Starting phenix.real_space_refine on Sun Feb 8 01:51:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vz8_32222/02_2026/7vz8_32222.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vz8_32222/02_2026/7vz8_32222.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 { model { file = "/net/cci-nas-00/data/ceres_data/7vz8_32222/02_2026/7vz8_32222.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vz8_32222/02_2026/7vz8_32222.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vz8_32222/02_2026/7vz8_32222.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vz8_32222/02_2026/7vz8_32222.map" } 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 27 5.49 5 S 283 5.16 5 C 25365 2.51 5 N 6210 2.21 5 O 7134 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 77 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39019 Number of models: 1 Model: "" Number of chains: 64 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: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 696 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "Y" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 597 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 63} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 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: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 342 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 40} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 10 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: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 740 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 1, 'TRANS': 95} Chain: "l" Number of atoms: 4782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4782 Classifications: {'peptide': 603} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 574} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "m" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 925 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "n" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 479 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} 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: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1028 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 116} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "w" Number of atoms: 2582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2582 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 303} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "Q" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "U" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} 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: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 91 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "b" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 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: "g" 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: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 34 Chain: "l" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 146 Unusual residues: {'CDL': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "m" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 93 Unusual residues: {'PEE': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "r" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 354 Unusual residues: {'CDL': 2, 'PEE': 1, 'PLX': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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: "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: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "S" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} 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: "W" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "c" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 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: "g" 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: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 64 Classifications: {'water': 64} Link IDs: {None: 63} Chain: "j" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "k" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "l" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 55 Classifications: {'water': 55} Link IDs: {None: 54} Chain: "m" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} 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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 83 Classifications: {'water': 83} Link IDs: {None: 82} Chain: "s" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 