0.000 ARG A 327 Details of bonding type rmsd link_NAG-ASN : bond 0.00219 ( 36) link_NAG-ASN : angle 1.70937 ( 108) link_BETA1-4 : bond 0.00384 ( 12) link_BETA1-4 : angle 1.98076 ( 36) hydrogen bonds : bond 0.03751 ( 630) hydrogen bonds : angle 4.47942 ( 1584) SS BOND : bond 0.00567 ( 45) SS BOND : angle 1.80327 ( 90) covalent geometry : bond 0.00366 (24789) covalent geometry : angle 0.54412 (33609) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 351 time to evaluate : 2.924 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8522 (tp40) cc_final: 0.8017 (tt0) REVERT: A 370 GLU cc_start: 0.7516 (mp0) cc_final: 0.7272 (mp0) REVERT: A 621 ASP cc_start: 0.8028 (m-30) cc_final: 0.7800 (m-30) REVERT: A 632 ASP cc_start: 0.8673 (t0) cc_final: 0.8385 (t0) REVERT: L 45 LYS cc_start: 0.8062 (tttt) cc_final: 0.7417 (ttmt) REVERT: L 53 ASN cc_start: 0.7719 (t0) cc_final: 0.7423 (t0) REVERT: D 31 ASN cc_start: 0.8616 (p0) cc_final: 0.8373 (p0) REVERT: D 52 THR cc_start: 0.8884 (p) cc_final: 0.8478 (t) REVERT: C 70 SER cc_start: 0.8837 (t) cc_final: 0.8576 (m) REVERT: C 82 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7836 (mp) REVERT: G 114 GLN cc_start: 0.8544 (tp40) cc_final: 0.7996 (tt0) REVERT: M 53 ASN cc_start: 0.7697 (t0) cc_final: 0.7271 (t0) REVERT: F 45 LYS cc_start: 0.8650 (tttt) cc_final: 0.8333 (tttt) REVERT: F 61 ARG cc_start: 0.7665 (ttp80) cc_final: 0.7454 (ttp80) REVERT: E 70 SER cc_start: 0.8810 (t) cc_final: 0.8549 (m) REVERT: B 95 MET cc_start: 0.8931 (OUTLIER) cc_final: 0.8724 (ptt) REVERT: B 114 GLN cc_start: 0.8415 (tp40) cc_final: 0.7924 (tt0) REVERT: B 341 MET cc_start: 0.8253 (ttp) cc_final: 0.7948 (tmm) REVERT: B 657 GLU cc_start: 0.8371 (tt0) cc_final: 0.8032 (tt0) REVERT: K 31 ASN cc_start: 0.8557 (p0) cc_final: 0.8228 (p0) REVERT: K 52 THR cc_start: 0.8774 (p) cc_final: 0.8380 (t) REVERT: J 70 SER cc_start: 0.8720 (t) cc_final: 0.8457 (m) REVERT: J 91 TYR cc_start: 0.8918 (m-80) cc_final: 0.8372 (m-10) outliers start: 67 outliers final: 60 residues processed: 386 average time/residue: 0.3684 time to fit residues: 220.7373 Evaluate side-chains 398 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 336 time to evaluate : 2.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 328 GLU Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 328 GLU Chi-restraints excluded: chain G residue 371 ILE Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 112 SER Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain E residue 97 MET Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 385 CYS Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 83 ILE Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 72 THR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 72 SER Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 108 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 242 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 260 optimal weight: 1.9990 chunk 178 optimal weight: 7.9990 chunk 261 optimal weight: 3.9990 chunk 206 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 157 optimal weight: 2.9990 chunk 262 optimal weight: 0.6980 chunk 214 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 HIS ** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 34 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.159004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.125918 restraints weight = 28563.226| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.70 r_work: 0.3318 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24882 Z= 0.158 Angle : 0.564 11.310 33843 Z= 0.288 Chirality : 0.045 0.196 3855 Planarity : 0.004 0.034 4239 Dihedral : 4.871 30.603 4278 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.64 % Allowed : 13.89 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.15), residues: 2976 helix: 0.27 (0.27), residues: 399 sheet: 0.07 (0.16), residues: 1002 loop : -0.59 (0.16), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 50 HIS 0.003 0.001 HIS A 249 PHE 0.019 0.001 PHE E 67 TYR 0.015 0.001 TYR B 402 ARG 0.008 0.000 ARG A 327 Details of bonding type rmsd link_NAG-ASN : bond 0.00262 ( 36) link_NAG-ASN : angle 1.74620 ( 108) link_BETA1-4 : bond 0.00391 ( 12) link_BETA1-4 : angle 1.98216 ( 36) hydrogen bonds : bond 0.03790 ( 630) hydrogen bonds : angle 4.49842 ( 1584) SS BOND : bond 0.00560 ( 45) SS BOND : angle 1.50694 ( 90) covalent geometry : bond 0.00381 (24789) covalent geometry : angle 0.54830 (33609) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 338 time to evaluate : 2.