Starting phenix.real_space_refine on Mon Jul 6 21:14:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7vwl_32155/07_2026/7vwl_32155.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vwl_32155/07_2026/7vwl_32155.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vwl_32155/07_2026/7vwl_32155.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vwl_32155/07_2026/7vwl_32155.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7vwl_32155/07_2026/7vwl_32155.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7vwl_32155/07_2026/7vwl_32155.cif" model { file = "/net/cci-nas-00/data/ceres_data/7vwl_32155/07_2026/7vwl_32155.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vwl_32155/07_2026/7vwl_32155.cif" } resolution = 2.7 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 29 5.49 5 S 285 5.16 5 C 25369 2.51 5 N 6204 2.21 5 O 7162 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 53 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 39049 Number of models: 1 Model: "" Number of chains: 62 Chain: "Q" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 333 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 7, 'TRANS': 32} Chain: "S" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 567 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "U" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 643 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 11, 'TRANS': 71} Chain: "V" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1021 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain: "W" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 949 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "X" Number of atoms: 702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 702 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "Y" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 600 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 6, 'TRANS': 63} Chain: "Z" Number of atoms: 674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 674 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 3, 'TRANS': 80} Chain: "a" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1165 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 10, 'TRANS': 129} Chain: "b" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 879 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 11, 'TRANS': 91} Chain breaks: 1 Chain: "c" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1315 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 20, 'TRANS': 135} Chain: "d" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1461 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 10, 'TRANS': 164} Chain: "e" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 890 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 10, 'TRANS': 96} Chain: "f" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 343 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 40} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "g" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1000 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 11, 'TRANS': 109} Chain: "h" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 867 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "i" Number of atoms: 2710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2710 Classifications: {'peptide': 347} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 328} Chain: "j" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 800 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain breaks: 1 Chain: "k" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 748 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "l" Number of atoms: 4773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4773 Classifications: {'peptide': 603} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 28, 'TRANS': 574} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "m" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 951 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 126} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "n" Number of atoms: 448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 448 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 2, 'TRANS': 53} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "o" Number of atoms: 1062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1062 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 11, 'TRANS': 116} Chain: "p" Number of atoms: 1534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1534 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 17, 'TRANS': 160} Chain: "r" Number of atoms: 3631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3631 Classifications: {'peptide': 459} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 438} Chain: "s" Number of atoms: 2394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2394 Classifications: {'peptide': 303} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 281} Chain breaks: 1 Chain: "u" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1398 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 12, 'TRANS': 158} Chain: "v" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1032 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 116} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "w" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2576 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 16, 'TRANS': 303} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "V" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 71 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 29 Chain: "X" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 143 Unusual residues: {'CDL': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "e" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PLX': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 165 Unusual residues: {'CDL': 1, 'PEE': 1, 'PLX': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 38 Chain: "j" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'PEE': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "l" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 157 Unusual residues: {'CDL': 1, 'PEE': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 45 Chain: "m" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "r" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 302 Unusual residues: {'CDL': 2, 'PEE': 1, 'PLX': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "s" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 79 Unusual residues: {' UQ': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {' UQ:plan-2': 1, ' UQ:plan-3': 1, ' UQ:plan-4': 1, ' UQ:plan-5': 1, ' UQ:plan-6': 1, ' UQ:plan-7': 1, ' UQ:plan-11': 1} Unresolved non-hydrogen planarities: 35 Chain: "u" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 63 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 37 Chain: "w" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "U" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "V" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "a" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "c" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "d" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "e" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "h" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "i" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 62 Classifications: {'water': 62} Link IDs: {None: 61} Chain: "j" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "k" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "l" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Chain: "m" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "n" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "p" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "r" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 84 Classifications: {'water': 84} Link IDs: {None: 83} Chain: "s" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 65 Classifications: {'water': 65} Link IDs: {None: 64} Chain: "u" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "w" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1' ADP w 401 " occ=0.50 ... (25 atoms not shown) pdb=" PB ADP w 401 " occ=0.50 Time building chain proxies: 6.57, per 1000 atoms: 0.17 Number of scatterers: 39049 At special positions: 0 Unit cell: (184.762, 186.911, 141.794, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 285 16.00 P 29 15.00 O 7162 8.00 N 6204 7.00 C 25369 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS V 95 " - pdb=" SG CYS V 115 " distance=2.27 Simple disulfide: pdb=" SG CYS d 113 " - pdb=" SG CYS d 125 " distance=2.04 Simple disulfide: pdb=" SG CYS h 33 " - pdb=" SG CYS h 66 " distance=2.92 Simple disulfide: pdb=" SG CYS h 43 " - pdb=" SG CYS h 56 " distance=2.04 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.47 Conformation dependent library (CDL) restraints added in 1.5 seconds 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8814 Finding SS restraints... Secondary structure from input PDB file: 218 helices and 6 sheets defined 71.0% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'Q' and resid 40 through 45 Processing helix chain 'Q' and resid 46 through 48 No H-bonds generated for 'chain 'Q' and resid 46 through 48' Processing helix chain 'Q' and resid 57 through 61 removed outlier: 4.135A pdb=" N HIS Q 60 " --> pdb=" O GLU Q 57 " (cutoff:3.500A) Processing helix chain 'S' and resid 1 through 4 Processing helix chain 'S' and resid 5 through 30 Proline residue: S 19 - end of helix Processing helix chain 'S' and resid 42 through 56 removed outlier: 4.314A pdb=" N GLY S 56 " --> pdb=" O ARG S 52 " (cutoff:3.500A) Processing helix chain 'S' and resid 65 through 69 Processing helix chain 'U' and resid 3 through 14 Processing helix chain 'U' and resid 16 through 32 Processing helix chain 'U' and resid 33 through 35 No H-bonds generated for 'chain 'U' and resid 33 through 35' Processing helix chain 'U' and resid 38 through 48 Processing helix chain 'U' and resid 78 through 84 Processing helix chain 'V' and resid 3 through 12 removed outlier: 4.112A pdb=" N ILE V 12 " --> pdb=" O LYS V 8 " (cutoff:3.500A) Processing helix chain 'V' and resid 17 through 44 removed outlier: 3.632A pdb=" N LYS V 21 " --> pdb=" O GLU V 17 " (cutoff:3.500A) Processing helix chain 'V' and resid 48 through 82 Processing helix chain 'V' and resid 86 through 106 removed outlier: 3.957A pdb=" N TYR V 90 " --> pdb=" O ASP V 86 " (cutoff:3.500A) Processing helix chain 'V' and resid 107 through 132 Processing helix chain 'W' and resid 33 through 98 Proline residue: W 73 - end of helix Processing helix chain 'W' and resid 99 through 101 No H-bonds generated for 'chain 'W' and resid 99 through 101' Processing helix chain 'W' and resid 120 through 125 removed outlier: 3.531A pdb=" N LEU W 124 " --> pdb=" O MET W 120 " (cutoff:3.500A) Processing helix chain 'W' and resid 129 through 143 removed outlier: 6.200A pdb=" N PHE W 140 " --> pdb=" O ALA W 136 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ILE W 141 " --> pdb=" O THR W 137 " (cutoff:3.500A) Processing helix chain 'X' and resid 75 through 89 Processing helix chain 'X' and resid 94 through 98 Processing helix chain 'X' and resid 111 through 127 Processing helix chain 'X' and resid 131 through 136 Processing helix chain 'X' and resid 140 through 153 Processing helix chain 'Y' and resid 51 through 76 removed outlier: 3.574A pdb=" N LEU Y 55 " --> pdb=" O THR Y 51 " (cutoff:3.500A) Processing helix chain 'Y' and resid 77 through 82 Processing helix chain 'Y' and resid 88 through 92 Processing helix chain 'Z' and resid 18 through 22 removed outlier: 3.741A pdb=" N TRP Z 22 " --> pdb=" O TYR Z 19 " (cutoff:3.500A) Processing helix chain 'Z' and resid 27 through 38 removed outlier: 3.876A pdb=" N THR Z 31 " --> pdb=" O THR Z 27 " (cutoff:3.500A) Processing helix chain 'Z' and resid 46 through 54 removed outlier: 5.222A pdb=" N TRP Z 51 " --> pdb=" O ASN Z 48 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER Z 54 " --> pdb=" O TRP Z 51 " (cutoff:3.500A) Processing helix chain 'Z' and resid 62 through 68 Processing helix chain 'Z' and resid 70 through 90 Processing helix chain 'a' and resid 61 through 93 Proline residue: a 81 - end of helix Processing helix chain 'a' and resid 108 through 113 removed outlier: 3.772A pdb=" N TYR a 112 " --> pdb=" O HIS a 109 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE a 113 " --> pdb=" O TRP a 110 " (cutoff:3.500A) Processing helix chain 'a' and resid 115 through 126 Processing helix chain 'a' and resid 128 through 164 removed outlier: 4.043A pdb=" N ASN a 132 " --> pdb=" O GLY a 128 " (cutoff:3.500A) Processing helix chain 'a' and resid 175 through 179 Processing helix chain 'b' and resid 5 through 26 Processing helix chain 'b' and resid 65 through 74 Processing helix chain 'b' and resid 75 through 89 Processing helix chain 'c' and resid 33 through 37 Processing helix chain 'c' and resid 44 through 55 Processing helix chain 'c' and resid 108 through 112 Processing helix chain 'c' and resid 125 through 150 Processing helix chain 'd' and resid 28 through 59 removed outlier: 3.926A pdb=" N TYR d 32 " --> pdb=" O ASN d 28 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ARG d 43 " --> pdb=" O LEU d 39 " (cutoff:3.500A) Proline residue: d 44 - end of helix removed outlier: 3.681A pdb=" N ASN d 59 " --> pdb=" O GLN d 55 " (cutoff:3.500A) Processing helix chain 'd' and resid 73 through 77 removed outlier: 3.512A pdb=" N CYS d 77 " --> pdb=" O ILE d 74 " (cutoff:3.500A) Processing helix chain 'd' and resid 81 through 118 removed outlier: 3.676A pdb=" N GLY d 118 " --> pdb=" O GLN d 114 " (cutoff:3.500A) Processing helix chain 'd' and resid 120 through 125 Processing helix chain 'd' and resid 125 through 144 Processing helix chain 'd' and resid 151 through 175 Processing helix chain 'e' and resid 65 through 70 removed outlier: 4.131A pdb=" N LYS e 69 " --> pdb=" O ASN e 65 " (cutoff:3.500A) Processing helix chain 'e' and resid 79 through 95 Processing helix chain 'e' and resid 97 through 108 removed outlier: 3.672A pdb=" N SER e 103 " --> pdb=" O LEU e 99 " (cutoff:3.500A) Processing