61 Classifications: {'water': 61} Link IDs: {None: 60} Chain: "u" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 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=0.62 ... (25 atoms not shown) pdb=" PB ADP w 401 " occ=0.62 Time building chain proxies: 7.98, per 1000 atoms: 0.20 Number of scatterers: 39019 At special positions: 0 Unit cell: (179.507, 192.681, 136.689, 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 283 16.00 P 27 15.00 O 7134 8.00 N 6210 7.00 C 25365 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS V 95 " - pdb=" SG CYS V 115 " distance=1.86 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=2.03 Simple disulfide: pdb=" SG CYS h 43 " - pdb=" SG CYS h 56 " distance=2.04 Simple disulfide: pdb=" SG CYS u 88 " - pdb=" SG CYS u 100 " distance=2.03 Simple disulfide: pdb=" SG CYS v 69 " - pdb=" SG CYS v 80 " 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: 3.11 Conformation dependent library (CDL) restraints added in 1.8 seconds 9164 Ramachandran restraints generated. 4582 Oldfield, 0 Emsley, 4582 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8806 Finding SS restraints... Secondary structure from input PDB file: 218 helices and 6 sheets defined 70.9% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 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: 4.248A 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: 3.530A pdb=" N ASN S 46 " --> pdb=" O SER S 42 " (cutoff:3.500A) removed outlier: 4.085A 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 36 removed outlier: 3.509A pdb=" N VAL U 20 " --> pdb=" O GLU U 16 " (cutoff:3.500A) Proline residue: U 33 - end of helix 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 11 Processing helix chain 'V' and resid 17 through 44 Processing helix chain 'V' and resid 48 through 82 Processing helix chain 'V' and resid 86 through 106 removed outlier: 4.144A 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 120 through 125 removed outlier: 3.606A pdb=" N LEU W 124 " --> pdb=" O MET W 120 " (cutoff:3.500A) Processing helix chain 'W' and resid 129 through 143 removed outlier: 6.357A pdb=" N PHE W 140 " --> pdb=" O ALA W 136 " (cutoff:3.500A) removed outlier: 5.570A 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 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: 3.515A 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 removed outlier: 3.613A pdb=" N TRP Y 92 " --> pdb=" O PRO Y 89 " (cutoff:3.500A) Processing helix chain 'Z' and resid 18 through 22 removed outlier: 3.548A pdb=" N TRP Z 22 " --> pdb=" O TYR Z 19 " (cutoff:3.500A) Processing helix chain 'Z' and resid 27 through 38 removed outlier: 3.768A pdb=" N THR Z 31 " --> pdb=" O THR Z 27 " (cutoff:3.500A) Processing helix chain 'Z' and resid 45 through 50 removed outlier: 3.935A pdb=" N GLU Z 49 " --> pdb=" O TRP Z 45 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA Z 50 " --> pdb=" O GLY Z 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 45 through 50' Processing helix chain 'Z' and resid 51 through 54 removed outlier: 3.713A pdb=" N SER Z 54 " --> pdb=" O TRP Z 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 51 through 54' 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: 3.659A pdb=" N TYR a 112 " --> pdb=" O HIS a 109 " (cutoff:3.500A) removed outlier: 3.882A 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: 4.103A 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 25 Processing helix chain 'b' and resid 65 through 75 Processing helix chain 'b' and resid 75 through 89 Processing helix chain 'c' and resid 33 through 37 removed outlier: 3.650A pdb=" N PHE c 37 " --> pdb=" O LYS c 34 " (cutoff:3.500A) 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 58 removed outlier: 4.045A pdb=" N TYR d 32 " --> pdb=" O ASN d 28 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ARG d 43 " --> pdb=" O LEU d 39 " (cutoff:3.500A) Proline residue: d 44 - end of helix Processing helix chain 'd' and resid 73 through 77 Processing helix chain 'd' and resid 81 through 118 removed outlier: 3.858A 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: 4.206A 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: 3.848A pdb=" N SER e 103 " --> pdb=" O LEU e 99 " (cutoff:3.500A) Processing helix chain 'e' and resid 114 through 132 removed outlier: 3.593A pdb=" N ALA e 118 " --> pdb=" O MET e 114 " (cutoff:3.500A) 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 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: 3.915A 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: 3.531A 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: 