Starting phenix.real_space_refine on Fri Sep 19 07:10:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9msd_48575/09_2025/9msd_48575.cif Found real_map, /net/cci-nas-00/data/ceres_data/9msd_48575/09_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_48575/09_2025/9msd_48575.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9msd_48575/09_2025/9msd_48575.map" model { file = "/net/cci-nas-00/data/ceres_data/9msd_48575/09_2025/9msd_48575.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9msd_48575/09_2025/9msd_48575.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 5.91, per 1000 atoms: 0.24 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: 2.06 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.08 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: 4.37 Time building geometry restraints manager: 2.72 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: 0.06 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: 4.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.350 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 22.970 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.690 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.032 0.004 ARG H 53 TYR 0.042 0.002 TYR F 96 PHE 0.051 0.003 PHE I 97 TRP 0.024 0.002 TRP A 479 HIS 0.006 0.002 HIS G 339 Details of bonding type rmsd covalent geometry : bond 0.00529 (24789) covalent geometry : angle 0.90940 (33609) SS BOND : bond 0.00401 ( 45) SS BOND : angle 1.89589 ( 90) hydrogen bonds : bond 0.18979 ( 630) hydrogen bonds : angle 7.55716 ( 1584) link_BETA1-4 : bond 0.00405 ( 12) link_BETA1-4 : angle 1.74333 ( 36) link_NAG-ASN : bond 0.00324 ( 36) link_NAG-ASN : angle 2.19123 ( 108) *********************** 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 : 0.966 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: 0.8082 (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: 0.7480 (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: 0.7907 (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: 0.1834 time to fit residues: 139.0661 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 : 0.973 ------------------------------------------------------------------------------- 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 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.2980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 9.9990 chunk 111 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 C 76 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.166214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.135599 restraints weight = 28710.274| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.58 r_work: 0.3414 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 24882 Z= 0.142 Angle : 0.602 12.720 33843 Z= 0.314 Chirality : 0.046 0.204 3855 Planarity : 0.004 0.034 4239 Dihedral : 6.912 71.674 4288 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.88 % Allowed : 10.52 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.15), residues: 2976 helix: -0.71 (0.26), residues: 408 sheet: -0.26 (0.15), residues: 1023 loop : -0.51 (0.15), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 327 TYR 0.019 0.001 TYR G 402 PHE 0.021 0.002 PHE I 97 TRP 0.022 0.002 TRP G 479 HIS 0.002 0.001 HIS G 287 Details of bonding type rmsd covalent geometry : bond 0.00329 (24789) covalent geometry : angle 0.58333 (33609) SS BOND : bond 0.00754 ( 45) SS BOND : angle 1.72298 ( 90) hydrogen bonds : bond 0.04651 ( 630) hydrogen bonds : angle 5.51237 ( 1584) link_BETA1-4 : bond 0.00645 ( 12) link_BETA1-4 : angle 1.85571 ( 36) link_NAG-ASN : bond 0.00317 ( 36) link_NAG-ASN : angle 1.99431 ( 108) *********************** 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 452 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 403 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8396 (tp40) cc_final: 0.7863 (tt0) REVERT: L 45 LYS cc_start: 0.8214 (tttt) cc_final: 0.7628 (ttmt) REVERT: L 53 ASN cc_start: 0.7793 (t0) cc_final: 0.7514 (t0) REVERT: D 31 ASN cc_start: 0.8408 (p0) cc_final: 0.8006 (p0) REVERT: C 70 SER cc_start: 0.8814 (t) cc_final: 0.8495 (m) REVERT: C 91 TYR cc_start: 0.8911 (m-80) cc_final: 0.8498 (m-10) REVERT: G 35 TRP cc_start: 0.8986 (m100) cc_final: 0.8594 (m-90) REVERT: G 114 GLN cc_start: 0.8596 (tp40) cc_final: 0.8090 (tt0) REVERT: G 241 ASN cc_start: 0.8246 (t0) cc_final: 0.7994 (t0) REVERT: G 278 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.8026 (ttp) REVERT: G 657 GLU cc_start: 0.8238 (tt0) cc_final: 0.7972 (tt0) REVERT: F 31 ASN cc_start: 0.8276 (p0) cc_final: 0.7875 (p0) REVERT: F 36 TYR cc_start: 0.8593 (m-80) cc_final: 0.8194 (m-80) REVERT: E 70 SER cc_start: 0.8805 (t) cc_final: 0.8489 (m) REVERT: E 91 TYR cc_start: 0.8870 (m-80) cc_final: 0.8493 (m-10) REVERT: B 114 GLN cc_start: 0.8379 (tp40) cc_final: 0.7866 (tt0) REVERT: B 341 MET cc_start: 0.7952 (ttp) cc_final: 0.7689 (tmm) REVERT: N 69 MET cc_start: 0.8560 (mtt) cc_final: 0.8165 (mtt) REVERT: O 61 ARG cc_start: 0.5598 (ptt-90) cc_final: 0.5358 (ptt-90) REVERT: K 74 THR cc_start: 0.7917 (m) cc_final: 0.7539 (p) REVERT: J 70 SER cc_start: 0.8659 (t) cc_final: 0.8273 (m) REVERT: J 91 TYR cc_start: 0.8786 (m-80) cc_final: 0.8434 (m-10) outliers start: 49 outliers final: 32 residues processed: 427 average time/residue: 0.1919 time to fit residues: 124.9165 Evaluate side-chains 389 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 356 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 247 CYS 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 76 ASN Chi-restraints excluded: chain C residue 94 THR 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 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 247 CYS 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 83 ILE Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain K residue 72 SER 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 41 optimal weight: 1.9990 chunk 228 optimal weight: 0.9980 chunk 149 optimal weight: 0.0030 chunk 133 optimal weight: 3.9990 chunk 216 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 168 optimal weight: 10.0000 chunk 130 optimal weight: 0.8980 chunk 240 optimal weight: 0.5980 chunk 231 optimal weight: 2.