helix chain 'e' and resid 114 through 133 Processing helix chain 'e' and resid 143 through 147 Processing helix chain 'f' and resid 40 through 74 Processing helix chain 'g' and resid 17 through 23 Processing helix chain 'g' and resid 30 through 51 Processing helix chain 'g' and resid 59 through 99 Processing helix chain 'g' and resid 100 through 103 Processing helix chain 'g' and resid 110 through 114 Processing helix chain 'h' and resid 5 through 11 Processing helix chain 'h' and resid 15 through 19 removed outlier: 3.506A pdb=" N THR h 19 " --> pdb=" O ARG h 16 " (cutoff:3.500A) Processing helix chain 'h' and resid 25 through 29 Processing helix chain 'h' and resid 33 through 45 Processing helix chain 'h' and resid 48 through 56 Processing helix chain 'h' and resid 56 through 69 Processing helix chain 'h' and resid 69 through 90 Processing helix chain 'h' and resid 95 through 100 removed outlier: 3.563A pdb=" N GLY h 100 " --> pdb=" O HIS h 97 " (cutoff:3.500A) Processing helix chain 'i' and resid 2 through 23 Processing helix chain 'i' and resid 25 through 45 removed outlier: 3.618A pdb=" N ILE i 41 " --> pdb=" O LEU i 37 " (cutoff:3.500A) Proline residue: i 42 - end of helix Processing helix chain 'i' and resid 49 through 81 Processing helix chain 'i' and resid 91 through 107 Processing helix chain 'i' and resid 113 through 122 removed outlier: 4.248A pdb=" N GLU i 117 " --> pdb=" O PHE i 113 " (cutoff:3.500A) Processing helix chain 'i' and resid 123 through 133 Processing helix chain 'i' and resid 135 through 145 Processing helix chain 'i' and resid 150 through 170 removed outlier: 3.764A pdb=" N LEU i 170 " --> pdb=" O GLY i 166 " (cutoff:3.500A) Processing helix chain 'i' and resid 174 through 192 Processing helix chain 'i' and resid 197 through 222 removed outlier: 3.539A pdb=" N THR i 201 " --> pdb=" O ASN i 197 " (cutoff:3.500A) Processing helix chain 'i' and resid 226 through 231 Processing helix chain 'i' and resid 232 through 236 Processing helix chain 'i' and resid 237 through 252 Processing helix chain 'i' and resid 259 through 273 removed outlier: 4.536A pdb=" N LYS i 263 " --> pdb=" O GLY i 259 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN i 273 " --> pdb=" O GLU i 269 " (cutoff:3.500A) Processing helix chain 'i' and resid 276 through 301 removed outlier: 4.278A pdb=" N LEU i 288 " --> pdb=" O MET i 284 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASN i 289 " --> pdb=" O THR i 285 " (cutoff:3.500A) Processing helix chain 'i' and resid 310 through 315 removed outlier: 3.785A pdb=" N LYS i 314 " --> pdb=" O ASN i 310 " (cutoff:3.500A) Processing helix chain 'i' and resid 325 through 335 Processing helix chain 'i' and resid 336 through 346 Proline residue: i 341 - end of helix Processing helix chain 'j' and resid 2 through 24 Processing helix chain 'j' and resid 25 through 27 No H-bonds generated for 'chain 'j' and resid 25 through 27' Processing helix chain 'j' and resid 52 through 73 removed outlier: 4.322A pdb=" N PHE j 56 " --> pdb=" O SER j 52 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU j 71 " --> pdb=" O LEU j 67 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU j 72 " --> pdb=" O GLU j 68 " (cutoff:3.500A) Processing helix chain 'j' and resid 74 through 79 removed outlier: 3.521A pdb=" N SER j 79 " --> pdb=" O LEU j 75 " (cutoff:3.500A) Processing helix chain 'j' and resid 83 through 108 Processing helix chain 'k' and resid 2 through 22 removed outlier: 3.571A pdb=" N MET k 6 " --> pdb=" O PRO k 2 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TYR k 22 " --> pdb=" O GLY k 18 " (cutoff:3.500A) Processing helix chain 'k' and resid 25 through 51 removed outlier: 3.625A pdb=" N SER k 29 " --> pdb=" O HIS k 25 " (cutoff:3.500A) Processing helix chain 'k' and resid 54 through 56 No H-bonds generated for 'chain 'k' and resid 54 through 56' Processing helix chain 'k' and resid 57 through 86 removed outlier: 4.715A pdb=" N ILE k 61 " --> pdb=" O ASN k 57 " (cutoff:3.500A) Processing helix chain 'k' and resid 89 through 93 removed outlier: 3.598A pdb=" N ASN k 92 " --> pdb=" O TYR k 89 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 15 removed outlier: 4.114A pdb=" N LEU l 12 " --> pdb=" O THR l 8 " (cutoff:3.500A) Processing helix chain 'l' and resid 16 through 22 Processing helix chain 'l' and resid 23 through 24 No H-bonds generated for 'chain 'l' and resid 23 through 24' Processing helix chain 'l' and resid 25 through 29 Processing helix chain 'l' and resid 31 through 58 removed outlier: 4.660A pdb=" N VAL l 49 " --> pdb=" O THR l 45 " (cutoff:3.500A) Proline residue: l 50 - end of helix Processing helix chain 'l' and resid 83 through 108 Proline residue: l 91 - end of helix removed outlier: 3.914A pdb=" N TRP l 106 " --> pdb=" O GLU l 102 " (cutoff:3.500A) Processing helix chain 'l' and resid 113 through 134 removed outlier: 3.512A pdb=" N PHE l 117 " --> pdb=" O PHE l 113 " (cutoff:3.500A) Processing helix chain 'l' and resid 136 through 156 Processing helix chain 'l' and resid 161 through 194 removed outlier: 3.513A pdb=" N ASN l 165 " --> pdb=" O ARG l 161 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLY l 181 " --> pdb=" O ILE l 177 " (cutoff:3.500A) Processing helix chain 'l' and resid 197 through 205 Processing helix chain 'l' and resid 209 through 224 removed outlier: 4.176A pdb=" N LEU l 213 " --> pdb=" O PRO l 209 " (cutoff:3.500A) Processing helix chain 'l' and resid 226 through 230 removed outlier: 3.740A pdb=" N HIS l 230 " --> pdb=" O PHE l 227 " (cutoff:3.500A) Processing helix chain 'l' and resid 231 through 236 Processing helix chain 'l' and resid 237 through 239 No H-bonds generated for 'chain 'l' and resid 237 through 239' Processing helix chain 'l' and resid 240 through 247 Processing helix chain 'l' and resid 254 through 263 Processing helix chain 'l' and resid 263 through 268 Processing helix chain 'l' and resid 271 through 293 Processing helix chain 'l' and resid 297 through 319 Processing helix chain 'l' and resid 321 through 350 removed outlier: 3.731A pdb=" N PHE l 334 " --> pdb=" O CYS l 330 " (cutoff:3.500A) Processing helix chain 'l' and resid 355 through 359 Processing helix chain 'l' and resid 366 through 382 Processing helix chain 'l' and resid 388 through 401 removed outlier: 4.714A pdb=" N LEU l 394 " --> pdb=" O TYR l 390 " (cutoff:3.500A) Processing helix chain 'l' and resid 405 through 432 removed outlier: 3.675A pdb=" N LEU l 432 " --> pdb=" O PHE l 428 " (cutoff:3.500A) Processing helix chain 'l' and resid 447 through 472 removed outlier: 3.692A pdb=" N LEU l 457 " --> pdb=" O SER l 453 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N GLY l 465 " --> pdb=" O SER l 461 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N PHE l 466 " --> pdb=" O ILE l 462 " (cutoff:3.500A) Processing helix chain 'l' and resid 483 through 488 removed outlier: 3.512A pdb=" N MET l 488 " --> pdb=" O LEU l 484 " (cutoff:3.500A) Processing helix chain 'l' and resid 488 through 507 removed outlier: 3.584A pdb=" N THR l 507 " --> pdb=" O GLU l 503 " (cutoff:3.500A) Processing helix chain 'l' and resid 508 through 510 No H-bonds generated for 'chain 'l' and resid 508 through 510' Processing helix chain 'l' and resid 517 through 525 Processing helix chain 'l' and resid 528 through 548 Proline residue: l 537 - end of helix removed outlier: 3.758A pdb=" N MET l 544 " --> pdb=" O HIS l 540 " (cutoff:3.500A) Processing helix chain 'l' and resid 556 through 562 removed outlier: 3.619A pdb=" N LEU l 562 " --> pdb=" O LEU l 558 " (cutoff:3.500A) Processing helix chain 'l' and resid 562 through 579 Processing helix chain 'l' and resid 583 through 603 removed outlier: 3.619A pdb=" N PHE l 602 " --> pdb=" O SER l 598 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN l 603 " --> pdb=" O MET l 599 " (cutoff:3.500A) Processing helix chain 'm' and resid 4 through 22 removed outlier: 3.574A pdb=" N SER m 22 " --> pdb=" O VAL m 18 " (cutoff:3.500A) Processing helix chain 'm' and resid 25 through 48 removed outlier: 3.549A pdb=" N GLY m 29 " --> pdb=" O SER m 25 " (cutoff:3.500A) Processing helix chain 'm' and resid 49 through 75 removed outlier: 3.876A pdb=" N LEU m 61 " --> pdb=" O PHE m 57 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU m 65 " --> pdb=" O LEU m 61 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N VAL m 66 " --> pdb=" O GLY m 62 " (cutoff:3.500A) Processing helix chain 'm' and resid 137 through 145 Processing helix chain 'm' and resid 145 through 150 Processing helix chain 'm' and resid 150 through 173 Processing helix chain 'n' and resid 7 through 12 Processing helix chain 'n' and resid 15 through 33 Processing helix chain 'o' and resid 15 through 18 Processing helix chain 'o' and resid 19 through 24 removed outlier: 3.978A pdb=" N TYR o 23 " --> pdb=" O ASP o 19 " (cutoff:3.500A) Processing helix chain 'o' and resid 26 through 52 Processing helix chain 'o' and resid 62 through 74 Processing helix chain 'o' and resid 76 through 80 Processing helix chain 'o' and resid 83 through 119 Proline residue: o 97 - end of helix Processing helix chain 'p' and resid 11 through 31 Processing helix chain 'p' and resid 33 through 50 Processing helix chain 'p' and resid 56 through 63 Processing helix chain 'p' and resid 64 through 74 Processing helix chain 'p' and resid 100 through 107 Processing helix chain 'p' and resid 108 through 114 removed outlier: 3.895A pdb=" N MET p 114 " --> pdb=" O SER p 110 " (cutoff:3.500A) Processing helix chain 'p' and resid 115 through 144 removed outlier: 3.540A pdb=" N PHE p 119 " --> pdb=" O TYR p 115 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU p 134 " --> pdb=" O ARG p 130 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS p 138 " --> pdb=" O GLU p 134 " (cutoff:3.500A) Processing helix chain 'p' and resid 167 through 172 Processing helix chain 'r' and resid 2 through 17 Proline residue: r 7 - end of helix removed outlier: 4.188A pdb=" N LEU r 12 " --> pdb=" O THR r 8 " (cutoff:3.500A) Proline residue: r 13 - end of helix Processing helix chain 'r' and resid 22 through 39 Processing helix chain 'r' and resid 40 through 43 removed outlier: 3.812A pdb=" N ASN r 43 " --> pdb=" O SER r 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 40 through 43' Processing helix chain 'r' and resid 61 through 81 removed outlier: 4.074A pdb=" N LEU r 65 " --> pdb=" O LEU r 61 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU r 73 " --> pdb=" O THR r 69 " (cutoff:3.500A) Proline residue: r 74 - end of helix Processing helix chain 'r' and resid 88 through 112 removed outlier: 3.527A pdb=" N THR r 111 " --> pdb=" O ILE r 107 " (cutoff:3.500A) Processing helix chain 'r' and resid 114 through 125 Processing helix chain 'r' and resid 125 through 137 removed outlier: 3.735A pdb=" N THR r 129 " --> pdb=" O THR r 125 " (cutoff:3.500A) Processing helix chain 'r' and resid 141 through 172 removed outlier: 4.012A pdb=" N THR r 153 " --> pdb=" O PHE r 149 " (cutoff:3.500A) Proline residue: r 159 - end of helix removed outlier: 3.535A pdb=" N VAL r 162 " --> pdb=" O LEU r 158 " (cutoff:3.500A) Processing helix chain 'r' and resid 175 through 182 Processing helix chain 'r' and resid 189 through 207 removed outlier: 4.562A pdb=" N ALA r 202 " --> pdb=" O ALA r 198 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N PHE r 203 " --> pdb=" O CYS r 199 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS r 206 " --> pdb=" O ALA r 202 " (cutoff:3.500A) Processing helix chain 'r' and resid 214 through 223 removed outlier: 4.126A pdb=" N LYS r 218 " --> pdb=" O LEU r 214 " (cutoff:3.500A) Processing helix chain 'r' and resid 224 through 234 Processing helix chain 'r' and resid 236 through 247 removed outlier: 4.216A pdb=" N GLY r 240 " --> pdb=" O LEU r 236 " (cutoff:3.500A) Processing helix chain 'r' and resid 253 through 278 removed outlier: 4.798A pdb=" N TYR r 259 " --> pdb=" O ASN r 255 " (cutoff:3.500A) Proline residue: r 260 - end of helix removed outlier: 3.991A pdb=" N ILE r 270 " --> pdb=" O MET r 266 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU r 277 " --> pdb=" O SER r 273 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG r 278 " --> pdb=" O SER r 274 " (cutoff:3.500A) Processing helix chain 'r' and resid 281 through 304 Processing helix chain 'r' and resid 305 through 338 removed outlier: 3.698A pdb=" N ARG r 336 " --> pdb=" O THR r 332 " (cutoff:3.500A) Processing helix chain 'r' and resid 352 through 367 Processing helix chain 'r' and resid 372 through 389 Processing helix chain 'r' and resid 391 through 416 removed outlier: 4.336A pdb=" N LEU r 395 " --> pdb=" O ILE r 391 " (cutoff:3.500A) Processing helix chain 'r' and resid 430 through 448 Proline residue: r 443 - end of helix Processing helix chain 'r' and resid 449 through 455 removed outlier: 6.524A pdb=" N LYS r 452 " --> pdb=" O LEU r 449 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU r 455 " --> pdb=" O LYS r 452 " (cutoff:3.500A) Processing helix chain 's' and resid 2 through 32 Proline residue: s 12 - end of helix removed outlier: 3.816A pdb=" N LEU s 22 " --> pdb=" O ALA s 18 " (cutoff:3.500A) Processing helix chain 's' and resid 46 through 58 Processing helix chain 's' and resid 67 through 85 Proline residue: s 75 - end of helix Processing helix chain 's' and resid 100 through 112 Processing helix chain 's' and resid 112 through 123 removed outlier: 4.200A pdb=" N ILE s 116 " --> pdb=" O ALA s 112 " (cutoff:3.500A) Processing helix chain 's' and resid 125 through 155 removed outlier: 3.873A pdb=" N THR s 145 " --> pdb=" O SER s 141 " (cutoff:3.500A) Processing helix chain 's' and resid 163 through 169 removed outlier: 3.698A pdb=" N THR s 167 " --> pdb=" O SER s 163 " (cutoff:3.500A) Processing helix chain 's' and resid 173 through 178 removed outlier: 4.003A pdb=" N THR s 177 " --> pdb=" O TRP s 173 " (cutoff:3.500A) Processing helix chain 's' and resid 178 through 193 removed outlier: 3.652A pdb=" N ALA s 182 " --> pdb=" O SER s 178 " (cutoff:3.500A) Processing helix chain 's' and resid 218 through 243 Processing helix chain 's' and resid 251 through 277 removed outlier: 4.423A pdb=" N