4.277A 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 146 through 149 Processing helix chain 'i' and resid 150 through 170 removed outlier: 3.772A 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: 3.610A 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 removed outlier: 3.622A pdb=" N THR i 241 " --> pdb=" O MET i 237 " (cutoff:3.500A) Processing helix chain 'i' and resid 259 through 273 removed outlier: 4.562A pdb=" N LYS i 263 " --> pdb=" O GLY i 259 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN i 273 " --> pdb=" O GLU i 269 " (cutoff:3.500A) Processing helix chain 'i' and resid 276 through 301 removed outlier: 4.317A pdb=" N LEU i 288 " --> pdb=" O MET i 284 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASN i 289 " --> pdb=" O THR i 285 " (cutoff:3.500A) Processing helix chain 'i' and resid 310 through 315 removed outlier: 3.890A 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 removed outlier: 3.558A pdb=" N SER i 344 " --> pdb=" O PRO i 341 " (cutoff:3.500A) 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: 3.814A pdb=" N PHE j 56 " --> pdb=" O SER j 52 " (cutoff:3.500A) Processing helix chain 'j' and resid 74 through 79 removed outlier: 3.518A 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 3 through 22 removed outlier: 3.822A pdb=" N TYR k 22 " --> pdb=" O GLY k 18 " (cutoff:3.500A) Processing helix chain 'k' and resid 25 through 51 removed outlier: 3.658A pdb=" N SER k 29 " --> pdb=" O HIS k 25 " (cutoff:3.500A) Processing helix chain 'k' and resid 53 through 56 Processing helix chain 'k' and resid 57 through 86 removed outlier: 4.634A pdb=" N ILE k 61 " --> pdb=" O ASN k 57 " (cutoff:3.500A) Processing helix chain 'k' and resid 89 through 93 Processing helix chain 'l' and resid 2 through 15 removed outlier: 4.444A pdb=" N SER l 6 " --> pdb=" O ASN l 2 " (cutoff:3.500A) removed outlier: 3.751A 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 57 removed outlier: 4.155A 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: 3.801A pdb=" N TRP l 106 " --> pdb=" O GLU l 102 " (cutoff:3.500A) Processing helix chain 'l' and resid 113 through 134 Processing helix chain 'l' and resid 136 through 156 Processing helix chain 'l' and resid 161 through 194 removed outlier: 3.968A 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: 4.233A pdb=" N LEU l 213 " --> pdb=" O PRO l 209 " (cutoff:3.500A) Processing helix chain 'l' and resid 226 through 230 removed outlier: 3.808A 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 270 through 293 removed outlier: 3.662A pdb=" N GLN l 274 " --> pdb=" O ASN l 270 " (cutoff:3.500A) Processing helix chain 'l' and resid 297 through 319 Processing helix chain 'l' and resid 321 through 350 removed outlier: 3.756A pdb=" N PHE l 334 " --> pdb=" O CYS l 330 " (cutoff:3.500A) Processing helix chain 'l' and resid 355 through 359 removed outlier: 3.593A pdb=" N MET l 359 " --> pdb=" O ILE l 356 " (cutoff:3.500A) Processing helix chain 'l' and resid 366 through 381 Processing helix chain 'l' and resid 388 through 401 removed outlier: 4.819A pdb=" N LEU l 394 " --> pdb=" O TYR l 390 " (cutoff:3.500A) Processing helix chain 'l' and resid 406 through 432 removed outlier: 3.670A pdb=" N LEU l 432 " --> pdb=" O PHE l 428 " (cutoff:3.500A) Processing helix chain 'l' and resid 447 through 472 removed outlier: 3.745A pdb=" N LEU l 457 " --> pdb=" O SER l 453 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N GLY l 465 " --> pdb=" O SER l 461 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N PHE l 466 " --> pdb=" O ILE l 462 " (cutoff:3.500A) Processing helix chain 'l' and resid 483 through 488 Processing helix chain 'l' and resid 488 through 507 removed outlier: 3.607A 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: 3.518A pdb=" N MET l 544 " --> pdb=" O HIS l 540 " (cutoff:3.500A) Processing helix chain 'l' and resid 556 through 562 removed outlier: 3.723A 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 602 removed outlier: 3.730A pdb=" N PHE l 602 " --> pdb=" O SER l 598 " (cutoff:3.500A) Processing helix chain 'm' and resid 5 through 22 Processing helix chain 'm' and resid 25 through 48 Processing helix chain 'm' and resid 49 through 75 removed outlier: 3.854A pdb=" N LEU m 61 " --> pdb=" O PHE m 57 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU m 65 " --> pdb=" O LEU m 61 " (cutoff:3.500A) removed outlier: 4.717A 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 150 through 174 removed outlier: 4.498A pdb=" N GLY m 174 " --> pdb=" O GLU m 170 " (cutoff:3.500A) Processing