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN A 339 HIS L 34 ASN D 69 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 = 0.3911 r_free = 0.3911 target = 0.165652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.134936 restraints weight = 28578.277| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.61 r_work: 0.3403 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 24882 Z= 0.131 Angle : 0.556 11.097 33843 Z= 0.289 Chirality : 0.045 0.187 3855 Planarity : 0.004 0.038 4239 Dihedral : 6.075 60.516 4278 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.18 % Allowed : 11.02 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.15), residues: 2976 helix: -0.31 (0.26), residues: 408 sheet: -0.02 (0.16), residues: 984 loop : -0.50 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 327 TYR 0.020 0.001 TYR A 402 PHE 0.013 0.001 PHE I 97 TRP 0.019 0.001 TRP I 50 HIS 0.003 0.001 HIS G 287 Details of bonding type rmsd covalent geometry : bond 0.00305 (24789) covalent geometry : angle 0.53950 (33609) SS BOND : bond 0.00692 ( 45) SS BOND : angle 1.66008 ( 90) hydrogen bonds : bond 0.03991 ( 630) hydrogen bonds : angle 5.01228 ( 1584) link_BETA1-4 : bond 0.00452 ( 12) link_BETA1-4 : angle 1.90142 ( 36) link_NAG-ASN : bond 0.00238 ( 36) link_NAG-ASN : angle 1.70066 ( 108) *********************** 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 426 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 369 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8429 (tp40) cc_final: 0.7866 (tt0) REVERT: A 370 GLU cc_start: 0.7573 (mp0) cc_final: 0.7273 (mp0) REVERT: L 21 ILE cc_start: 0.7820 (mt) cc_final: 0.7330 (mt) REVERT: L 45 LYS cc_start: 0.8170 (tttt) cc_final: 0.7771 (ttmt) REVERT: D 31 ASN cc_start: 0.8437 (p0) cc_final: 0.8162 (p0) REVERT: D 69 ASN cc_start: 0.8364 (m-40) cc_final: 0.8090 (t0) REVERT: C 70 SER cc_start: 0.8799 (t) cc_final: 0.8506 (m) REVERT: C 82 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7887 (mp) REVERT: C 91 TYR cc_start: 0.8954 (m-80) cc_final: 0.8559 (m-80) REVERT: G 35 TRP cc_start: 0.9007 (m100) cc_final: 0.8616 (m-90) REVERT: G 114 GLN cc_start: 0.8582 (tp40) cc_final: 0.8102 (tt0) REVERT: G 241 ASN cc_start: 0.8343 (t0) cc_final: 0.8083 (t0) REVERT: G 278 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.8039 (ttp) REVERT: M 21 ILE cc_start: 0.8122 (mt) cc_final: 0.7670 (mt) REVERT: F 31 ASN cc_start: 0.8301 (p0) cc_final: 0.7981 (p0) REVERT: F 69 ASN cc_start: 0.8040 (m110) cc_final: 0.7837 (t0) REVERT: F 73 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7490 (tp) REVERT: E 70 SER cc_start: 0.8800 (t) cc_final: 0.8502 (m) REVERT: E 91 TYR cc_start: 0.8865 (m-80) cc_final: 0.8475 (m-10) REVERT: B 114 GLN cc_start: 0.8409 (tp40) cc_final: 0.7870 (tt0) REVERT: B 341 MET cc_start: 0.8042 (ttp) cc_final: 0.7697 (tmm) REVERT: N 76 ARG cc_start: 0.8010 (mtm-85) cc_final: 0.7725 (mtm-85) REVERT: K 61 ARG cc_start: 0.7162 (ttp80) cc_final: 0.6753 (ttp80) REVERT: J 70 SER cc_start: 0.8604 (t) cc_final: 0.8259 (m) REVERT: J 91 TYR cc_start: 0.8863 (m-80) cc_final: 0.8474 (m-10) outliers start: 57 outliers final: 29 residues processed: 403 average time/residue: 0.1754 time to fit residues: 108.7514 Evaluate side-chains 379 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 347 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain H residue 7 SER 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 82 LEU Chi-restraints excluded: chain C residue 94 THR 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 I residue 7 SER 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 B residue 120 VAL Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 243 SER 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 N residue 7 SER Chi-restraints excluded: chain N residue 82 SER Chi-restraints excluded: chain N residue 83 ILE Chi-restraints excluded: chain K residue 95 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 203 optimal weight: 3.9990 chunk 241 optimal weight: 2.9990 chunk 245 optimal weight: 1.9990 chunk 69 optimal weight: 9.9990 chunk 57 optimal weight: 3.9990 chunk 206 optimal weight: 0.5980 chunk 63 optimal weight: 7.9990 chunk 261 optimal weight: 7.9990 chunk 292 optimal weight: 3.9990 chunk 198 optimal weight: 0.8980 chunk 239 optimal weight: 0.6980 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 L 53 ASN G 216 HIS ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 53 ASN ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 34 ASN O 38 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.159954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.127347 restraints weight = 28759.724| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.67 r_work: 0.3307 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 24882 Z= 0.213 Angle : 0.611 11.123 33843 Z= 0.315 Chirality : 0.047 0.203 3855 Planarity : 0.004 0.039 4239 Dihedral : 6.023 56.806 4278 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.14 % Allowed : 11.33 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.15), residues: 2976 helix: -0.36 (0.26), residues: 417 sheet: 0.02 (0.15), residues: 1044 loop : -0.67 (0.15), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 327 TYR 0.021 0.002 TYR B 402 PHE 0.015 0.002 PHE I 97 TRP 0.019 0.002 TRP H 50 HIS 0.006 0.001 HIS B 287 Details of bonding type rmsd covalent geometry : bond 0.00517 (24789) covalent geometry : angle 0.59394 (33609) SS BOND : bond 0.00721 ( 45) SS BOND : angle 1.62455 ( 90) hydrogen bonds : bond 0.04328 ( 630) hydrogen bonds : angle 4.86868 ( 1584) link_BETA1-4 : bond 0.00371 ( 12) link_BETA1-4 : angle 2.02935 ( 36) link_NAG-ASN : bond 0.00270 ( 36) link_NAG-ASN : angle 1.85959 ( 108) *********************** 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 451 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 369 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8457 (tp40) cc_final: 0.7915 (tt0) REVERT: A 370 GLU cc_start: 0.7592 (mp0) cc_final: 0.7317 (mp0) REVERT: L 21 ILE cc_start: 0.7904 (mt) cc_final: 0.7408 (mt) REVERT: L 45 LYS cc_start: 0.8171 (tttt) cc_final: 0.7576 (ttmt) REVERT: L 53 ASN cc_start: 0.7761 (OUTLIER) cc_final: 0.7404 (t0) REVERT: D 31 ASN cc_start: 0.8610 (p0) cc_final: 0.8320 (p0) REVERT: C 70 SER cc_start: 0.8817 (t) cc_final: 0.8534 (m) REVERT: C 76 ASN cc_start: 0.9050 (OUTLIER) cc_final: 0.8801 (m-40) REVERT: C 82 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7950 (mp) REVERT: C 91 TYR cc_start: 0.9041 (m-80) cc_final: 0.8630 (m-80) REVERT: G 114 GLN cc_start: 0.8626 (tp40) cc_final: 0.8081 (tt0) REVERT: G 664 ASP cc_start: 0.7162 (OUTLIER) cc_final: 0.6817 (t0) REVERT: M 5 THR cc_start: 0.8172 (m) cc_final: 0.7952 (m) REVERT: M 21 ILE cc_start: 0.8229 (mt) cc_final: 0.7713 (mt) REVERT: M 53 ASN cc_start: 0.7810 (OUTLIER) cc_final: 0.7472 (t0) REVERT: F 73 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7693 (tp) REVERT: E 43 LYS cc_start: 0.7636 (mmtt) cc_final: 0.7066 (pttp) REVERT: E 70 SER cc_start: 0.8867 (t) cc_final: 0.8547 (m) REVERT: B 114 GLN cc_start: 0.8468 (tp40) cc_final: 0.7939 (tt0) REVERT: B 341 MET cc_start: 0.8230 (ttp) cc_final: 0.7946 (tmm) REVERT: B 657 GLU cc_start: 0.8365 (tt0) cc_final: 0.7976 (tt0) REVERT: K 61 ARG cc_start: 0.7316 (ttp80) cc_final: 0.6944 (ttp80) REVERT: J 41 PRO cc_start: 0.8597 (Cg_exo) cc_final: 0.8204 (Cg_endo) REVERT: J 70 SER cc_start: 0.8677 (t) cc_final: 0.8334 (m) REVERT: J 91 TYR cc_start: 0.8931 (m-80) cc_final: 0.8540 (m-10) outliers start: 82 outliers final: 54 residues processed: 414 average time/residue: 0.1889 time to fit residues: 120.9254 Evaluate side-chains 399 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 339 time to evaluate : 0.927 ------------------------------------------------------------------------------- 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 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 L residue 53 ASN 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 97 ILE Chi-restraints excluded: chain C residue 62 SER 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 213 ILE Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 408 ASN 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 53 ASN 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 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 B residue 120 VAL Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 408 ASN 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 11 VAL Chi-restraints excluded: chain N residue 82 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 108 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 203 optimal weight: 2.9990 chunk 228 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 77 optimal weight: 5.9990 chunk 235 optimal weight: 0.9980 chunk 134 optimal weight: 0.6980 chunk 237 optimal weight: 7.9990 chunk 213 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 6 optimal weight: 0.0030 chunk 234 optimal weight: 0.8980 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN D 79 GLN G 203 GLN E 81 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.162283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.130811 restraints weight = 28510.949| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 1.62 r_work: 0.3350 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24882 Z= 0.122 Angle : 0.541 10.031 33843 Z= 0.278 Chirality : 0.044 0.192 3855 Planarity : 0.003 0.035 4239 Dihedral : 5.508 49.177 4278 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.83 % Allowed : 12.67 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.15), residues: 2976 helix: -0.11 (0.26), residues: 417 sheet: 0.14 (0.16), residues: 993 loop : -0.61 (0.15), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 327 TYR 0.017 0.001 TYR G 402 PHE 0.011 0.001 PHE B 383 TRP 0.019 0.001 TRP H 50 HIS 0.002 0.001 HIS G 287 Details of bonding type rmsd covalent geometry : bond 0.00284 (24789) covalent geometry : angle 0.52534 (33609) SS BOND : bond 0.00505 ( 45) SS BOND : angle 1.38179 ( 90) hydrogen bonds : bond 0.03736 ( 630) hydrogen bonds : angle 4.64395 ( 1584) link_BETA1-4 : bond 0.00399 ( 12) link_BETA1-4 : angle 1.97051 ( 36) link_NAG-ASN : bond 0.00229 ( 36) link_NAG-ASN : angle 1.69850 ( 108) *********************** 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 425 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 351 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8447 (tp40) cc_final: 0.7952 (tt0) REVERT: A 370 GLU cc_start: 0.7482 (mp0) cc_final: 0.7222 (mp0) REVERT: A 632 ASP cc_start: 0.8572 (t0) cc_final: 