TYR s 255 " --> pdb=" O THR s 251 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR s 277 " --> pdb=" O ILE s 273 " (cutoff:3.500A) Processing helix chain 's' and resid 281 through 312 removed outlier: 5.181A pdb=" N LEU s 294 " --> pdb=" O TRP s 290 " (cutoff:3.500A) Proline residue: s 295 - end of helix Proline residue: s 308 - end of helix Processing helix chain 'u' and resid 10 through 14 Processing helix chain 'u' and resid 21 through 36 removed outlier: 4.956A pdb=" N HIS u 30 " --> pdb=" O LYS u 26 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N HIS u 31 " --> pdb=" O ALA u 27 " (cutoff:3.500A) Processing helix chain 'u' and resid 36 through 51 removed outlier: 3.655A pdb=" N ASN u 40 " --> pdb=" O CYS u 36 " (cutoff:3.500A) Processing helix chain 'u' and resid 52 through 55 Processing helix chain 'u' and resid 56 through 92 removed outlier: 4.002A pdb=" N ALA u 79 " --> pdb=" O LYS u 75 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N GLU u 80 " --> pdb=" O ARG u 76 " (cutoff:3.500A) Proline residue: u 81 - end of helix removed outlier: 3.614A pdb=" N SER u 92 " --> pdb=" O CYS u 88 " (cutoff:3.500A) Processing helix chain 'u' and resid 97 through 99 No H-bonds generated for 'chain 'u' and resid 97 through 99' Processing helix chain 'u' and resid 100 through 116 Processing helix chain 'v' and resid 3 through 10 Processing helix chain 'v' and resid 12 through 16 Processing helix chain 'v' and resid 26 through 30 removed outlier: 3.951A pdb=" N GLY v 30 " --> pdb=" O PRO v 27 " (cutoff:3.500A) Processing helix chain 'v' and resid 42 through 49 removed outlier: 3.503A pdb=" N MET v 46 " --> pdb=" O THR v 42 " (cutoff:3.500A) Processing helix chain 'v' and resid 59 through 73 removed outlier: 3.621A pdb=" N LEU v 63 " --> pdb=" O CYS v 59 " (cutoff:3.500A) Processing helix chain 'v' and resid 76 through 79 Processing helix chain 'v' and resid 80 through 125 removed outlier: 3.947A pdb=" N GLN v 84 " --> pdb=" O CYS v 80 " (cutoff:3.500A) Processing helix chain 'w' and resid 39 through 46 Processing helix chain 'w' and resid 69 through 82 Processing helix chain 'w' and resid 93 through 97 Processing helix chain 'w' and resid 113 through 120 Processing helix chain 'w' and resid 126 through 154 Processing helix chain 'w' and resid 166 through 176 removed outlier: 4.148A pdb=" N LEU w 170 " --> pdb=" O ASP w 166 " (cutoff:3.500A) Processing helix chain 'w' and resid 180 through 196 removed outlier: 3.747A pdb=" N VAL w 184 " --> pdb=" O ARG w 180 " (cutoff:3.500A) Processing helix chain 'w' and resid 210 through 222 removed outlier: 3.762A pdb=" N GLY w 222 " --> pdb=" O ILE w 218 " (cutoff:3.500A) Processing helix chain 'w' and resid 225 through 229 Processing helix chain 'w' and resid 230 through 244 Processing helix chain 'w' and resid 244 through 251 Processing helix chain 'w' and resid 265 through 276 removed outlier: 3.940A pdb=" N VAL w 269 " --> pdb=" O ASP w 265 " (cutoff:3.500A) Processing helix chain 'w' and resid 287 through 299 Processing helix chain 'w' and resid 300 through 305 removed outlier: 3.615A pdb=" N VAL w 304 " --> pdb=" O ASN w 300 " (cutoff:3.500A) Processing helix chain 'w' and resid 306 through 310 removed outlier: 3.924A pdb=" N THR w 309 " --> pdb=" O ASN w 306 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE w 310 " --> pdb=" O TYR w 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 306 through 310' Processing helix chain 'w' and resid 320 through 333 Processing helix chain 'w' and resid 351 through 355 Processing sheet with id=AA1, first strand: chain 'U' and resid 57 through 58 removed outlier: 6.724A pdb=" N LEU U 57 " --> pdb=" O VAL u 131 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'a' and resid 97 through 98 removed outlier: 5.670A pdb=" N GLU a 97 " --> pdb=" O TYR d 63 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'b' and resid 97 through 98 removed outlier: 7.317A pdb=" N ASN l 65 " --> pdb=" O PHE l 80 " (cutoff:3.500A) removed outlier: 9.177A pdb=" N PHE l 80 " --> pdb=" O ASN l 65 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N HIS l 67 " --> pdb=" O LEU l 78 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LEU l 78 " --> pdb=" O HIS l 67 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N MET l 69 " --> pdb=" O LEU l 76 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'i' and resid 307 through 308 Processing sheet with id=AA5, first strand: chain 'r' and resid 50 through 51 Processing sheet with id=AA6, first strand: chain 'w' and resid 84 through 86 removed outlier: 6.374A pdb=" N ARG w 84 " --> pdb=" O VAL w 158 " (cutoff:3.500A) 2317 hydrogen bonds defined for protein. 6723 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.48 Time building geometry restraints manager: 4.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 6132 1.32 - 1.46: 14885 1.46 - 1.60: 18115 1.60 - 1.74: 56 1.74 - 1.89: 516 Bond restraints: 39704 Sorted by residual: bond pdb=" C3' ADP w 401 " pdb=" C4' ADP w 401 " ideal model delta sigma weight residual 1.524 1.299 0.225 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C18 UQ s 402 " pdb=" C19 UQ s 402 " ideal model delta sigma weight residual 1.336 1.556 -0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" CB7 CDL i 401 " pdb=" OB8 CDL i 401 " ideal model delta sigma weight residual 1.334 1.454 -0.120 1.10e-02 8.26e+03 1.19e+02 bond pdb=" CB7 CDL a 201 " pdb=" OB8 CDL a 201 " ideal model delta sigma weight residual 1.334 1.452 -0.118 1.10e-02 8.26e+03 1.16e+02 bond pdb=" CA7 CDL a 201 " pdb=" OA8 CDL a 201 " ideal model delta sigma weight residual 1.334 1.452 -0.118 1.10e-02 8.26e+03 1.14e+02 ... (remaining 39699 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.38: 52956 3.38 - 6.76: 596 6.76 - 10.14: 78 10.14 - 13.52: 18 13.52 - 16.89: 10 Bond angle restraints: 53658 Sorted by residual: angle pdb=" C11 CDL u 201 " pdb=" CA5 CDL u 201 " pdb=" OA6 CDL u 201 " ideal model delta sigma weight residual 111.33 121.31 -9.98 1.32e+00 5.72e-01 5.70e+01 angle pdb=" C11 CDL i 401 " pdb=" CA5 CDL i 401 " pdb=" OA6 CDL i 401 " ideal model delta sigma weight residual 111.33 121.24 -9.91 1.32e+00 5.72e-01 5.62e+01 angle pdb=" N MET i 89 " pdb=" CA MET i 89 " pdb=" C MET i 89 " ideal model delta sigma weight residual 111.28 119.17 -7.89 1.09e+00 8.42e-01 5.24e+01 angle pdb=" C51 CDL a 201 " pdb=" CB5 CDL a 201 " pdb=" OB6 CDL a 201 " ideal model delta sigma weight residual 111.33 120.45 -9.12 1.32e+00 5.72e-01 4.76e+01 angle pdb=" C11 CDL r 503 " pdb=" CA5 CDL r 503 " pdb=" OA6 CDL r 503 " ideal model delta sigma weight residual 111.33 120.29 -8.96 1.32e+00 5.72e-01 4.60e+01 ... (remaining 53653 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.58: 23136 33.58 - 67.16: 703 67.16 - 100.74: 65 100.74 - 134.33: 9 134.33 - 167.91: 9 Dihedral angle restraints: 23922 sinusoidal: 10284 harmonic: 13638 Sorted by residual: dihedral pdb=" C5' ADP w 401 " pdb=" O5' ADP w 401 " pdb=" PA ADP w 401 " pdb=" O2A ADP w 401 " ideal model delta sinusoidal sigma weight residual -60.00 107.91 -167.91 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" CA MET s 91 " pdb=" C MET s 91 " pdb=" N PRO s 92 " pdb=" CA PRO s 92 " ideal model delta harmonic sigma weight residual 0.00 -33.97 33.97 0 5.00e+00 4.00e-02 4.62e+01 dihedral pdb=" CA THR r 111 " pdb=" C THR r 111 " pdb=" N ALA r 112 " pdb=" CA ALA r 112 " ideal model delta harmonic sigma weight residual 180.00 153.37 26.63 0 5.00e+00 4.00e-02 2.84e+01 ... (remaining 23919 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 5431 0.085 - 0.170: 368 0.170 - 0.255: 27 0.255 - 0.341: 7 0.341 - 0.426: 2 Chirality restraints: 5835 Sorted by residual: chirality pdb=" CA TRP u 86 " pdb=" N TRP u 86 " pdb=" C TRP u 86 " pdb=" CB TRP u 86 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.53e+00 chirality pdb=" C6 PLX a 202 " pdb=" C7 PLX a 202 " pdb=" O6 PLX a 202 " pdb=" O7 PLX a 202 " both_signs ideal model delta sigma weight residual False 2.01 2.39 -0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" C6 PLX i 402 " pdb=" C7 PLX i 402 " pdb=" O6 PLX i 402 " pdb=" O7 PLX i 402 " both_signs ideal model delta sigma weight residual False 2.01 2.35 -0.34 2.00e-01 2.50e+01 2.88e+00 ... (remaining 5832 not shown) Planarity restraints: 6566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 UQ s 402 " -0.432 2.00e-02 2.50e+03 4.40e-01 2.42e+03 pdb=" C11 UQ s 402 " -0.055 2.00e-02 2.50e+03 pdb=" C7 UQ s 402 " -0.513 2.00e-02 2.50e+03 pdb=" C8 UQ s 402 " 0.581 2.00e-02 2.50e+03 pdb=" C9 UQ s 402 " 0.420 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 UQ s 402 " -0.191 2.00e-02 2.50e+03 2.21e-01 6.09e+02 pdb=" C18 UQ s 402 " 0.132 2.00e-02 2.50e+03 pdb=" C19 UQ s 402 " 0.351 2.00e-02 2.50e+03 pdb=" C20 UQ s 402 " -0.038 2.00e-02 2.50e+03 pdb=" C21 UQ s 402 " -0.255 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 UQ s 402 " 0.073 2.00e-02 2.50e+03 1.71e-01 3.67e+02 pdb=" C13 UQ s 402 " 0.013 2.00e-02 2.50e+03 pdb=" C14 UQ s 402 " -0.330 2.00e-02 2.50e+03 pdb=" C15 UQ s 402 " 0.082 2.00e-02 2.50e+03 pdb=" C16 UQ s 402 " 0.162 2.00e-02 2.50e+03 ... (remaining 6563 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 563 2.64 - 3.21: 35802 3.21 - 3.77: 63529 3.77 - 4.34: 89755 4.34 - 4.90: 144629 Nonbonded interactions: 334278 Sorted by model distance: nonbonded pdb=" N GLN u 103 " pdb=" OE1 GLN u 103 " model vdw 2.079 3.120 nonbonded pdb=" OH TYR o 23 " pdb=" OE1 GLU p 68 " model vdw 2.079 3.040 nonbonded pdb=" O HOH l 821 " pdb=" O HOH l 824 " model vdw 2.090 3.040 nonbonded pdb=" O PRO s 316 " pdb=" O HOH s 501 " model vdw 2.091 3.040 nonbonded pdb=" O THR s 193 " pdb=" O HOH s 502 " model vdw 2.113 3.040 ... (remaining 334273 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: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.340 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: 0.040 Extract box with map and model: 1.230 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 31.610 Find NCS groups from input model: 0.330 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: 0.000 Load rotamer database and sin/cos tables:7.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 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 : 0.008 0.887 39709 Z= 0.457 Angle : 0.914 34.554 53666 Z= 0.477 Chirality : 0.047 0.426 5835 Planarity : 0.008 0.440 6566 Dihedral : 16.093 167.908 15096 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.01 % Favored : 95.90 % Rotamer: Outliers : 0.20 % Allowed : 0.32 % Favored : 99.48 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.35 % 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 are not related in a simple way. whole: 1.41 (0.12), residues: 4586 helix: 1.74 (0.09), residues: 2933 sheet: -0.44 (1.04), residues: 25 loop : -0.50 (0.15), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG g 51 TYR 0.024 0.001 TYR e 128 PHE 0.030 0.002 PHE l 498 TRP 0.054 0.001 TRP l 68 HIS 0.005 0.001 HIS p 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00703 / 0.40 (39704) covalent geometry : angle 0.89908 / 0.47 (53658) SS BOND : bond 0.45950 / 14.87 ( 4) SS BOND : angle 13.27843 / 8.67 ( 8) hydrogen bonds : bond 0.13903 / 9.28 ( 2317) hydrogen bonds : angle 5.40853 / 3.83 ( 6723) Misc. bond : bond 0.00091 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 823 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 815 time to evaluate : 1.438 Fit side-chains REVERT: X 77 GLU cc_start: 0.7904 (tp30) cc_final: 0.7298 (tp30) REVERT: g 92 MET cc_start: 0.8639 (ttp) cc_final: 0.8436 (ttm) REVERT: m 57 PHE cc_start: 0.7697 (t80) cc_final: 0.7102 (t80) REVERT: s 51 ASP cc_start: 0.8016 (m-30) cc_final: 0.7786 (m-30) REVERT: w 62 VAL cc_start: 0.8039 (t) cc_final: 0.7835 (m) REVERT: w 120 ASP cc_start: 0.7173 (t70) cc_final: 0.6753 (t0) outliers start: 8 outliers final: 4 residues processed: 819 average time/residue: 0.7581 time to fit residues: 741.3825 Evaluate side-chains 678 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 674 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain i residue 278 MET Chi-restraints excluded: chain l residue 597 ILE Chi-restraints excluded: chain v residue 8 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 432 optimal weight: 3.9990 chunk 197 optimal weight: 0.6980 chunk 388 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 5.9990 chunk 401 optimal weight: 6.9990 chunk 424 optimal weight: 5.