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8519 (tp40) cc_final: 0.8021 (tt0) REVERT: A 621 ASP cc_start: 0.8024 (m-30) cc_final: 0.7788 (m-30) REVERT: A 632 ASP cc_start: 0.8652 (t0) cc_final: 0.8373 (t0) REVERT: L 45 LYS cc_start: 0.8054 (tttt) cc_final: 0.7408 (ttmt) REVERT: L 53 ASN cc_start: 0.7730 (t0) cc_final: 0.7422 (t0) REVERT: D 31 ASN cc_start: 0.8629 (p0) cc_final: 0.8383 (p0) REVERT: C 70 SER cc_start: 0.8829 (t) cc_final: 0.8566 (m) REVERT: C 82 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7845 (mp) REVERT: G 114 GLN cc_start: 0.8525 (tp40) cc_final: 0.7982 (tt0) REVERT: G 278 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.8320 (ttp) REVERT: G 412 SER cc_start: 0.8781 (t) cc_final: 0.8485 (m) REVERT: M 53 ASN cc_start: 0.7702 (t0) cc_final: 0.7277 (t0) REVERT: F 45 LYS cc_start: 0.8646 (tttt) cc_final: 0.8334 (tttt) REVERT: F 61 ARG cc_start: 0.7671 (ttp80) cc_final: 0.7441 (ttp80) REVERT: E 70 SER cc_start: 0.8813 (t) cc_final: 0.8553 (m) REVERT: B 95 MET cc_start: 0.8901 (OUTLIER) cc_final: 0.8695 (ptt) REVERT: B 114 GLN cc_start: 0.8418 (tp40) cc_final: 0.7924 (tt0) REVERT: B 341 MET cc_start: 0.8253 (ttp) cc_final: 0.7946 (tmm) REVERT: B 657 GLU cc_start: 0.8319 (tt0) cc_final: 0.7972 (tt0) REVERT: K 31 ASN cc_start: 0.8566 (p0) cc_final: 0.8257 (p0) REVERT: K 52 THR cc_start: 0.8881 (p) cc_final: 0.8489 (t) REVERT: J 43 LYS cc_start: 0.7947 (mmtt) cc_final: 0.7421 (mttm) REVERT: J 70 SER cc_start: 0.8741 (t) cc_final: 0.8458 (m) REVERT: J 91 TYR cc_start: 0.8911 (m-80) cc_final: 0.8360 (m-10) outliers start: 69 outliers final: 62 residues processed: 374 average time/residue: 0.3673 time to fit residues: 214.5236 Evaluate side-chains 400 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 335 time to evaluate : 2.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 328 GLU Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 278 MET Chi-restraints excluded: chain G residue 328 GLU Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 112 SER Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain E residue 97 MET Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 385 CYS Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 83 ILE Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 72 THR Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 72 SER Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 108 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 142 optimal weight: 1.9990 chunk 264 optimal weight: 1.9990 chunk 212 optimal weight: 0.5980 chunk 118 optimal weight: 0.0470 chunk 32 optimal weight: 1.9990 chunk 8 optimal weight: 0.0070 chunk 15 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 155 optimal weight: 30.0000 chunk 273 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 34 ASN ** G 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 61 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.159951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.127722 restraints weight = 28596.982| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.69 r_work: 0.3331 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24882 Z= 0.129 Angle : 0.553 11.508 33843 Z= 0.282 Chirality : 0.044 0.208 3855 Planarity : 0.004 0.034 4239 Dihedral : 4.745 28.462 4278 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.45 % Allowed : 14.20 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.15), residues: 2976 helix: 0.39 (0.27), residues: 399 sheet: 0.08 (0.16), residues: 999 loop : -0.67 (0.15), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 50 HIS 0.003 0.001 HIS G 216 PHE 0.018 0.001 PHE E 67 TYR 0.017 0.001 TYR B 402 ARG 0.008 0.000 ARG A 327 Details of bonding type rmsd link_NAG-ASN : bond 0.00256 ( 36) link_NAG-ASN : angle 1.68501 ( 108) link_BETA1-4 : bond 0.00416 ( 12) link_BETA1-4 : angle 1.92920 ( 36) hydrogen bonds : bond 0.03597 ( 630) hydrogen bonds : angle 4.42624 ( 1584) SS BOND : bond 0.00519 ( 45) SS BOND : angle 1.84054 ( 90) covalent geometry : bond 0.00307 (24789) covalent geometry : angle 0.53446 (33609) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15903.88 seconds wall clock time: 279 minutes 51.09 seconds (16791.09 seconds total)