helix chain 'n' and resid 7 through 12 Processing helix chain 'n' and resid 15 through 35 removed outlier: 3.559A pdb=" N GLU n 33 " --> pdb=" O ARG n 29 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS n 34 " --> pdb=" O ARG n 30 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU n 35 " --> pdb=" O SER n 31 " (cutoff:3.500A) Processing helix chain 'n' and resid 36 through 39 Processing helix chain 'o' and resid 15 through 23 Proline residue: o 20 - end of helix 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 49 Processing helix chain 'p' and resid 50 through 52 No H-bonds generated for 'chain 'p' and resid 50 through 52' Processing helix chain 'p' and resid 56 through 63 removed outlier: 3.625A pdb=" N ALA p 60 " --> pdb=" O ASP p 56 " (cutoff:3.500A) Processing helix chain 'p' and resid 65 through 74 Processing helix chain 'p' and resid 92 through 98 removed outlier: 4.447A pdb=" N CYS p 96 " --> pdb=" O ARG p 93 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS p 98 " --> pdb=" O GLU p 95 " (cutoff:3.500A) Processing helix chain 'p' and resid 100 through 107 Processing helix chain 'p' and resid 108 through 114 removed outlier: 4.049A pdb=" N MET p 114 " --> pdb=" O SER p 110 " (cutoff:3.500A) Processing helix chain 'p' and resid 115 through 144 removed outlier: 3.593A pdb=" N PHE p 119 " --> pdb=" O TYR p 115 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU p 134 " --> pdb=" O ARG p 130 " (cutoff:3.500A) removed outlier: 3.935A 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: 4.206A 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: 3.548A 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 82 removed outlier: 4.190A pdb=" N LEU r 65 " --> pdb=" O LEU r 61 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU r 73 " --> pdb=" O THR r 69 " (cutoff:3.500A) Proline residue: r 74 - end of helix removed outlier: 4.405A pdb=" N SER r 82 " --> pdb=" O MET r 78 " (cutoff:3.500A) Processing helix chain 'r' and resid 88 through 112 Processing helix chain 'r' and resid 114 through 125 Processing helix chain 'r' and resid 125 through 137 removed outlier: 3.815A pdb=" N THR r 129 " --> pdb=" O THR r 125 " (cutoff:3.500A) Processing helix chain 'r' and resid 141 through 171 removed outlier: 3.857A pdb=" N THR r 153 " --> pdb=" O PHE r 149 " (cutoff:3.500A) Proline residue: r 159 - end of helix Processing helix chain 'r' and resid 175 through 182 Processing helix chain 'r' and resid 189 through 207 removed outlier: 4.509A pdb=" N ALA r 202 " --> pdb=" O ALA r 198 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N PHE r 203 " --> pdb=" O CYS r 199 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS r 206 " --> pdb=" O ALA r 202 " (cutoff:3.500A) Processing helix chain 'r' and resid 214 through 223 removed outlier: 4.123A 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: 4.028A pdb=" N GLY r 240 " --> pdb=" O LEU r 236 " (cutoff:3.500A) Processing helix chain 'r' and resid 248 through 250 No H-bonds generated for 'chain 'r' and resid 248 through 250' Processing helix chain 'r' and resid 253 through 258 Processing helix chain 'r' and resid 258 through 278 removed outlier: 4.029A pdb=" N ILE r 270 " --> pdb=" O MET r 266 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU r 277 " --> pdb=" O SER r 273 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG r 278 " --> pdb=" O SER r 274 " (cutoff:3.500A) Processing helix chain 'r' and resid 281 through 304 removed outlier: 3.572A pdb=" N GLN r 304 " --> pdb=" O ALA r 300 " (cutoff:3.500A) Processing helix chain 'r' and resid 305 through 338 removed outlier: 3.926A pdb=" N ARG r 336 " --> pdb=" O THR r 332 " (cutoff:3.500A) Processing helix chain 'r' and resid 347 through 352 removed outlier: 4.161A pdb=" N LEU r 351 " --> pdb=" O GLY r 347 " (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: 4.278A pdb=" N LEU r 395 " --> pdb=" O ILE r 391 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR r 414 " --> pdb=" O MET r 410 " (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: 6.495A pdb=" N LYS r 452 " --> pdb=" O LEU r 449 " (cutoff:3.500A) Processing helix chain 's' and resid 2 through 32 Proline residue: s 12 - end of helix removed outlier: 3.835A pdb=" N THR s 21 " --> pdb=" O VAL s 17 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LEU s 22 " --> pdb=" O ALA s 18 " (cutoff:3.500A) Processing helix chain 's' and resid 46 through 57 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 122 removed outlier: 4.210A pdb=" N ILE s 116 " --> pdb=" O ALA s 112 " (cutoff:3.500A) Processing helix chain 's' and