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... V 129 GLN X 115 GLN Y 83 HIS c 127 ASN d 131 GLN e 65 ASN f 61 GLN h 27 HIS i 49 ASN i 91 ASN i 150 ASN ** i 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 59 GLN l 175 ASN l 205 ASN ** l 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 518 GLN n 14 HIS p 141 GLN r 51 ASN r 175 ASN r 390 ASN s 230 ASN s 287 HIS u 77 HIS u 95 GLN ** v 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 85 HIS ** v 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 107 GLN w 306 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.139400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.115854 restraints weight = 47581.056| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.27 r_work: 0.3118 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2998 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 39709 Z= 0.160 Angle : 0.619 9.071 53666 Z= 0.315 Chirality : 0.043 0.193 5835 Planarity : 0.005 0.058 6566 Dihedral : 14.646 168.107 5977 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.69 % Favored : 96.27 % Rotamer: Outliers : 2.02 % Allowed : 8.29 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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 are not related in a simple way. whole: 1.75 (0.12), residues: 4586 helix: 1.99 (0.09), residues: 2949 sheet: -0.40 (1.06), residues: 25 loop : -0.36 (0.16), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG n 30 TYR 0.020 0.002 TYR l 422 PHE 0.029 0.002 PHE i 292 TRP 0.028 0.001 TRP l 68 HIS 0.006 0.001 HIS v 4 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (39704) covalent geometry : angle 0.61911 / 0.32 (53658) SS BOND : bond 0.00834 / 0.30 ( 4) SS BOND : angle 1.51194 / 0.94 ( 8) hydrogen bonds : bond 0.05733 / 3.83 ( 2317) hydrogen bonds : angle 4.37642 / 3.14 ( 6723) Misc. bond : bond 0.00061 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 800 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 718 time to evaluate : 1.514 Fit side-chains revert: symmetry clash REVERT: Q 46 GLN cc_start: 0.8198 (mt0) cc_final: 0.7910 (mt0) REVERT: S 4 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7700 (mp0) REVERT: S 31 ASN cc_start: 0.8708 (m-40) cc_final: 0.8314 (m110) REVERT: a 163 ARG cc_start: 0.8917 (OUTLIER) cc_final: 0.8136 (mtp180) REVERT: c 141 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8733 (mp) REVERT: c 185 GLU cc_start: 0.6964 (OUTLIER) cc_final: 0.6254 (tm-30) REVERT: e 143 ASP cc_start: 0.8259 (p0) cc_final: 0.8045 (p0) REVERT: h 6 VAL cc_start: 0.9036 (t) cc_final: 0.8770 (m) REVERT: h 81 ARG cc_start: 0.7678 (ttp-110) cc_final: 0.7461 (mtm-85) REVERT: i 100 MET cc_start: 0.8748 (OUTLIER) cc_final: 0.8318 (mtm) REVERT: i 147 GLN cc_start: 0.8555 (pm20) cc_final: 0.8266 (pm20) REVERT: i 281 LEU cc_start: 0.8691 (mp) cc_final: 0.8463 (mp) REVERT: l 410 LEU cc_start: 0.8364 (mt) cc_final: 0.8095 (mt) REVERT: m 31 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8022 (mt) REVERT: m 57 PHE cc_start: 0.8020 (t80) cc_final: 0.7372 (t80) REVERT: p 44 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.8217 (tpt) REVERT: s 51 ASP cc_start: 0.8348 (m-30) cc_final: 0.7896 (m-30) REVERT: s 134 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.7472 (mpt-90) REVERT: v 105 GLU cc_start: 0.8011 (tm-30) cc_final: 0.7766 (tm-30) REVERT: w 120 ASP cc_start: 0.7661 (t70) cc_final: 0.7282 (t0) outliers start: 82 outliers final: 35 residues processed: 749 average time/residue: 0.7574 time to fit residues: 679.5191 Evaluate side-chains 712 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 669 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 4 GLU Chi-restraints excluded: chain S residue 52 ARG Chi-restraints excluded: chain S residue 69 ILE Chi-restraints excluded: chain U residue 18 VAL Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 77 SER Chi-restraints excluded: chain V residue 4 THR Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain Z residue 24 ILE Chi-restraints excluded: chain Z residue 31 THR Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain a residue 163 ARG Chi-restraints excluded: chain c residue 141 LEU Chi-restraints excluded: chain c residue 185 GLU Chi-restraints excluded: chain d residue 33 LEU Chi-restraints excluded: chain d residue 36 ILE Chi-restraints excluded: chain d residue 52 ILE Chi-restraints excluded: chain d residue 55 GLN Chi-restraints excluded: chain e residue 62 GLU Chi-restraints excluded: chain e residue 125 LEU Chi-restraints excluded: chain f residue 48 LEU Chi-restraints excluded: chain i residue 100 MET Chi-restraints excluded: chain i residue 257 LEU Chi-restraints excluded: chain i residue 323 MET Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 66 ASP Chi-restraints excluded: chain l residue 191 THR Chi-restraints excluded: chain l residue 308 SER Chi-restraints excluded: chain l residue 544 MET Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain m residue 31 LEU Chi-restraints excluded: chain o residue 88 LEU Chi-restraints excluded: chain p residue 21 LYS Chi-restraints excluded: chain p residue 44 MET Chi-restraints excluded: chain p residue 57 MET Chi-restraints excluded: chain r residue 138 ASN Chi-restraints excluded: chain r residue 337 VAL Chi-restraints excluded: chain s residue 7 LEU Chi-restraints excluded: chain s residue 134 ARG Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain w residue 257 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 152 optimal weight: 4.9990 chunk 320 optimal weight: 6.9990 chunk 146 optimal weight: 7.9990 chunk 8 optimal weight: 0.6980 chunk 132 optimal weight: 7.9990 chunk 72 optimal weight: 7.9990 chunk 143 optimal weight: 6.9990 chunk 422 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 256 optimal weight: 6.9990 chunk 380 optimal weight: 7.9990 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... V 129 GLN X 115 GLN c 127 ASN ** e 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 132 ASN f 61 GLN g 63 GLN i 310 ASN l 59 GLN l 320 ASN ** l 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 126 ASN p 141 GLN r 304 GLN s 287 HIS u 77 HIS ** v 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 107 GLN w 219 GLN w 306 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.133060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.109204 restraints weight = 47327.029| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 1.19 r_work: 0.3042 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2915 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2915 r_free = 0.2915 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2915 r_free = 0.2915 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2915 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8992 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 39709 Z= 0.309 Angle : 0.778 13.613 53666 Z= 0.395 Chirality : 0.051 0.287 5835 Planarity : 0.006 0.056 6566 Dihedral : 14.336 172.014 5968 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.12 % Favored : 95.84 % Rotamer: Outliers : 3.42 % Allowed : 10.56 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 are not related in a simple way. whole: 1.21 (0.12), residues: 4586 helix: 1.56 (0.09), residues: 2965 sheet: -0.62 (1.15), residues: 23 loop : -0.57 (0.16), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG l 357 TYR 0.034 0.003 TYR c 184 PHE 0.029 0.003 PHE i 292 TRP 0.028 0.002 TRP l 68 HIS 0.010 0.002 HIS c 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00762 / 0.31 (39704) covalent geometry : angle 0.77805 / 0.39 (53658) SS BOND : bond 0.00851 / 0.40 ( 4) SS BOND : angle 2.28333 / 1.44 ( 8) hydrogen bonds : bond 0.07458 / 5.00 ( 2317) hydrogen bonds : angle 4.59405 / 3.33 ( 6723) Misc. bond : bond 0.00123 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 820 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 681 time to evaluate : 1.440 Fit side-chains revert: symmetry clash REVERT: S 4 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7778 (mp0) REVERT: S 31 ASN cc_start: 0.8733 (m-40) cc_final: 0.8242 (m110) REVERT: V 17 GLU cc_start: 0.6679 (tt0) cc_final: 0.6448 (tt0) REVERT: Y 51 THR cc_start: 0.8296 (m) cc_final: 0.8011 (p) REVERT: a 148 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7700 (mp0) REVERT: a 163 ARG cc_start: 0.9035 (OUTLIER) cc_final: 0.8127 (mtp180) REVERT: d 55 GLN cc_start: 0.8977 (OUTLIER) cc_final: 0.8015 (mp10) REVERT: e 146 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8271 (ttpp) REVERT: g 4 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.8313 (mmm) REVERT: h 80 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.8172 (tttt) REVERT: i 100 MET cc_start: 0.8913 (OUTLIER) cc_final: 0.8560 (mtm) REVERT: i 236 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8243 (tttp) REVERT: l 331 MET cc_start: 0.9122 (OUTLIER) cc_final: 0.8098 (mmp) REVERT: l 410 LEU cc_start: 0.8600 (mt) cc_final: 0.8389 (mt) REVERT: l 580 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.6808 (mp-120) REVERT: m 3 MET cc_start: 0.2548 (mmm) cc_final: 0.2245 (mmt) REVERT: m 31 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8198 (mt) REVERT: m 57 PHE cc_start: 0.8113 (t80) cc_final: 0.7382 (t80) REVERT: p 44 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.8336 (tpt) REVERT: p 139 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.6852 (tm-30) REVERT: r 398 MET cc_start: 0.8144 (tpt) cc_final: 0.7924 (tpt) REVERT: s 1 MET cc_start: 0.7647 (OUTLIER) cc_final: 0.7271 (mmm) REVERT: s 51 ASP cc_start: 0.8477 (m-30) cc_final: 0.8044 (m-30) REVERT: s 134 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7762 (mpt-90) REVERT: v 109 LEU cc_start: 0.7584 (mt) cc_final: 0.7098 (mt) REVERT: w 116 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.7947 (mtpp) REVERT: w 120 ASP cc_start: 0.7795 (t70) cc_final: 0.7291 (t70) REVERT: w 184 VAL cc_start: 0.8494 (OUTLIER) cc_final: 0.8194 (t) REVERT: w 185 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7690 (mp0) outliers start: 139 outliers final: 62 residues processed: 748 average time/residue: 0.7180 time to fit residues: 643.2861 Evaluate side-chains 735 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 654 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 4 GLU Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 52 ARG Chi-restraints excluded: chain S residue 69 ILE Chi-restraints excluded: chain U residue 18 VAL Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 77 SER Chi-restraints excluded: chain V residue 4 THR Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain Z residue 24 ILE Chi-restraints excluded: chain Z residue 31 THR Chi-restraints excluded: chain a residue 148 GLU Chi-restraints excluded: chain a residue 163 ARG Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 141 LEU Chi-restraints excluded: chain c residue 185 GLU Chi-restraints excluded: chain d residue 33 LEU Chi-restraints excluded: chain d residue 36 ILE Chi-restraints excluded: chain d residue 52 ILE Chi-restraints excluded: chain d residue 55 GLN Chi-restraints excluded: chain d residue 127 LYS Chi-restraints excluded: chain e residue 116 GLU Chi-restraints excluded: chain e residue 125 LEU Chi-restraints excluded: chain e residue 146 LYS Chi-restraints excluded: chain f residue 48 LEU Chi-restraints excluded: chain g residue 4 MET Chi-restraints excluded: chain g residue 28 LEU Chi-restraints excluded: chain h residue 80 LYS Chi-restraints excluded: chain i residue 4 ILE Chi-restraints excluded: chain i residue 100 MET Chi-restraints excluded: chain i residue 236 LYS Chi-restraints excluded: chain i residue 239 VAL Chi-restraints excluded: chain i residue 257 LEU Chi-restraints excluded: chain i residue 299 SER Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 66 ASP Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 33 LEU Chi-restraints excluded: chain l residue 190 LEU Chi-restraints excluded: chain l residue 191 THR Chi-restraints excluded: chain l residue 308 SER Chi-restraints excluded: chain l residue 331 MET Chi-restraints excluded: chain l residue 469 SER Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 580 GLN Chi-restraints excluded: chain m residue 31 LEU Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain o residue 88 LEU Chi-restraints excluded: chain p residue 21 LYS Chi-restraints excluded: chain p residue 44 MET Chi-restraints excluded: chain p residue 57 MET Chi-restraints excluded: chain p residue 139 GLN Chi-restraints excluded: chain p residue 151 THR Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 303 ILE Chi-restraints excluded: chain r residue 337 VAL Chi-restraints excluded: chain r residue 401 MET Chi-restraints excluded: chain s residue 1 MET Chi-restraints excluded: chain s residue 7 LEU Chi-restraints excluded: chain s residue 10 ILE Chi-restraints excluded: chain s residue 57 THR Chi-restraints excluded: chain s residue 109 SER Chi-restraints excluded: chain s residue 134 ARG Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain u residue 6 GLU Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 63 VAL Chi-restraints excluded: chain u residue 78 CYS Chi-restraints excluded: chain u residue 111 VAL Chi-restraints excluded: chain u residue 139 GLU Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain w residue 76 GLU Chi-restraints excluded: chain w residue 116 LYS Chi-restraints excluded: chain w residue 184 VAL Chi-restraints excluded: chain w residue 185 GLU Chi-restraints excluded: chain w residue 227 MET Chi-restraints excluded: chain w residue 257 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 110 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 102 optimal weight: 0.8980 chunk 186 optimal weight: 1.9990 chunk 304 optimal weight: 3.9990 chunk 421 optimal weight: 0.9980 chunk 386 optimal weight: 1.9990 chunk 424 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 149 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... V 129 GLN c 127 ASN ** e 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 145 ASN g 63 GLN i 49 ASN i 221 HIS i 322 GLN l 320 ASN ** l 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 126 ASN p 75 GLN p 141 GLN ** v 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 107 GLN w 306 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.138462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.115250 restraints weight = 47526.726| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.26 r_work: 0.3123 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3003 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3003 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 39709 Z= 0.131 Angle : 0.572 9.205 53666 Z= 0.292 Chirality : 0.041 0.190 5835 Planarity : 0.005 0.049 6566 Dihedral : 13.305 177.912 5968 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.69 % Favored : 96.27 % Rotamer: Outliers : 2.68 % Allowed : 12.26 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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 are not related in a simple way. whole: 1.73 (0.13), residues: 4586 helix: 1.99 (0.09), residues: 2970 sheet: -1.04 (1.03), residues: 25 loop : -0.41 (0.16), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG n 47 TYR 0.021 0.001 TYR l 422 PHE 0.029 0.001 PHE i 292 TRP 0.020 0.001 TRP l 144 HIS 0.006 0.001 HIS p 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (39704) covalent geometry : angle 0.57127 / 0.29 (53658) SS BOND : bond 0.00446 / 0.22 ( 4) SS BOND : angle 2.00357 / 1.28 ( 8) hydrogen bonds : bond 0.05122 / 3.42 ( 2317) hydrogen bonds : angle 4.23719 / 3.07 ( 6723) Misc. bond : bond 0.00045 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 813 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 704 time to evaluate : 1.519 Fit side-chains REVERT: S 4 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.8058 (mm-30) REVERT: S 31 ASN cc_start: 0.8712 (m-40) cc_final: 0.8284 (m110) REVERT: X 81 ASP cc_start: 0.8463 (m-30) cc_final: 