0.8299 (t0) REVERT: L 45 LYS cc_start: 0.8144 (tttt) cc_final: 0.7529 (ttmt) REVERT: L 53 ASN cc_start: 0.7915 (t0) cc_final: 0.7708 (t0) REVERT: D 31 ASN cc_start: 0.8629 (p0) cc_final: 0.8342 (p0) REVERT: D 73 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7693 (tp) REVERT: C 70 SER cc_start: 0.8816 (t) cc_final: 0.8555 (m) REVERT: C 76 ASN cc_start: 0.9105 (OUTLIER) cc_final: 0.8745 (m-40) REVERT: C 82 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7905 (mp) REVERT: C 91 TYR cc_start: 0.9035 (m-80) cc_final: 0.8628 (m-80) REVERT: G 114 GLN cc_start: 0.8582 (tp40) cc_final: 0.8063 (tt0) REVERT: G 664 ASP cc_start: 0.7096 (OUTLIER) cc_final: 0.6867 (t0) REVERT: M 21 ILE cc_start: 0.8202 (mt) cc_final: 0.7709 (mt) REVERT: F 36 TYR cc_start: 0.8656 (m-80) cc_final: 0.8293 (m-80) REVERT: F 73 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7674 (tp) REVERT: E 70 SER cc_start: 0.8811 (t) cc_final: 0.8521 (m) REVERT: B 114 GLN cc_start: 0.8381 (tp40) cc_final: 0.7936 (tt0) REVERT: B 341 MET cc_start: 0.8114 (ttp) cc_final: 0.7900 (tmm) REVERT: B 657 GLU cc_start: 0.8285 (tt0) cc_final: 0.7897 (tt0) REVERT: K 31 ASN cc_start: 0.8461 (p0) cc_final: 0.8134 (p0) REVERT: K 61 ARG cc_start: 0.7357 (ttp80) cc_final: 0.6856 (ttp80) REVERT: J 70 SER cc_start: 0.8675 (t) cc_final: 0.8371 (m) REVERT: J 91 TYR cc_start: 0.8942 (m-80) cc_final: 0.8506 (m-10) outliers start: 74 outliers final: 48 residues processed: 395 average time/residue: 0.1878 time to fit residues: 114.3008 Evaluate side-chains 388 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 335 time to evaluate : 0.931 ------------------------------------------------------------------------------- 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 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 72 THR Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain D residue 33 VAL 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 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 213 ILE 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 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 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 243 SER 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 612 SER Chi-restraints excluded: chain B residue 664 ASP Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 62 LYS Chi-restraints excluded: chain N residue 83 ILE Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 95 THR 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 45 optimal weight: 3.9990 chunk 293 optimal weight: 7.9990 chunk 152 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 264 optimal weight: 10.0000 chunk 38 optimal weight: 0.5980 chunk 130 optimal weight: 0.8980 chunk 200 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 158 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** L 34 ASN D 79 GLN ** G 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 276 ASN G 463 ASN ** B 229 ASN ** 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 = 0.3863 r_free = 0.3863 target = 0.160926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.128600 restraints weight = 28570.416| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.65 r_work: 0.3358 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2417 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= 0.127 Angle : 0.534 9.663 33843 Z= 0.274 Chirality : 0.044 0.186 3855 Planarity : 0.003 0.035 4239 Dihedral : 5.181 42.748 4278 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.53 % Allowed : 13.09 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.15), residues: 2976 helix: 0.01 (0.27), residues: 417 sheet: 0.19 (0.16), residues: 993 loop : -0.60 (0.15), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 327 TYR 0.016 0.001 TYR G 402 PHE 0.014 0.001 PHE A 383 TRP 0.018 0.001 TRP H 50 HIS 0.003 0.001 HIS G 216 Details of bonding type rmsd covalent geometry : bond 0.00301 (24789) covalent geometry : angle 0.51855 (33609) SS BOND : bond 0.00534 ( 45) SS BOND : angle 1.39992 ( 90) hydrogen bonds : bond 0.03645 ( 630) hydrogen bonds : angle 4.53313 ( 1584) link_BETA1-4 : bond 0.00442 ( 12) link_BETA1-4 : angle 2.00563 ( 36) link_NAG-ASN : bond 0.00217 ( 36) link_NAG-ASN : angle 1.64156 ( 108) *********************** 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 407 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 341 time to evaluate : 0.969 Fit side-chains revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8440 (tp40) cc_final: 0.7904 (tt0) REVERT: A 370 GLU cc_start: 0.7511 (mp0) cc_final: 0.7261 (mp0) REVERT: A 632 ASP cc_start: 0.8612 (t0) cc_final: 0.8319 (t0) REVERT: L 45 LYS cc_start: 0.8096 (tttt) cc_final: 0.7467 (ttmt) REVERT: L 53 ASN cc_start: 0.7864 (t0) cc_final: 0.7548 (t0) REVERT: D 31 ASN cc_start: 0.8644 (p0) cc_final: 0.8352 (p0) REVERT: D 73 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7646 (tp) REVERT: C 70 SER cc_start: 0.8808 (t) cc_final: 0.8547 (m) REVERT: C 76 ASN cc_start: 0.9083 (OUTLIER) cc_final: 0.8714 (m-40) REVERT: C 82 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7866 (mp) REVERT: C 91 TYR cc_start: 0.9022 (m-80) cc_final: 0.8592 (m-80) REVERT: G 114 GLN cc_start: 0.8525 (tp40) cc_final: 0.7990 (tt0) REVERT: G 664 ASP cc_start: 0.7025 (OUTLIER) cc_final: 0.6807 (t0) REVERT: I 82 ARG cc_start: 0.8349 (mpp80) cc_final: 0.8146 (mpp80) REVERT: M 21 ILE cc_start: 0.8166 (mt) cc_final: 0.7680 (mt) REVERT: F 36 TYR cc_start: 0.8664 (m-80) cc_final: 0.8277 (m-80) REVERT: F 61 ARG cc_start: 0.7593 (ttp80) cc_final: 0.7335 (ttp80) REVERT: F 73 