0.8190 (m-30) REVERT: Y 51 THR cc_start: 0.8215 (m) cc_final: 0.7953 (p) REVERT: a 69 LYS cc_start: 0.8854 (mttp) cc_final: 0.8652 (mttt) REVERT: a 148 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7622 (mp0) REVERT: a 153 GLU cc_start: 0.8713 (tp30) cc_final: 0.8392 (tt0) REVERT: a 163 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.8168 (mtp180) REVERT: b 115 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7336 (pm20) REVERT: c 185 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6261 (tm-30) REVERT: d 55 GLN cc_start: 0.8827 (OUTLIER) cc_final: 0.7905 (mp10) REVERT: h 6 VAL cc_start: 0.9034 (t) cc_final: 0.8744 (m) REVERT: h 80 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.8098 (tttm) REVERT: i 90 PHE cc_start: 0.6411 (m-80) cc_final: 0.6067 (m-80) REVERT: i 100 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8535 (mtm) REVERT: i 147 GLN cc_start: 0.8553 (pm20) cc_final: 0.8282 (pm20) REVERT: j 66 ASP cc_start: 0.8599 (OUTLIER) cc_final: 0.8163 (m-30) REVERT: l 45 THR cc_start: 0.8909 (t) cc_final: 0.8622 (m) REVERT: l 314 MET cc_start: 0.8902 (mmm) cc_final: 0.8699 (mmt) REVERT: l 331 MET cc_start: 0.9062 (OUTLIER) cc_final: 0.8061 (mmp) REVERT: m 31 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7964 (mt) REVERT: m 57 PHE cc_start: 0.8051 (t80) cc_final: 0.7307 (t80) REVERT: p 135 ARG cc_start: 0.7029 (OUTLIER) cc_final: 0.6145 (mtm110) REVERT: p 176 GLU cc_start: 0.7514 (tp30) cc_final: 0.7133 (pm20) REVERT: r 398 MET cc_start: 0.8026 (tpt) cc_final: 0.7802 (tpt) REVERT: s 1 MET cc_start: 0.7600 (OUTLIER) cc_final: 0.7211 (mmm) REVERT: s 51 ASP cc_start: 0.8374 (m-30) cc_final: 0.7902 (m-30) REVERT: s 134 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.7527 (mpt-90) REVERT: v 54 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.8205 (pp30) REVERT: v 109 LEU cc_start: 0.7412 (mt) cc_final: 0.6924 (mt) REVERT: w 116 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.7816 (mtpp) REVERT: w 120 ASP cc_start: 0.7659 (t70) cc_final: 0.7375 (t0) REVERT: w 272 ASP cc_start: 0.7787 (m-30) cc_final: 0.7547 (m-30) outliers start: 109 outliers final: 36 residues processed: 755 average time/residue: 0.7109 time to fit residues: 645.3906 Evaluate side-chains 728 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 676 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 4 GLU Chi-restraints excluded: chain S residue 66 LEU Chi-restraints excluded: chain S residue 69 ILE Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain Z residue 24 ILE Chi-restraints excluded: chain Z residue 39 ARG Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain a residue 148 GLU Chi-restraints excluded: chain a residue 163 ARG Chi-restraints excluded: chain b residue 115 GLU Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 185 GLU Chi-restraints excluded: chain d residue 52 ILE Chi-restraints excluded: chain d residue 55 GLN Chi-restraints excluded: chain d residue 127 LYS Chi-restraints excluded: chain e residue 125 LEU Chi-restraints excluded: chain f residue 48 LEU Chi-restraints excluded: chain g residue 28 LEU Chi-restraints excluded: chain h residue 80 LYS Chi-restraints excluded: chain i residue 100 MET Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 60 ILE Chi-restraints excluded: chain j residue 66 ASP Chi-restraints excluded: chain l residue 308 SER Chi-restraints excluded: chain l residue 331 MET Chi-restraints excluded: chain l residue 469 SER Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain m residue 31 LEU Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain o residue 88 LEU Chi-restraints excluded: chain p residue 57 MET Chi-restraints excluded: chain p residue 135 ARG Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 122 PHE Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 337 VAL Chi-restraints excluded: chain s residue 1 MET Chi-restraints excluded: chain s residue 10 ILE Chi-restraints excluded: chain s residue 91 MET Chi-restraints excluded: chain s residue 134 ARG Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 100 CYS Chi-restraints excluded: chain u residue 111 VAL Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain w residue 116 LYS Chi-restraints excluded: chain w residue 184 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 380 optimal weight: 6.9990 chunk 345 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 404 optimal weight: 7.9990 chunk 304 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 chunk 347 optimal weight: 0.9990 chunk 242 optimal weight: 8.9990 chunk 326 optimal weight: 8.9990 chunk 60 optimal weight: 7.9990 chunk 221 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... V 129 GLN X 101 ASN c 127 ASN ** e 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 145 ASN i 49 ASN l 320 ASN ** l 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 405 ASN o 126 ASN p 141 GLN r 390 ASN s 194 ASN u 77 HIS v 4 HIS ** v 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 107 GLN w 219 GLN w 306 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.136908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.113497 restraints weight = 47140.463| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.25 r_work: 0.3096 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2975 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.2975 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 39709 Z= 0.162 Angle : 0.604 9.398 53666 Z= 0.306 Chirality : 0.042 0.196 5835 Planarity : 0.005 0.050 6566 Dihedral : 12.953 177.436 5968 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.90 % Favored : 96.05 % Rotamer: Outliers : 3.05 % Allowed : 13.04 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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 are not related in a simple way. whole: 1.76 (0.13), residues: 4586 helix: 1.99 (0.09), residues: 2987 sheet: -1.04 (1.03), residues: 25 loop : -0.38 (0.16), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG g 51 TYR 0.022 0.002 TYR m 70 PHE 0.029 0.002 PHE i 292 TRP 0.016 0.001 TRP u 86 HIS 0.010 0.001 HIS p 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (39704) covalent geometry : angle 0.60320 / 0.31 (53658) SS BOND : bond 0.00578 / 0.28 ( 4) SS BOND : angle 1.69554 / 1.06 ( 8) hydrogen bonds : bond 0.05543 / 3.71 ( 2317) hydrogen bonds : angle 4.24094 / 3.08 ( 6723) Misc. bond : bond 0.00102 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 812 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 688 time to evaluate : 1.411 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 4 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.8083 (mm-30) REVERT: S 31 ASN cc_start: 0.8718 (m-40) cc_final: 0.8244 (m110) REVERT: S 66 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7849 (mp) REVERT: W 131 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6724 (pm20) REVERT: X 81 ASP cc_start: 0.8508 (m-30) cc_final: 0.8214 (m-30) REVERT: Y 51 THR cc_start: 0.8234 (m) cc_final: 0.7940 (p) REVERT: Z 31 THR cc_start: 0.8505 (OUTLIER) cc_final: 0.8283 (t) REVERT: a 69 LYS cc_start: 0.8857 (mttp) cc_final: 0.8646 (mttt) REVERT: a 148 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7696 (mp0) REVERT: a 163 ARG cc_start: 0.8940 (OUTLIER) cc_final: 0.8168 (mtp180) REVERT: b 115 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7291 (pm20) REVERT: c 185 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6368 (tm-30) REVERT: d 38 ASP cc_start: 0.7629 (OUTLIER) cc_final: 0.7404 (t70) REVERT: d 55 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.7922 (mp10) REVERT: e 116 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8233 (mt-10) REVERT: e 146 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8172 (ttpp) REVERT: f 64 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7619 (mp0) REVERT: h 80 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.8082 (tttm) REVERT: i 90 PHE cc_start: 0.6573 (m-80) cc_final: 0.6365 (m-80) REVERT: i 100 MET cc_start: 0.8863 (OUTLIER) cc_final: 0.8535 (mtm) REVERT: j 66 ASP cc_start: 0.8596 (OUTLIER) cc_final: 0.7862 (m-30) REVERT: l 45 THR cc_start: 0.8944 (t) cc_final: 0.8674 (m) REVERT: l 314 MET cc_start: 0.8924 (mmm) cc_final: 0.8714 (mmt) REVERT: l 331 MET cc_start: 0.9077 (OUTLIER) cc_final: 0.8117 (mmp) REVERT: l 580 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.6900 (mp-120) REVERT: m 31 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8024 (mt) REVERT: m 57 PHE cc_start: 0.8099 (t80) cc_final: 0.7332 (t80) REVERT: p 44 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.8270 (tpt) REVERT: p 135 ARG cc_start: 0.7052 (OUTLIER) cc_final: 0.6152 (mtm110) REVERT: p 139 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.6322 (tm-30) REVERT: p 176 GLU cc_start: 0.7507 (tp30) cc_final: 0.7018 (pm20) REVERT: r 398 MET cc_start: 0.8040 (tpt) cc_final: 0.7804 (tpt) REVERT: s 1 MET cc_start: 0.7627 (OUTLIER) cc_final: 0.7245 (mmm) REVERT: s 51 ASP cc_start: 0.8374 (m-30) cc_final: 0.7882 (m-30) REVERT: s 134 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7577 (mpt-90) REVERT: v 109 LEU cc_start: 0.7452 (mt) cc_final: 0.6929 (mt) REVERT: w 116 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.7822 (mtpp) REVERT: w 120 ASP cc_start: 0.7716 (t70) cc_final: 0.7437 (t0) REVERT: w 227 MET cc_start: 0.7338 (OUTLIER) cc_final: 0.6402 (mtt) REVERT: w 272 ASP cc_start: 0.7823 (m-30) cc_final: 0.7561 (m-30) outliers start: 124 outliers final: 59 residues processed: 749 average time/residue: 0.7628 time to fit residues: 685.9541 Evaluate side-chains 746 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 661 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 4 GLU Chi-restraints excluded: chain S residue 52 ARG Chi-restraints excluded: chain S residue 66 LEU Chi-restraints excluded: chain S residue 69 ILE Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 77 SER Chi-restraints excluded: chain V residue 4 THR Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain W residue 131 GLU Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain X residue 155 TYR Chi-restraints excluded: chain Y residue 40 ILE Chi-restraints excluded: chain Z residue 24 ILE Chi-restraints excluded: chain Z residue 31 THR Chi-restraints excluded: chain Z residue 39 ARG Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain a residue 148 GLU Chi-restraints excluded: chain a residue 163 ARG Chi-restraints excluded: chain b residue 115 GLU Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 141 LEU Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain c residue 185 GLU Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 38 ASP Chi-restraints excluded: chain d residue 52 ILE Chi-restraints excluded: chain d residue 55 GLN Chi-restraints excluded: chain e residue 116 GLU Chi-restraints excluded: chain e residue 125 LEU Chi-restraints excluded: chain e residue 146 LYS Chi-restraints excluded: chain f residue 48 LEU Chi-restraints excluded: chain f residue 64 GLU Chi-restraints excluded: chain g residue 28 LEU Chi-restraints excluded: chain h residue 80 LYS Chi-restraints excluded: chain i residue 100 MET Chi-restraints excluded: chain i residue 211 MET Chi-restraints excluded: chain i residue 299 SER Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 60 ILE Chi-restraints excluded: chain j residue 66 ASP Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 58 MET Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 191 THR Chi-restraints excluded: chain l residue 308 SER Chi-restraints excluded: chain l residue 331 MET Chi-restraints excluded: chain l residue 469 SER Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 580 GLN Chi-restraints excluded: chain m residue 31 LEU Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain o residue 50 GLN Chi-restraints excluded: chain o residue 88 LEU Chi-restraints excluded: chain p residue 21 LYS Chi-restraints excluded: chain p residue 44 MET Chi-restraints excluded: chain p residue 57 MET Chi-restraints excluded: chain p residue 135 ARG Chi-restraints excluded: chain p residue 139 GLN Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 122 PHE Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 303 ILE Chi-restraints excluded: chain r residue 337 VAL Chi-restraints excluded: chain r residue 401 MET Chi-restraints excluded: chain r residue 442 LEU Chi-restraints excluded: chain s residue 1 MET Chi-restraints excluded: chain s residue 10 ILE Chi-restraints excluded: chain s residue 91 MET Chi-restraints excluded: chain s residue 134 ARG Chi-restraints excluded: chain s residue 144 VAL Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 78 CYS Chi-restraints excluded: chain u residue 100 CYS Chi-restraints excluded: chain u residue 111 VAL Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain w residue 116 LYS Chi-restraints excluded: chain w residue 184 VAL Chi-restraints excluded: chain w residue 227 MET Chi-restraints excluded: chain w residue 257 GLN Chi-restraints excluded: chain w residue 347 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 319 optimal weight: 1.9990 chunk 337 optimal weight: 0.7980 chunk 440 optimal weight: 6.9990 chunk 447 optimal weight: 4.9990 chunk 240 optimal weight: 1.9990 chunk 364 optimal weight: 2.9990 chunk 188 optimal weight: 5.9990 chunk 333 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 133 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... V 129 GLN X 115 GLN c 127 ASN d 134 GLN ** e 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 145 ASN i 49 ASN l 320 ASN ** l 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 405 ASN o 126 ASN p 141 GLN u 77 HIS ** v 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 107 GLN w 306 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.136658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.112720 restraints weight = 47431.126| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.21 r_work: 0.3085 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2996 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 39709 Z= 0.176 Angle : 0.621 11.415 53666 Z= 0.315 Chirality : 0.043 0.199 5835 Planarity : 0.005 0.050 6566 Dihedral : 12.713 165.533 5968 