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7615 (tp) REVERT: E 70 SER cc_start: 0.8794 (t) cc_final: 0.8519 (m) REVERT: B 114 GLN cc_start: 0.8383 (tp40) cc_final: 0.7902 (tt0) REVERT: B 341 MET cc_start: 0.8175 (ttp) cc_final: 0.7859 (tmm) REVERT: B 657 GLU cc_start: 0.8278 (tt0) cc_final: 0.7920 (tt0) REVERT: K 31 ASN cc_start: 0.8455 (p0) cc_final: 0.8112 (p0) REVERT: K 61 ARG cc_start: 0.7328 (ttp80) cc_final: 0.6796 (ttp80) REVERT: K 69 ASN cc_start: 0.8497 (m-40) cc_final: 0.8067 (t0) REVERT: J 70 SER cc_start: 0.8652 (t) cc_final: 0.8349 (m) REVERT: J 91 TYR cc_start: 0.8901 (m-80) cc_final: 0.8443 (m-10) outliers start: 66 outliers final: 56 residues processed: 374 average time/residue: 0.1739 time to fit residues: 100.7922 Evaluate side-chains 394 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 333 time to evaluate : 0.897 ------------------------------------------------------------------------------- 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 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 H residue 48 MET Chi-restraints excluded: chain L residue 33 LEU 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 73 LEU Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 76 ASN Chi-restraints excluded: chain C residue 82 MET 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 426 MET Chi-restraints excluded: chain G residue 463 ASN 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 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 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 243 SER 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 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 62 LYS Chi-restraints excluded: chain N residue 83 ILE Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 62 SER 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 123 optimal weight: 4.9990 chunk 147 optimal weight: 1.9990 chunk 206 optimal weight: 0.7980 chunk 13 optimal weight: 0.4980 chunk 104 optimal weight: 3.9990 chunk 106 optimal weight: 0.5980 chunk 195 optimal weight: 2.9990 chunk 221 optimal weight: 1.9990 chunk 273 optimal weight: 4.9990 chunk 213 optimal weight: 0.9980 chunk 165 optimal weight: 8.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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** ** G 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 GLN ** B 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.159880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.127479 restraints weight = 28658.856| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.68 r_work: 0.3335 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2531 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= 0.153 Angle : 0.546 9.883 33843 Z= 0.279 Chirality : 0.045 0.190 3855 Planarity : 0.004 0.034 4239 Dihedral : 5.085 39.416 4278 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.91 % Allowed : 13.09 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.15), residues: 2976 helix: -0.01 (0.27), residues: 417 sheet: 0.14 (0.16), residues: 1002 loop : -0.59 (0.15), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 327 TYR 0.016 0.001 TYR G 402 PHE 0.011 0.001 PHE B 383 TRP 0.017 0.001 TRP I 50 HIS 0.003 0.001 HIS G 339 Details of bonding type rmsd covalent geometry : bond 0.00365 (24789) covalent geometry : angle 0.53043 (33609) SS BOND : bond 0.00560 ( 45) SS BOND : angle 1.40255 ( 90) hydrogen bonds : bond 0.03743 ( 630) hydrogen bonds : angle 4.51713 ( 1584) link_BETA1-4 : bond 0.00386 ( 12) link_BETA1-4 : angle 2.01912 ( 36) link_NAG-ASN : bond 0.00218 ( 36) link_NAG-ASN : angle 1.68330 ( 108) *********************** 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 420 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 344 time to evaluate : 0.874 Fit side-chains revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8490 (tp40) cc_final: 0.7955 (tt0) REVERT: A 246 GLN cc_start: 0.6727 (OUTLIER) cc_final: 0.6335 (tt0) REVERT: A 632 ASP cc_start: 0.8635 (t0) cc_final: 0.8361 (t0) REVERT: L 45 LYS cc_start: 0.8098 (tttt) cc_final: 0.7469 (ttmt) REVERT: L 53 ASN cc_start: 0.7877 (t0) cc_final: 0.7552 (t0) REVERT: D 31 ASN cc_start: 0.8652 (p0) cc_final: 0.8377 (p0) REVERT: D 73 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7691 (tp) REVERT: C 41 PRO cc_start: 0.8642 (Cg_exo) cc_final: 0.8384 (Cg_endo) REVERT: C 70 SER cc_start: 0.8812 (t) cc_final: 0.8556 (m) REVERT: C 76 ASN cc_start: 0.9114 (OUTLIER) cc_final: 0.8740 (m-40) REVERT: C 82 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7896 (mp) REVERT: G 114 GLN cc_start: 0.8542 (tp40) cc_final: 0.7998 (tt0) REVERT: G 664 ASP cc_start: 0.7065 (OUTLIER) cc_final: 0.6845 (t0) REVERT: F 45 LYS cc_start: 0.8603 (tttt) cc_final: 0.8273 (tttt) REVERT: F 61 ARG cc_start: 0.7607 (ttp80) cc_final: 0.7330 (ttp80) REVERT: F 73 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7715 (tp) REVERT: E 70 SER cc_start: 0.8817 (t) cc_final: 0.8533 (m) REVERT: B 114 GLN cc_start: 0.8420 (tp40) cc_final: 0.7945 (tt0) REVERT: B 341 MET cc_start: 0.8219 (ttp) cc_final: 0.7893 (tmm) REVERT: B 657 GLU cc_start: 0.8322 (tt0) cc_final: 0.7993 (tt0) REVERT: K 31 ASN cc_start: 0.8496 (p0) cc_final: 0.8165 (p0) REVERT: K 61 ARG cc_start: 0.7403 (ttp80) cc_final: 0.6861 (ttp80) REVERT: J 43 LYS cc_start: 0.7798 (mmtt) cc_final: 0.7447 (mttm) REVERT: J 70 SER cc_start: 0.8656 (t) cc_final: 0.8360 (m) REVERT: J 91 TYR cc_start: 0.8919 (m-80) cc_final: 0.8442 (m-10) outliers start: 76 outliers final: 65 residues processed: 384 average time/residue: 0.1822 time to fit residues: 108.6670 Evaluate side-chains 403 