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.97 % Favored : 95.99 % Rotamer: Outliers : 3.47 % Allowed : 12.82 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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 are not related in a simple way. whole: 1.71 (0.13), residues: 4586 helix: 1.94 (0.09), residues: 2993 sheet: -1.12 (1.06), residues: 23 loop : -0.39 (0.16), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG g 51 TYR 0.020 0.002 TYR c 184 PHE 0.030 0.002 PHE i 292 TRP 0.017 0.001 TRP l 144 HIS 0.009 0.001 HIS p 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (39704) covalent geometry : angle 0.62063 / 0.31 (53658) SS BOND : bond 0.00772 / 0.39 ( 4) SS BOND : angle 1.78375 / 1.11 ( 8) hydrogen bonds : bond 0.05755 / 3.85 ( 2317) hydrogen bonds : angle 4.26882 / 3.10 ( 6723) Misc. bond : bond 0.00087 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 809 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 668 time to evaluate : 1.721 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 46 GLN cc_start: 0.8485 (mt0) cc_final: 0.8114 (pt0) REVERT: S 31 ASN cc_start: 0.8726 (m-40) cc_final: 0.8277 (m110) REVERT: S 66 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7929 (mp) REVERT: W 108 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8007 (tt0) REVERT: X 77 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7517 (tp30) REVERT: X 81 ASP cc_start: 0.8515 (m-30) cc_final: 0.8258 (m-30) REVERT: X 153 ASP cc_start: 0.8266 (m-30) cc_final: 0.8039 (m-30) REVERT: Y 51 THR cc_start: 0.8277 (m) cc_final: 0.8003 (p) REVERT: Y 78 ASP cc_start: 0.7819 (OUTLIER) cc_final: 0.7385 (m-30) REVERT: a 69 LYS cc_start: 0.8881 (mttp) cc_final: 0.8678 (mttt) REVERT: a 148 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7732 (mp0) REVERT: b 115 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7293 (pm20) REVERT: c 185 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6421 (tm-30) REVERT: d 38 ASP cc_start: 0.7670 (OUTLIER) cc_final: 0.7445 (t70) REVERT: d 55 GLN cc_start: 0.8886 (OUTLIER) cc_final: 0.7974 (mp10) REVERT: e 146 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8191 (ttpp) REVERT: f 64 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7661 (mp0) REVERT: h 6 VAL cc_start: 0.9051 (t) cc_final: 0.8768 (m) REVERT: h 80 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.8099 (tttm) REVERT: i 100 MET cc_start: 0.8888 (OUTLIER) cc_final: 0.8572 (mtm) REVERT: i 147 GLN cc_start: 0.8600 (pm20) cc_final: 0.8294 (pm20) REVERT: i 236 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.8134 (tttp) REVERT: l 45 THR cc_start: 0.8936 (t) cc_final: 0.8673 (m) REVERT: l 331 MET cc_start: 0.9096 (OUTLIER) cc_final: 0.8095 (mmp) REVERT: l 410 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8120 (mp) REVERT: l 580 GLN cc_start: 0.8107 (OUTLIER) cc_final: 0.6962 (mp-120) REVERT: m 31 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8058 (mt) REVERT: m 57 PHE cc_start: 0.8095 (t80) cc_final: 0.7283 (t80) REVERT: o 120 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7550 (ptpt) REVERT: p 44 MET cc_start: 0.8663 (OUTLIER) cc_final: 0.8353 (tpt) REVERT: p 135 ARG cc_start: 0.7163 (OUTLIER) cc_final: 0.6281 (mtm110) REVERT: p 176 GLU cc_start: 0.7503 (tp30) cc_final: 0.7160 (pm20) REVERT: r 398 MET cc_start: 0.8062 (tpt) cc_final: 0.7841 (tpt) REVERT: s 1 MET cc_start: 0.7615 (OUTLIER) cc_final: 0.7243 (mmm) REVERT: s 51 ASP cc_start: 0.8407 (m-30) cc_final: 0.7932 (m-30) REVERT: s 134 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7633 (mpt-90) REVERT: v 109 LEU cc_start: 0.7505 (mt) cc_final: 0.6993 (mt) REVERT: w 116 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.7863 (mtpp) REVERT: w 120 ASP cc_start: 0.7718 (t70) cc_final: 0.7169 (t70) REVERT: w 184 VAL cc_start: 0.8407 (OUTLIER) cc_final: 0.8105 (t) REVERT: w 227 MET cc_start: 0.7341 (OUTLIER) cc_final: 0.6467 (mtt) REVERT: w 272 ASP cc_start: 0.7861 (m-30) cc_final: 0.7581 (m-30) outliers start: 141 outliers final: 62 residues processed: 740 average time/residue: 0.7715 time to fit residues: 688.1501 Evaluate side-chains 739 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 651 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 52 ARG Chi-restraints excluded: chain S residue 66 LEU Chi-restraints excluded: chain S residue 69 ILE Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 77 SER Chi-restraints excluded: chain V residue 4 THR Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain W residue 108 GLU Chi-restraints excluded: chain X residue 77 GLU Chi-restraints excluded: chain X residue 155 TYR Chi-restraints excluded: chain Y residue 40 ILE Chi-restraints excluded: chain Y residue 78 ASP Chi-restraints excluded: chain Z residue 24 ILE Chi-restraints excluded: chain Z residue 39 ARG Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain a residue 148 GLU Chi-restraints excluded: chain b residue 115 GLU Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 141 LEU Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain c residue 185 GLU Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 38 ASP Chi-restraints excluded: chain d residue 52 ILE Chi-restraints excluded: chain d residue 55 GLN Chi-restraints excluded: chain e residue 116 GLU Chi-restraints excluded: chain e residue 125 LEU Chi-restraints excluded: chain e residue 146 LYS Chi-restraints excluded: chain f residue 48 LEU Chi-restraints excluded: chain f residue 64 GLU Chi-restraints excluded: chain g residue 28 LEU Chi-restraints excluded: chain g residue 92 MET Chi-restraints excluded: chain h residue 80 LYS Chi-restraints excluded: chain i residue 100 MET Chi-restraints excluded: chain i residue 211 MET Chi-restraints excluded: chain i residue 236 LYS Chi-restraints excluded: chain i residue 239 VAL Chi-restraints excluded: chain i residue 299 SER Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 60 ILE Chi-restraints excluded: chain j residue 66 ASP Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 58 MET Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 190 LEU Chi-restraints excluded: chain l residue 191 THR Chi-restraints excluded: chain l residue 271 LYS Chi-restraints excluded: chain l residue 308 SER Chi-restraints excluded: chain l residue 331 MET Chi-restraints excluded: chain l residue 410 LEU Chi-restraints excluded: chain l residue 469 SER Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 580 GLN Chi-restraints excluded: chain m residue 31 LEU Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain o residue 88 LEU Chi-restraints excluded: chain o residue 120 LYS Chi-restraints excluded: chain p residue 21 LYS Chi-restraints excluded: chain p residue 44 MET Chi-restraints excluded: chain p residue 57 MET Chi-restraints excluded: chain p residue 135 ARG Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 111 THR Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 303 ILE Chi-restraints excluded: chain r residue 337 VAL Chi-restraints excluded: chain r residue 401 MET Chi-restraints excluded: chain r residue 442 LEU Chi-restraints excluded: chain s residue 1 MET Chi-restraints excluded: chain s residue 109 SER Chi-restraints excluded: chain s residue 134 ARG Chi-restraints excluded: chain s residue 144 VAL Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain u residue 6 GLU Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 78 CYS Chi-restraints excluded: chain u residue 100 CYS Chi-restraints excluded: chain u residue 111 VAL Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain w residue 76 GLU Chi-restraints excluded: chain w residue 116 LYS Chi-restraints excluded: chain w residue 184 VAL Chi-restraints excluded: chain w residue 227 MET Chi-restraints excluded: chain w residue 347 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 37 optimal weight: 0.8980 chunk 286 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 291 optimal weight: 1.9990 chunk 107 optimal weight: 20.0000 chunk 194 optimal weight: 3.9990 chunk 156 optimal weight: 0.6980 chunk 340 optimal weight: 8.9990 chunk 152 optimal weight: 3.9990 chunk 394 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... V 129 GLN c 127 ASN e 65 ASN f 61 GLN l 320 ASN ** l 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 405 ASN o 126 ASN p 141 GLN s 194 ASN u 77 HIS ** v 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 219 GLN w 299 GLN w 306 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.137249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.113586 restraints weight = 47125.599| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.19 r_work: 0.3110 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2985 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2985 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 39709 Z= 0.150 Angle : 0.591 11.615 53666 Z= 0.300 Chirality : 0.042 0.246 5835 Planarity : 0.005 0.050 6566 Dihedral : 12.321 151.288 5968 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.84 % Favored : 96.12 % Rotamer: Outliers : 3.10 % Allowed : 13.54 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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 are not related in a simple way. whole: 1.83 (0.13), residues: 4586 helix: 2.04 (0.09), residues: 2989 sheet: -0.86 (1.05), residues: 22 loop : -0.36 (0.16), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG g 51 TYR 0.020 0.001 TYR r 406 PHE 0.030 0.002 PHE i 292 TRP 0.019 0.001 TRP l 144 HIS 0.005 0.001 HIS p 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (39704) covalent geometry : angle 0.59068 / 0.30 (53658) SS BOND : bond 0.00421 / 0.20 ( 4) SS BOND : angle 1.75015 / 1.10 ( 8) hydrogen bonds : bond 0.05344 / 3.57 ( 2317) hydrogen bonds : angle 4.20514 / 3.05 ( 6723) Misc. bond : bond 0.00059 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 799 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 673 time to evaluate : 1.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 46 GLN cc_start: 0.8472 (mt0) cc_final: 0.8121 (pt0) REVERT: S 31 ASN cc_start: 0.8751 (m-40) cc_final: 0.8324 (m110) REVERT: S 66 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7921 (mp) REVERT: W 108 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.8003 (tt0) REVERT: X 77 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7851 (tp30) REVERT: Y 51 THR cc_start: 0.8248 (m) cc_final: 0.7972 (p) REVERT: Y 78 ASP cc_start: 0.7802 (OUTLIER) cc_final: 0.7305 (m-30) REVERT: a 69 LYS cc_start: 0.8859 (mttp) cc_final: 0.8657 (mttt) REVERT: a 148 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7710 (mp0) REVERT: b 115 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7327 (pm20) REVERT: c 185 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6379 (tm-30) REVERT: d 38 ASP cc_start: 0.7646 (OUTLIER) cc_final: 0.7427 (t70) REVERT: d 55 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.7932 (mp10) REVERT: e 146 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8114 (ttpp) REVERT: h 6 VAL cc_start: 0.9036 (t) cc_final: 0.8762 (m) REVERT: h 80 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.8112 (tttm) REVERT: i 100 MET cc_start: 0.8877 (OUTLIER) cc_final: 0.8547 (mtm) REVERT: i 147 GLN cc_start: 0.8574 (pm20) cc_final: 0.8274 (pm20) REVERT: i 236 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.8117 (tttp) REVERT: l 45 THR cc_start: 0.8921 (t) cc_final: 0.8661 (m) REVERT: l 331 MET cc_start: 0.9069 (OUTLIER) cc_final: 0.8119 (mmp) REVERT: l 525 MET cc_start: 0.9107 (OUTLIER) cc_final: 0.7684 (mpp) REVERT: l 580 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.6943 (mp-120) REVERT: m 31 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8010 (mt) REVERT: m 57 PHE cc_start: 0.8063 (t80) cc_final: 0.7247 (t80) REVERT: o 120 LYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7524 (ptpt) REVERT: p 135 ARG cc_start: 0.7018 (OUTLIER) cc_final: 0.6076 (mtm110) REVERT: p 176 GLU cc_start: 0.7506 (tp30) cc_final: 0.7155 (pm20) REVERT: r 398 MET cc_start: 0.8040 (tpt) cc_final: 0.7808 (tpt) REVERT: s 1 MET cc_start: 0.7624 (OUTLIER) cc_final: 0.7263 (mmm) REVERT: s 51 ASP cc_start: 0.8407 (m-30) cc_final: 0.7938 (m-30) REVERT: s 134 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7586 (mpt-90) REVERT: v 83 GLU cc_start: 0.8462 (mp0) cc_final: 0.8226 (mp0) REVERT: v 109 LEU cc_start: 0.7502 (mt) cc_final: 0.7007 (mt) REVERT: w 116 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.7918 (mtpp) REVERT: w 120 ASP cc_start: 0.7695 (t70) cc_final: 0.7440 (t0) REVERT: w 184 VAL cc_start: 0.8403 (OUTLIER) cc_final: 0.8122 (t) REVERT: w 227 MET cc_start: 0.7317 (OUTLIER) cc_final: 0.6397 (mtt) REVERT: w 272 ASP cc_start: 0.7854 (m-30) cc_final: 0.7581 (m-30) outliers start: 126 outliers final: 64 residues processed: 732 average time/residue: 0.7744 time to fit residues: 682.7014 Evaluate side-chains 742 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 654 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 52 ARG Chi-restraints excluded: chain S residue 66 LEU Chi-restraints excluded: chain S residue 69 ILE Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 77 SER Chi-restraints excluded: chain V residue 4 THR Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain W residue 108 GLU Chi-restraints excluded: chain X residue 77 GLU Chi-restraints excluded: chain X residue 155 TYR Chi-restraints excluded: chain Y residue 40 ILE Chi-restraints excluded: chain Y residue 78 ASP Chi-restraints excluded: chain Z residue 24 ILE Chi-restraints excluded: chain Z residue 39 ARG Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain a residue 148 GLU Chi-restraints excluded: chain b residue 115 GLU Chi-restraints excluded: chain c residue 86 ARG Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain c residue 185 GLU Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 38 ASP Chi-restraints excluded: chain d residue 52 ILE Chi-restraints excluded: chain d residue 55 GLN Chi-restraints excluded: chain e residue 99 LEU Chi-restraints excluded: chain e residue 125 LEU Chi-restraints excluded: chain e residue 146 LYS Chi-restraints excluded: chain f residue 48 LEU Chi-restraints excluded: chain g residue 28 LEU Chi-restraints excluded: chain g residue 92 MET Chi-restraints excluded: chain h residue 80 LYS Chi-restraints excluded: chain i residue 100 MET Chi-restraints excluded: chain i residue 211 MET Chi-restraints excluded: chain i residue 236 LYS Chi-restraints excluded: chain i residue 239 VAL Chi-restraints excluded: chain i residue 299 SER Chi-restraints excluded: chain i residue 311 MET Chi-restraints excluded: chain i residue 323 MET Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 60 ILE Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 26 LEU Chi-restraints excluded: chain k residue 58 MET Chi-restraints excluded: chain l residue 21 MET Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 271 LYS Chi-restraints excluded: chain l residue 308 SER Chi-restraints excluded: chain l residue 331 MET Chi-restraints excluded: chain l residue 469 SER Chi-restraints excluded: chain l residue 525 MET Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 580 GLN Chi-restraints excluded: chain m residue 31 LEU Chi-restraints excluded: chain o residue 88 LEU Chi-restraints excluded: chain o residue 120 LYS Chi-restraints excluded: chain p residue 21 LYS Chi-restraints excluded: chain p residue 57 MET Chi-restraints excluded: chain p residue 135 ARG Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 111 THR Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 303 ILE Chi-restraints excluded: chain r residue 337 VAL Chi-restraints excluded: chain r residue 401 MET Chi-restraints excluded: chain r residue 442 LEU Chi-restraints excluded: chain s residue 1 MET Chi-restraints excluded: chain s residue 10 ILE Chi-restraints excluded: chain s residue 91 MET Chi-restraints excluded: chain s residue 134 ARG Chi-restraints excluded: chain s residue 144 VAL Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 78 CYS Chi-restraints excluded: chain u residue 100 CYS Chi-restraints excluded: chain u residue 111 VAL Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain w residue 116 LYS Chi-restraints excluded: chain w residue 184 VAL Chi-restraints excluded: chain w residue 214 ILE Chi-restraints excluded: chain w residue 227 MET Chi-restraints excluded: chain w residue 347 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 57 optimal weight: 7.9990 chunk 271 optimal weight: 7.9990 chunk 201 optimal weight: 6.9990 chunk 151 optimal weight: 7.9990 chunk 301 optimal weight: 2.9990 chunk 412 optimal weight: 1.9990 chunk 362 optimal weight: 0.9980 chunk 162 optimal weight: 3.9990 chunk 258 optimal weight: 0.9980 chunk 320 optimal weight: 4.9990 chunk 270 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... V 129 GLN c 115 ASN c 127 ASN e 65 ASN i 49 ASN l 136 ASN l 320 ASN ** l 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 405 ASN o 126 ASN p 141 GLN u 77 HIS ** v 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 306 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.137621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.113965 restraints weight = 47183.031| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.19 r_work: 0.3115 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3018 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3018 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 39709 Z= 0.146 Angle : 0.589 12.291 53666 Z= 0.298 Chirality : 0.042 0.214 5835 Planarity : 0.005 0.050 6566 Dihedral : 11.960 148.312 5968 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.88 % Favored : 96.08 % Rotamer: Outliers : 2.86 % Allowed : 14.28 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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 are not related in a simple way. whole: 1.88 (0.13), residues: 4586 helix: 2.08 (0.09), residues: 2983 sheet: -0.90 (1.04), residues: 22 loop : -0.33 (0.16), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG o 10 TYR 0.020 0.001 TYR r 406 PHE 0.030 0.002 PHE i 292 TRP 0.018 0.001 TRP l 144 HIS 0.006 0.001 HIS u 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (39704) covalent geometry : angle 0.58897 / 0.30 (53658) SS BOND : bond 0.00435 / 0.21 ( 4) SS BOND : angle 1.61022 / 1.00 ( 8) hydrogen bonds : bond 0.05238 / 3.50 ( 2317) hydrogen bonds : angle 4.18402 / 3.04 ( 6723) Misc. bond : bond 0.00063 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 785 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 669 time to evaluate : 1.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 46 GLN cc_start: 0.8478 (mt0) cc_final: 0.8148 (pt0) REVERT: S 31 ASN cc_start: 0.8771 (m-40) cc_final: 0.8355 (m110) REVERT: S 66 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7900 (mp) REVERT: W 108 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8015 (tt0) REVERT: X 77 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7832 (tp30) REVERT: Y 51 THR cc_start: 0.8256 (m) cc_final: 0.7980 (p) REVERT: a 69 LYS cc_start: 0.8866 (mttp) cc_final: 0.8662 (mttt) REVERT: a 148 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7716 (mp0) REVERT: b 115 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7359 (pm20) REVERT: c 185 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6351 (tm-30) REVERT: d 38 ASP cc_start: 0.7634 (OUTLIER) cc_final: 0.7420 (t70) REVERT: d 55 GLN cc_start: 0.8856 (OUTLIER) cc_final: 0.7912 (mp10) REVERT: e 65 ASN cc_start: 0.8417 (t0) cc_final: 0.8144 (t0) REVERT: e 81 ILE cc_start: 0.8646 (mm) cc_final: 0.8437 (mp) REVERT: e 146 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8143 (ttpp) REVERT: h 6 VAL cc_start: 0.9039 (t) cc_final: 0.8763 (m) REVERT: h 80 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.8091 (tttm) REVERT: i 100 MET cc_start: 0.8880 (OUTLIER) cc_final: 0.8558 (mtm) REVERT: i 147 GLN cc_start: 0.8580 (pm20) cc_final: 0.8279 (pm20) REVERT: i 236 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.8130 (tttp) REVERT: l 45 THR cc_start: 0.8914 (t) cc_final: 0.8655 (m) REVERT: l 331 MET cc_start: 0.9068 (OUTLIER) cc_final: 0.8126 (mmp) REVERT: l 580 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.6900 (mp-120) REVERT: m 3 MET cc_start: 0.2218 (mmm) cc_final: 0.1218 (pp-130) REVERT: m 31 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8009 (mt) REVERT: m 57 PHE cc_start: 0.8060 (t80) cc_final: 0.7240 (t80) REVERT: o 120 LYS cc_start: 0.7946 (OUTLIER) cc_final: 0.7514 (ptpt) REVERT: p 44 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8328 (tpt) REVERT: p 57 MET cc_start: 0.7686 (OUTLIER) cc_final: 0.7469 (tpp) REVERT: p 135 ARG cc_start: 0.6959 (OUTLIER) cc_final: 0.6008 (mtm110) REVERT: p 176 GLU cc_start: 0.7519 (tp30) cc_final: 0.7147 (pm20) REVERT: r 398 MET cc_start: 0.8018 (tpt) cc_final: 0.7794 (tpt) REVERT: s 1 MET cc_start: 0.7661 (OUTLIER) cc_final: 0.7309 (mmm) REVERT: s 51 ASP cc_start: 0.8400 (m-30) cc_final: 0.7912 (m-30) REVERT: s 134 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7587 (mpt-90) REVERT: v 83 GLU cc_start: 0.8450 (mp0) cc_final: 0.8210 (mp0) REVERT: v 109 LEU cc_start: 0.7491 (mt) cc_final: 0.7000 (mt) REVERT: w 120 ASP cc_start: 0.7687 (t70) cc_final: 0.7440 (t0) REVERT: w 184 VAL cc_start: 0.8409 (OUTLIER) cc_final: 0.8143 (t) REVERT: w 227 MET cc_start: 0.7303 (OUTLIER) cc_final: 0.6400 (mtt) REVERT: w 272 ASP cc_start: 0.7849 (m-30) cc_final: 0.7564 (m-30) outliers start: 116 outliers final: 61 residues processed: 732 average time/residue: 0.7507 time to fit residues: 662.3767 Evaluate side-chains 736 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 652 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 52 ARG Chi-restraints excluded: chain S residue 66 LEU Chi-restraints excluded: chain S residue 69 ILE Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 77 SER Chi-restraints excluded: chain V residue 4 THR Chi-restraints excluded: chain V residue 107 SER Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain W residue 108 GLU Chi-restraints excluded: chain X residue 77 GLU Chi-restraints excluded: chain X residue 155 TYR Chi-restraints excluded: chain Y residue 40 ILE Chi-restraints excluded: chain Z residue 24 ILE Chi-restraints excluded: chain Z residue 39 ARG Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain a residue 148 GLU Chi-restraints excluded: chain b residue 115 GLU Chi-restraints excluded: chain c residue 86 ARG Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain c residue 185 GLU Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 38 ASP Chi-restraints excluded: chain d residue 52 ILE Chi-restraints excluded: chain d residue 55 GLN Chi-restraints excluded: chain e residue 125 LEU Chi-restraints excluded: chain e residue 146 LYS Chi-restraints excluded: chain f residue 48 LEU Chi-restraints excluded: chain g residue 28 LEU Chi-restraints excluded: chain g residue 92 MET Chi-restraints excluded: chain h residue 80 LYS Chi-restraints excluded: chain i residue 100 MET Chi-restraints excluded: chain i residue 211 MET Chi-restraints excluded: chain i residue 236 LYS Chi-restraints excluded: chain i residue 239 VAL Chi-restraints excluded: chain i residue 299 SER Chi-restraints excluded: chain i residue 311 MET Chi-restraints excluded: chain i residue 323 MET Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 60 ILE Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 58 MET Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 271 LYS Chi-restraints excluded: chain l residue 308 SER Chi-restraints excluded: chain l residue 331 MET Chi-restraints excluded: chain l residue 469 SER Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 580 GLN Chi-restraints excluded: chain m residue 31 LEU Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain o residue 50 GLN Chi-restraints excluded: chain o residue 88 LEU Chi-restraints excluded: chain o residue 120 LYS Chi-restraints excluded: chain p residue 21 LYS Chi-restraints excluded: chain p residue 44 MET Chi-restraints excluded: chain p residue 57 MET Chi-restraints excluded: chain p residue 135 ARG Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 111 THR Chi-restraints excluded: chain r residue 122 PHE Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 337 VAL Chi-restraints excluded: chain r residue 401 MET Chi-restraints excluded: chain r residue 442 LEU Chi-restraints excluded: chain s residue 1 MET Chi-restraints excluded: chain s residue 10 ILE Chi-restraints excluded: chain s residue 134 ARG Chi-restraints excluded: chain s residue 144 VAL Chi-restraints excluded: chain s residue 150 LEU Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain u residue 23 SER Chi-restraints excluded: chain u residue 78 CYS Chi-restraints excluded: chain u residue 100 CYS Chi-restraints excluded: chain u residue 111 VAL Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain w residue 184 VAL Chi-restraints excluded: chain w residue 227 MET Chi-restraints excluded: chain w residue 347 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 387 optimal weight: 5.9990 chunk 88 optimal weight: 0.6980 chunk 199 optimal weight: 0.8980 chunk 176 optimal weight: 4.9990 chunk 177 optimal weight: 0.9980 chunk 320 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 224 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 220 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... V 129 GLN c 115 ASN c 127 ASN f 61 GLN i 49 ASN l 136 ASN l 274 GLN ** l 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 126 ASN p 141 GLN s 194 ASN u 77 HIS ** v 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 306 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.140876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.117538 restraints weight = 47466.948| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.28 r_work: 0.3158 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3034 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3034 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 39709 Z= 0.118 Angle : 0.551 14.555 53666 Z= 0.278 Chirality : 0.040 0.240 5835 Planarity : 0.004 0.050 6566 Dihedral : 11.312 145.191 5968 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.60 % Favored : 96.38 % Rotamer: Outliers : 2.19 % Allowed : 15.21 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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 are not related in a simple way. whole: 2.09 (0.13), residues: 4586 helix: 2.25 (0.09), residues: 2979 sheet: -0.91 (1.00), residues: 24 loop : -0.25 (0.17), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG o 10 TYR 0.024 0.001 TYR l 422 PHE 0.031 0.001 PHE i 292 TRP 0.023 0.001 TRP l 144 HIS 0.006 0.001 HIS u 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (39704) covalent geometry : angle 0.55036 / 0.28 (53658) SS BOND : bond 0.00375 / 0.18 ( 4) SS BOND : angle 1.59302 / 1.00 ( 8) hydrogen bonds : bond 0.04469 / 2.99 ( 2317) hydrogen bonds : angle 4.07421 / 2.96 ( 6723) Misc. bond : bond 0.00010 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 770 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 681 time to evaluate : 1.608 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 46 GLN cc_start: 0.8442 (mt0) cc_final: 0.8153 (pt0) REVERT: S 31 ASN cc_start: 0.8800 (m-40) cc_final: 0.8434 (m110) REVERT: S 66 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7869 (mp) REVERT: W 108 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7971 (tt0) REVERT: W 131 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.6756 (pm20) REVERT: X 77 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7821 (tp30) REVERT: Y 51 THR cc_start: 0.8166 (m) cc_final: 0.7885 (p) REVERT: Y 78 ASP cc_start: 0.7679 (OUTLIER) cc_final: 0.7446 (p0) REVERT: Z 80 VAL cc_start: 0.7906 (t) cc_final: 0.7650 (t) REVERT: a 69 LYS cc_start: 0.8865 (mttp) cc_final: 0.8655 (mttt) REVERT: a 148 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7681 (mp0) REVERT: a 178 LEU cc_start: 0.8980 (mt) cc_final: 0.8768 (mt) REVERT: b 115 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7344 (pm20) REVERT: c 185 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6222 (tm-30) REVERT: e 81 ILE cc_start: 0.8603 (mm) cc_final: 0.8395 (mp) REVERT: h 6 VAL cc_start: 0.9011 (t) cc_final: 0.8784 (m) REVERT: i 90 PHE cc_start: 0.6530 (m-80) cc_final: 0.6291 (m-80) REVERT: i 100 