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 332 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 239 CYS Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 328 GLU 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 A residue 625 ASN 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 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 73 LEU 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 76 ASN Chi-restraints excluded: chain C residue 82 MET 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 328 GLU 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 M residue 72 THR 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 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 239 CYS Chi-restraints excluded: chain B residue 243 SER 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 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 62 LYS Chi-restraints excluded: chain N residue 83 ILE Chi-restraints excluded: chain O residue 33 LEU 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 108 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 104 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 227 optimal weight: 2.9990 chunk 279 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 189 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 214 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 34 ASN D 79 GLN ** G 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 463 ASN B 216 HIS ** B 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.155578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.122436 restraints weight = 28815.465| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.70 r_work: 0.3274 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 24882 Z= 0.270 Angle : 0.651 10.962 33843 Z= 0.332 Chirality : 0.049 0.219 3855 Planarity : 0.004 0.051 4239 Dihedral : 5.757 46.854 4278 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.25 % Allowed : 13.01 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.15), residues: 2976 helix: -0.32 (0.26), residues: 417 sheet: 0.02 (0.16), residues: 1008 loop : -0.70 (0.15), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 327 TYR 0.021 0.002 TYR K 49 PHE 0.014 0.002 PHE A 317 TRP 0.014 0.002 TRP H 50 HIS 0.005 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00656 (24789) covalent geometry : angle 0.63339 (33609) SS BOND : bond 0.00619 ( 45) SS BOND : angle 1.71876 ( 90) hydrogen bonds : bond 0.04536 ( 630) hydrogen bonds : angle 4.84984 ( 1584) link_BETA1-4 : bond 0.00336 ( 12) link_BETA1-4 : angle 2.11535 ( 36) link_NAG-ASN : bond 0.00292 ( 36) link_NAG-ASN : angle 2.02545 ( 108) *********************** 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 426 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 341 time to evaluate : 0.984 Fit side-chains revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8563 (tp40) cc_final: 0.8035 (tt0) REVERT: A 246 GLN cc_start: 0.7240 (OUTLIER) cc_final: 0.6844 (tt0) REVERT: L 45 LYS cc_start: 0.8092 (tttt) cc_final: 0.7501 (ttmt) REVERT: L 53 ASN cc_start: 0.7794 (t0) cc_final: 0.7485 (t0) REVERT: D 31 ASN cc_start: 0.8664 (p0) cc_final: 0.8413 (p0) REVERT: D 73 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7626 (tp) REVERT: C 70 SER cc_start: 0.8873 (t) cc_final: 0.8615 (m) REVERT: C 76 ASN cc_start: 0.9130 (OUTLIER) cc_final: 0.8807 (m-40) REVERT: C 82 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7935 (mp) REVERT: G 114 GLN cc_start: 0.8577 (tp40) cc_final: 0.8032 (tt0) REVERT: G 463 ASN cc_start: 0.8555 (OUTLIER) cc_final: 0.7473 (m-40) REVERT: F 61 ARG cc_start: 0.7689 (ttp80) cc_final: 0.7369 (ttp80) REVERT: E 70 SER cc_start: 0.8842 (t) cc_final: 0.8560 (m) REVERT: B 95 MET cc_start: 0.8949 (OUTLIER) cc_final: 0.8666 (ptt) REVERT: B 114 GLN cc_start: 0.8471 (tp40) cc_final: 0.7968 (tt0) REVERT: B 341 MET cc_start: 0.8301 (ttp) cc_final: 0.7918 (tmm) REVERT: B 460 LYS cc_start: 0.8208 (mmtm) cc_final: 0.7893 (mmtt) REVERT: K 31 ASN cc_start: 0.8566 (p0) cc_final: 0.8243 (p0) REVERT: K 52 THR cc_start: 0.8963 (p) cc_final: 0.8572 (t) REVERT: J 43 LYS cc_start: 0.7829 (mmtt) cc_final: 0.7422 (mttm) REVERT: J 70 SER cc_start: 0.8743 (t) cc_final: 0.8434 (m) REVERT: J 91 TYR cc_start: 0.8960 (m-80) cc_final: 0.8480 (m-10) outliers start: 85 outliers final: 68 residues processed: 392 average time/residue: 0.1858 time to fit residues: 112.4734 Evaluate side-chains 403 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 329 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 246 GLN 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 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 73 LEU Chi-restraints excluded: chain D residue 79 GLN 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 76 ASN Chi-restraints excluded: chain C residue 82 MET 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 G residue 120 VAL Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 232 THR Chi-restraints excluded: chain G residue 328 GLU Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain G residue 463 ASN 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 M residue 72 THR 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 72 SER 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 95 MET Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 243 SER 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 B residue 664 ASP Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 62 LYS Chi-restraints excluded: chain N residue 80 MET Chi-restraints excluded: chain N residue 82 SER Chi-restraints excluded: chain N residue 83 