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.8482 (mtm) REVERT: i 147 GLN cc_start: 0.8517 (pm20) cc_final: 0.8220 (pm20) REVERT: i 281 LEU cc_start: 0.8623 (mp) cc_final: 0.8418 (mp) REVERT: i 284 MET cc_start: 0.7754 (mmt) cc_final: 0.7385 (mmt) REVERT: l 45 THR cc_start: 0.8866 (t) cc_final: 0.8611 (m) REVERT: l 331 MET cc_start: 0.8988 (OUTLIER) cc_final: 0.8206 (mmp) REVERT: l 472 ILE cc_start: 0.8130 (pt) cc_final: 0.7930 (mm) REVERT: l 525 MET cc_start: 0.9093 (OUTLIER) cc_final: 0.7614 (mpp) REVERT: l 571 MET cc_start: 0.8686 (ttp) cc_final: 0.8337 (ttm) REVERT: l 580 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.6911 (mp-120) REVERT: m 3 MET cc_start: 0.2001 (mmm) cc_final: 0.1530 (mtp) REVERT: m 31 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7900 (mt) REVERT: m 57 PHE cc_start: 0.8027 (t80) cc_final: 0.7211 (t80) REVERT: o 120 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7456 (ptpt) REVERT: p 44 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.8445 (tpp) REVERT: p 176 GLU cc_start: 0.7528 (tp30) cc_final: 0.7121 (pm20) REVERT: r 398 MET cc_start: 0.7967 (tpt) cc_final: 0.7742 (tpt) REVERT: s 1 MET cc_start: 0.7687 (OUTLIER) cc_final: 0.7332 (mmm) REVERT: s 51 ASP cc_start: 0.8380 (m-30) cc_final: 0.7889 (m-30) REVERT: s 134 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.7460 (mpt-90) REVERT: v 54 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.8293 (pp30) REVERT: v 83 GLU cc_start: 0.8432 (mp0) cc_final: 0.8202 (mp0) REVERT: w 120 ASP cc_start: 0.7633 (t70) cc_final: 0.7362 (t0) REVERT: w 227 MET cc_start: 0.7234 (OUTLIER) cc_final: 0.6402 (mtt) REVERT: w 272 ASP cc_start: 0.7719 (m-30) cc_final: 0.7454 (m-30) outliers start: 89 outliers final: 37 residues processed: 724 average time/residue: 0.7312 time to fit residues: 637.1353 Evaluate side-chains 711 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 655 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 52 ARG Chi-restraints excluded: chain S residue 66 LEU Chi-restraints excluded: chain S residue 69 ILE Chi-restraints excluded: chain U residue 77 SER Chi-restraints excluded: chain V residue 107 SER Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain W residue 108 GLU Chi-restraints excluded: chain W residue 131 GLU Chi-restraints excluded: chain X residue 77 GLU Chi-restraints excluded: chain Y residue 78 ASP Chi-restraints excluded: chain Z residue 39 ARG Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain a residue 148 GLU Chi-restraints excluded: chain b residue 115 GLU Chi-restraints excluded: chain c residue 86 ARG Chi-restraints excluded: chain c residue 141 LEU Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain c residue 185 GLU Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 52 ILE Chi-restraints excluded: chain d residue 55 GLN Chi-restraints excluded: chain f residue 48 LEU Chi-restraints excluded: chain i residue 100 MET Chi-restraints excluded: chain i residue 211 MET Chi-restraints excluded: chain i residue 323 MET Chi-restraints excluded: chain j residue 105 GLU Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 308 SER Chi-restraints excluded: chain l residue 331 MET Chi-restraints excluded: chain l residue 469 SER Chi-restraints excluded: chain l residue 525 MET Chi-restraints excluded: chain l residue 580 GLN Chi-restraints excluded: chain m residue 31 LEU Chi-restraints excluded: chain o residue 50 GLN Chi-restraints excluded: chain o residue 88 LEU Chi-restraints excluded: chain o residue 120 LYS Chi-restraints excluded: chain p residue 21 LYS Chi-restraints excluded: chain p residue 44 MET Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 111 THR Chi-restraints excluded: chain r residue 122 PHE Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 337 VAL Chi-restraints excluded: chain r residue 401 MET Chi-restraints excluded: chain s residue 1 MET Chi-restraints excluded: chain s residue 10 ILE Chi-restraints excluded: chain s residue 134 ARG Chi-restraints excluded: chain s residue 150 LEU Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain u residue 100 CYS Chi-restraints excluded: chain u residue 111 VAL Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain w residue 227 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 316 optimal weight: 2.9990 chunk 320 optimal weight: 0.9990 chunk 209 optimal weight: 0.9990 chunk 410 optimal weight: 0.0170 chunk 25 optimal weight: 9.9990 chunk 253 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 285 optimal weight: 6.9990 chunk 419 optimal weight: 1.9990 chunk 188 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.8024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... V 129 GLN b 83 HIS c 115 ASN c 127 ASN f 61 GLN ** l 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 126 ASN p 141 GLN s 194 ASN s 287 HIS u 77 HIS ** v 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 239 ASN w 306 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.141353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.118066 restraints weight = 47378.238| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.26 r_work: 0.3175 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3063 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3063 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 39709 Z= 0.116 Angle : 0.552 13.617 53666 Z= 0.277 Chirality : 0.040 0.278 5835 Planarity : 0.004 0.050 6566 Dihedral : 10.903 140.502 5968 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.73 % Favored : 96.25 % Rotamer: Outliers : 1.65 % Allowed : 15.87 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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 are not related in a simple way. whole: 2.17 (0.13), residues: 4586 helix: 2.30 (0.09), residues: 2983 sheet: -0.82 (1.00), residues: 24 loop : -0.19 (0.17), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG o 10 TYR 0.023 0.001 TYR l 422 PHE 0.031 0.001 PHE i 292 TRP 0.020 0.001 TRP c 145 HIS 0.006 0.001 HIS u 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (39704) covalent geometry : angle 0.55135 / 0.28 (53658) SS BOND : bond 0.00309 / 0.15 ( 4) SS BOND : angle 1.94174 / 1.25 ( 8) hydrogen bonds : bond 0.04410 / 2.95 ( 2317) hydrogen bonds : angle 4.04359 / 2.94 ( 6723) Misc. bond : bond 0.00054 / 0.03 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9172 Ramachandran restraints generated. 4586 Oldfield, 0 Emsley, 4586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 754 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 687 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 46 GLN cc_start: 0.8415 (mt0) cc_final: 0.8160 (pt0) REVERT: S 31 ASN cc_start: 0.8816 (m-40) cc_final: 0.8458 (m110) REVERT: S 66 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7807 (mp) REVERT: W 108 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7969 (tt0) REVERT: W 131 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6696 (pm20) REVERT: X 77 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7790 (tp30) REVERT: Y 51 THR cc_start: 0.8172 (m) cc_final: 0.7905 (p) REVERT: Y 78 ASP cc_start: 0.7670 (OUTLIER) cc_final: 0.7402 (p0) REVERT: Z 31 THR cc_start: 0.8566 (p) cc_final: 0.8351 (t) REVERT: Z 80 VAL cc_start: 0.7887 (t) cc_final: 0.7631 (t) REVERT: a 148 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7657 (mp0) REVERT: a 178 LEU cc_start: 0.8971 (mt) cc_final: 0.8760 (mt) REVERT: b 21 ARG cc_start: 0.7830 (mtm180) cc_final: 0.7437 (mtp85) REVERT: b 115 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7357 (pm20) REVERT: c 185 GLU cc_start: 0.7065 (OUTLIER) cc_final: 0.6218 (tm-30) REVERT: d 43 ARG cc_start: 0.7760 (mmt-90) cc_final: 0.7511 (mmt90) REVERT: e 81 ILE cc_start: 0.8612 (mm) cc_final: 0.8409 (mp) REVERT: i 90 PHE cc_start: 0.6340 (m-80) cc_final: 0.6086 (m-80) REVERT: i 100 MET cc_start: 0.8835 (mtp) cc_final: 0.8466 (mtm) REVERT: i 147 GLN cc_start: 0.8541 (pm20) cc_final: 0.8228 (pm20) REVERT: i 281 LEU cc_start: 0.8604 (mp) cc_final: 0.8404 (mp) REVERT: i 284 MET cc_start: 0.7732 (mmt) cc_final: 0.7406 (mmt) REVERT: l 45 THR cc_start: 0.8865 (t) cc_final: 0.8621 (m) REVERT: l 331 MET cc_start: 0.8975 (OUTLIER) cc_final: 0.8210 (mmp) REVERT: l 525 MET cc_start: 0.9091 (OUTLIER) cc_final: 0.7625 (mpp) REVERT: l 571 MET cc_start: 0.8701 (ttp) cc_final: 0.8352 (ttm) REVERT: l 580 GLN cc_start: 0.7973 (OUTLIER) cc_final: 0.6804 (mp-120) REVERT: m 3 MET cc_start: 0.1833 (mmm) cc_final: 0.1422 (mtp) REVERT: m 31 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7896 (mt) REVERT: o 120 LYS cc_start: 0.7901 (OUTLIER) cc_final: 0.7460 (ptpt) REVERT: p 44 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.8435 (tpp) REVERT: p 176 GLU cc_start: 0.7527 (tp30) cc_final: 0.7129 (pm20) REVERT: r 398 MET cc_start: 0.7961 (tpt) cc_final: 0.7734 (tpt) REVERT: s 51 ASP cc_start: 0.8343 (m-30) cc_final: 0.7862 (m-30) REVERT: s 134 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7421 (mpt-90) REVERT: v 16 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8261 (mm-30) REVERT: v 52 MET cc_start: 0.7491 (OUTLIER) cc_final: 0.7066 (mmt) REVERT: v 54 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.8313 (pp30) REVERT: v 83 GLU cc_start: 0.8385 (mp0) cc_final: 0.8153 (mp0) REVERT: v 105 GLU cc_start: 0.8283 (tp30) cc_final: 0.7915 (tm-30) REVERT: v 116 GLU cc_start: 0.7467 (mt-10) cc_final: 0.6446 (pt0) REVERT: w 120 ASP cc_start: 0.7547 (t70) cc_final: 0.7318 (t0) REVERT: w 227 MET cc_start: 0.7226 (OUTLIER) cc_final: 0.6398 (mtt) REVERT: w 272 ASP cc_start: 0.7647 (m-30) cc_final: 0.7386 (m-30) outliers start: 67 outliers final: 34 residues processed: 719 average time/residue: 0.7080 time to fit residues: 612.1351 Evaluate side-chains 720 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 668 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 52 ARG Chi-restraints excluded: chain S residue 66 LEU Chi-restraints excluded: chain S residue 69 ILE Chi-restraints excluded: chain U residue 77 SER Chi-restraints excluded: chain V residue 107 SER Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain W residue 108 GLU Chi-restraints excluded: chain W residue 131 GLU Chi-restraints excluded: chain X residue 77 GLU Chi-restraints excluded: chain Y residue 78 ASP Chi-restraints excluded: chain a residue 148 GLU Chi-restraints excluded: chain b residue 115 GLU Chi-restraints excluded: chain c residue 86 ARG Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain c residue 185 GLU Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 52 ILE Chi-restraints excluded: chain d residue 55 GLN Chi-restraints excluded: chain f residue 48 LEU Chi-restraints excluded: chain i residue 211 MET Chi-restraints excluded: chain j residue 105 GLU Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 308 SER Chi-restraints excluded: chain l residue 331 MET Chi-restraints excluded: chain l residue 469 SER Chi-restraints excluded: chain l residue 525 MET Chi-restraints excluded: chain l residue 580 GLN Chi-restraints excluded: chain m residue 31 LEU Chi-restraints excluded: chain o residue 50 GLN Chi-restraints excluded: chain o residue 120 LYS Chi-restraints excluded: chain p residue 21 LYS Chi-restraints excluded: chain p residue 44 MET Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 111 THR Chi-restraints excluded: chain r residue 122 PHE Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 207 MET Chi-restraints excluded: chain r residue 337 VAL Chi-restraints excluded: chain r residue 401 MET Chi-restraints excluded: chain s residue 10 ILE Chi-restraints excluded: chain s residue 134 ARG Chi-restraints excluded: chain s residue 144 VAL Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain u residue 100 CYS Chi-restraints excluded: chain u residue 111 VAL Chi-restraints excluded: chain v residue 52 MET Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain w residue 227 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 263 optimal weight: 5.9990 chunk 87 optimal weight: 0.0670 chunk 50 optimal weight: 1.9990 chunk 348 optimal weight: 5.9990 chunk 432 optimal weight: 6.9990 chunk 222 optimal weight: 3.9990 chunk 367 optimal weight: 4.9990 chunk 58 optimal weight: 0.0870 chunk 124 optimal weight: 0.0570 chunk 131 optimal weight: 0.0970 chunk 314 optimal weight: 0.0030 overall best weight: 0.0622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... V 129 GLN c 115 ASN c 127 ASN d 131 GLN ** e 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 49 ASN ** l 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 79 ASN o 126 ASN p 76 HIS p 141 GLN s 287 HIS u 77 HIS ** v 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 239 ASN w 306 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.147730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.124981 restraints weight = 48031.389| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.29 r_work: 0.3262 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3137 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (14 function evaluations) r_final: 0.3137 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 39709 Z= 0.105 Angle : 0.525 15.423 53666 Z= 0.262 Chirality : 0.038 0.292 5835 Planarity : 0.004 0.052 6566 Dihedral : 10.167 133.489 5968 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.36 % Favored : 96.62 % Rotamer: Outliers : 1.03 % Allowed : 16.76 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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 are not related in a simple way. whole: 2.32 (0.13), residues: 4586 helix: 2.43 (0.09), residues: 2976 sheet: -0.62 (1.04), residues: 24 loop : -0.15 (0.17), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG o 10 TYR 0.028 0.001 TYR l 422 PHE 0.035 0.001 PHE l 335 TRP 0.029 0.001 TRP l 144 HIS 0.006 0.001 HIS u 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (39704) covalent geometry : angle 0.52511 / 0.26 (53658) SS BOND : bond 0.00287 / 0.14 ( 4) SS BOND : angle 1.50710 / 0.95 ( 8) hydrogen bonds : bond 0.03618 / 2.42 ( 2317) hydrogen bonds : angle 3.92765 / 2.86 ( 6723) Misc. bond : bond 0.00013 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18998.42 seconds wall clock time: 323 minutes 17.04 seconds (19397.04 seconds total)