ILE Chi-restraints excluded: chain O residue 33 LEU 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 62 SER 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 260 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 121 optimal weight: 0.6980 chunk 65 optimal weight: 0.0970 chunk 99 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 chunk 8 optimal weight: 0.4980 chunk 40 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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** D 39 HIS ** G 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 463 ASN ** B 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 34 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.161481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.129679 restraints weight = 28618.246| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.65 r_work: 0.3328 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 24882 Z= 0.118 Angle : 0.548 10.802 33843 Z= 0.281 Chirality : 0.044 0.200 3855 Planarity : 0.004 0.037 4239 Dihedral : 5.239 38.937 4278 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.53 % Allowed : 13.89 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.15), residues: 2976 helix: -0.01 (0.27), residues: 417 sheet: 0.08 (0.16), residues: 996 loop : -0.68 (0.15), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 327 TYR 0.017 0.001 TYR G 402 PHE 0.013 0.001 PHE B 383 TRP 0.018 0.001 TRP I 50 HIS 0.003 0.001 HIS G 216 Details of bonding type rmsd covalent geometry : bond 0.00274 (24789) covalent geometry : angle 0.53264 (33609) SS BOND : bond 0.00515 ( 45) SS BOND : angle 1.44808 ( 90) hydrogen bonds : bond 0.03619 ( 630) hydrogen bonds : angle 4.54047 ( 1584) link_BETA1-4 : bond 0.00416 ( 12) link_BETA1-4 : angle 1.92783 ( 36) link_NAG-ASN : bond 0.00239 ( 36) link_NAG-ASN : angle 1.73080 ( 108) *********************** 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 408 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 342 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8517 (tp40) cc_final: 0.8039 (tt0) REVERT: A 154 MET cc_start: 0.8689 (mtm) cc_final: 0.8476 (mtt) REVERT: A 621 ASP cc_start: 0.7977 (m-30) cc_final: 0.7763 (m-30) REVERT: A 632 ASP cc_start: 0.8645 (t0) cc_final: 0.8359 (t0) REVERT: H 53 ARG cc_start: 0.7621 (tpt170) cc_final: 0.7416 (tpt170) REVERT: L 45 LYS cc_start: 0.8106 (tttt) cc_final: 0.7506 (ttmt) REVERT: L 53 ASN cc_start: 0.7621 (t0) cc_final: 0.7303 (t0) REVERT: D 31 ASN cc_start: 0.8552 (p0) cc_final: 0.8313 (p0) REVERT: C 70 SER cc_start: 0.8855 (t) cc_final: 0.8608 (m) REVERT: C 76 ASN cc_start: 0.9102 (OUTLIER) cc_final: 0.8775 (m-40) REVERT: C 82 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7878 (mp) REVERT: G 114 GLN cc_start: 0.8505 (tp40) cc_final: 0.8009 (tt0) REVERT: G 463 ASN cc_start: 0.8469 (OUTLIER) cc_final: 0.7873 (m-40) REVERT: F 61 ARG cc_start: 0.7724 (ttp80) cc_final: 0.7454 (ttp80) REVERT: E 70 SER cc_start: 0.8804 (t) cc_final: 0.8552 (m) REVERT: B 95 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8658 (ptt) REVERT: B 114 GLN cc_start: 0.8411 (tp40) cc_final: 0.7944 (tt0) REVERT: B 657 GLU cc_start: 0.8313 (tt0) cc_final: 0.7989 (tt0) REVERT: K 31 ASN cc_start: 0.8558 (p0) cc_final: 0.8240 (p0) REVERT: K 52 THR cc_start: 0.8859 (p) cc_final: 0.8479 (t) REVERT: J 43 LYS cc_start: 0.7770 (mmtt) cc_final: 0.7395 (mttm) REVERT: J 70 SER cc_start: 0.8684 (t) cc_final: 0.8423 (m) REVERT: J 91 TYR cc_start: 0.8922 (m-80) cc_final: 0.8405 (m-10) REVERT: J 97 MET cc_start: 0.8564 (mtp) cc_final: 0.8342 (mtp) outliers start: 66 outliers final: 55 residues processed: 378 average time/residue: 0.1865 time to fit residues: 109.0019 Evaluate side-chains 390 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 331 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL 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 426 MET Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 595 ILE 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 97 ILE Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 76 ASN 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 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 426 MET Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain G residue 463 ASN Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 11 VAL 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 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 95 MET Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain B residue 328 GLU 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 N residue 7 SER Chi-restraints excluded: chain N residue 62 LYS Chi-restraints excluded: chain N residue 82 SER Chi-restraints excluded: chain N residue 83 ILE 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 95 THR Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 62 SER 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 184 optimal weight: 0.6980 chunk 170 optimal weight: 0.9980 chunk 223 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 259 optimal weight: 0.9980 chunk 113 optimal weight: 0.0070 chunk 244 optimal weight: 3.9990 chunk 292 optimal weight: 0.0670 chunk 19 optimal weight: 0.0040 chunk 183 optimal weight: 5.9990 chunk 264 optimal weight: 0.6980 overall best weight: 0.2948 ------------------------------------------------------------------------------- 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 L 34 ASN ** G 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 ASN B 339 HIS N 61 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.161860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.129887 restraints weight = 28595.726| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 1.64 r_work: 0.3375 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 24882 Z= 0.098 Angle : 0.523 11.504 33843 Z= 0.268 Chirality : 0.043 0.239 3855 Planarity : 0.003 0.034 4239 Dihedral : 4.712 30.313 4278 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.91 % Allowed : 14.70 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.15), residues: 2976 helix: 0.32 (0.28), residues: 408 sheet: 0.21 (0.16), residues: 996 loop : -0.64 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 327 TYR 0.017 0.001 TYR G 402 PHE 0.013 0.001 PHE I 63 TRP 0.021 0.001 TRP I 50 HIS 0.004 0.001 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00219 (24789) covalent geometry : angle 0.50909 (33609) SS BOND : bond 0.00481 ( 45) SS BOND : angle 1.30362 ( 90) hydrogen bonds : bond 0.03298 ( 630) hydrogen bonds : angle 4.30103 ( 1584) link_BETA1-4 : bond 0.00480 ( 12) link_BETA1-4 : angle 1.93258 ( 36) link_NAG-ASN : bond 0.00219 ( 36) link_NAG-ASN : angle 1.55827 ( 108) ********************** 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 401 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 351 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8474 (tp40) cc_final: 0.8002 (tt0) REVERT: A 530 MET cc_start: 0.9295 (mtp) cc_final: 0.9020 (mtp) REVERT: A 621 ASP cc_start: 0.7979 (m-30) cc_final: 0.7760 (m-30) REVERT: A 632 ASP cc_start: 0.8600 (t0) cc_final: 0.8324 (t0) REVERT: L 45 LYS cc_start: 0.8065 (tttt) cc_final: 0.7435 (ttmt) REVERT: L 53 ASN cc_start: 0.7617 (t0) cc_final: 0.7280 (t0) REVERT: D 31 ASN cc_start: 0.8584 (p0) cc_final: 0.8340 (p0) REVERT: C 70 SER cc_start: 0.8797 (t) cc_final: 0.8555 (m) REVERT: C 76 ASN cc_start: 0.9076 (OUTLIER) cc_final: 0.8715 (m-40) REVERT: C 82 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7855 (mp) REVERT: G 114 GLN cc_start: 0.8459 (tp40) cc_final: 0.7961 (tt0) REVERT: G 412 SER cc_start: 0.8726 (t) cc_final: 0.8465 (m) REVERT: G 463 ASN cc_start: 0.8382 (p0) cc_final: 0.8169 (m-40) REVERT: F 62 PHE cc_start: 0.8516 (m-80) cc_final: 0.8151 (m-80) REVERT: E 70 SER cc_start: 0.8788 (t) cc_final: 0.8538 (m) REVERT: B 114 GLN cc_start: 0.8391 (tp40) cc_final: 0.7907 (tt0) REVERT: B 278 MET cc_start: 0.8355 (ttp) cc_final: 0.8019 (mmt) REVERT: B 341 MET cc_start: 0.8188 (ttp) cc_final: 0.7911 (tmm) REVERT: B 657 GLU cc_start: 0.8265 (tt0) cc_final: 0.7940 (tt0) REVERT: K 31 ASN cc_start: 0.8483 (p0) cc_final: 0.8198 (p0) REVERT: K 52 THR cc_start: 0.8797 (p) cc_final: 0.8405 (t) REVERT: J 43 LYS cc_start: 0.7708 (mmtt) cc_final: 0.7376 (mttm) REVERT: J 70 SER cc_start: 0.8645 (t) cc_final: 0.8375 (m) REVERT: J 91 TYR cc_start: 0.8857 (m-80) cc_final: 0.8318 (m-10) REVERT: J 97 MET cc_start: 0.8390 (mtp) cc_final: 0.8142 (mtp) outliers start: 50 outliers final: 39 residues processed: 376 average time/residue: 0.1847 time to fit residues: 107.2549 Evaluate side-chains 375 residues out of total 2613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 334 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 328 GLU Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 595 ILE 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 76 ASN Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 213 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 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 95 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 232 THR Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 328 GLU 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 N residue 51 ILE Chi-restraints excluded: chain N residue 82 SER Chi-restraints excluded: chain N residue 83 ILE Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 62 SER 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 116 optimal weight: 0.0270 chunk 96 optimal weight: 4.9990 chunk 200 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 153 optimal weight: 2.9990 chunk 154 optimal weight: 9.9990 chunk 209 optimal weight: 1.9990 chunk 179 optimal weight: 0.8980 chunk 219 optimal weight: 2.9990 chunk 250 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 overall best weight: 0.9640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN G 229 ASN G 463 ASN I 61 GLN B 229 ASN O 34 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.161726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.132297 restraints weight = 28730.811| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.63 r_work: 0.3339 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24882 Z= 0.154 Angle : 0.567 10.948 33843 Z= 0.290 Chirality : 0.045 0.307 3855 Planarity : 0.004 0.035 4239 Dihedral : 4.820 32.224 4278 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.84 % Allowed : 15.04 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.15), residues: 2976 helix: 0.34 (0.27), residues: 399 sheet: 0.21 (0.16), residues: 996 loop : -0.69 (0.15), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 327 TYR 0.018 0.001 TYR K 32 PHE 0.011 0.001 PHE B 383 TRP 0.017 0.001 TRP I 50 HIS 0.004 0.001 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00371 (24789) covalent geometry : angle 0.54732 (33609) SS BOND : bond 0.00517 ( 45) SS BOND : angle 1.81412 ( 90) hydrogen bonds : bond 0.03698 ( 630) hydrogen bonds : angle 4.42859 ( 1584) link_BETA1-4 : bond 0.00437 ( 12) link_BETA1-4 : angle 1.97760 ( 36) link_NAG-ASN : bond 0.00256 ( 36) link_NAG-ASN : angle 1.87858 ( 108) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6580.75 seconds wall clock time: 113 minutes 29.32 seconds (6809.32 seconds total)