resid 125 through 155 removed outlier: 3.845A pdb=" N THR s 145 " --> pdb=" O SER s 141 " (cutoff:3.500A) Processing helix chain 's' and resid 163 through 169 removed outlier: 3.688A pdb=" N THR s 167 " --> pdb=" O SER s 163 " (cutoff:3.500A) Processing helix chain 's' and resid 173 through 178 removed outlier: 3.890A pdb=" N THR s 177 " --> pdb=" O TRP s 173 " (cutoff:3.500A) Processing helix chain 's' and resid 178 through 193 removed outlier: 3.687A 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: 4.427A pdb=" N TYR s 255 " --> pdb=" O THR s 251 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR s 277 " --> pdb=" O ILE s 273 " (cutoff:3.500A) Processing helix chain 's' and resid 281 through 312 removed outlier: 5.028A 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 21 through 28 Processing helix chain 'u' and resid 28 through 36 Processing helix chain 'u' and resid 36 through 51 removed outlier: 3.587A 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 78 Processing helix chain 'u' and resid 78 through 92 removed outlier: 3.858A pdb=" N SER u 92 " --> pdb=" O CYS u 88 " (cutoff:3.500A) Processing helix chain 'u' and resid 100 through 115 removed outlier: 3.524A pdb=" N GLN u 104 " --> pdb=" O CYS u 100 " (cutoff:3.500A) Processing helix chain 'v' and resid 3 through 11 Processing helix chain 'v' and resid 12 through 16 Processing helix chain 'v' and resid 42 through 49 Processing helix chain 'v' and resid 59 through 73 Processing helix chain 'v' and resid 81 through 125 Processing helix chain 'w' and resid 39 through 46 Processing helix chain 'w' and resid 49 through 53 Processing helix chain 'w' and resid 69 through 82 Processing helix chain 'w' and resid 94 through 98 removed outlier: 3.560A pdb=" N THR w 98 " --> pdb=" O ASP w 95 " (cutoff:3.500A) Processing helix chain 'w' and resid 113 through 120 removed outlier: 3.512A pdb=" N PHE w 117 " --> pdb=" O SER w 113 " (cutoff:3.500A) Processing helix chain 'w' and resid 126 through 154 Processing helix chain 'w' and resid 166 through 176 removed outlier: 4.067A pdb=" N LEU w 170 " --> pdb=" O ASP w 166 " (cutoff:3.500A) Processing helix chain 'w' and resid 180 through 196 removed outlier: 3.603A pdb=" N VAL w 184 " --> pdb=" O ARG w 180 " (cutoff:3.500A) Processing helix chain 'w' and resid 210 through 222 removed outlier: 3.608A 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 251 removed outlier: 3.594A pdb=" N LEU w 234 " --> pdb=" O THR w 230 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LEU w 246 " --> pdb=" O LYS w 242 " (cutoff:3.500A) Proline residue: w 247 - end of helix Processing helix chain 'w' and resid 265 through 276 removed outlier: 4.048A 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 Processing helix chain 'w' and resid 306 through 310 removed outlier: 3.900A pdb=" N THR w 309 " --> pdb=" O ASN w 306 " (cutoff:3.500A) removed outlier: 3.765A 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 334 removed outlier: 3.587A pdb=" N LEU w 334 " --> pdb=" O LYS w 330 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'U' and resid 57 through 58 removed outlier: 6.565A 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 99 Processing sheet with id=AA3, first strand: chain 'b' and resid 97 through 99 removed outlier: 5.745A pdb=" N ILE l 62 " --> pdb=" O MET l 82 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N MET l 82 " --> pdb=" O ILE l 62 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N SER l 64 " --> pdb=" O PHE l 80 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N PHE l 80 " --> pdb=" O SER l 64 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TRP l 66 " --> pdb=" O LEU l 78 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LEU l 76 " --> pdb=" O TRP l 68 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N THR l 70 " --> pdb=" O VAL l 74 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL l 74 " --> pdb=" O THR l 70 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'c' and resid 151 through 152 Processing sheet with id=AA5, first strand: chain 'i' and resid 307 through 308 Processing sheet with id=AA6, first strand: chain 'w' and resid 84 through 86 removed outlier: 6.457A pdb=" N ARG w 84 " --> pdb=" O VAL w 158 " (cutoff:3.500A) 2305 hydrogen bonds defined for protein. 6705 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: 6.48 Time building geometry restraints manager: 4.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5863 1.31 - 1.44: 10781 1.44 - 1.56: 22358 1.56 - 1.69: 164 1.69 - 1.82: 511 Bond restraints: 39677 Sorted by residual: bond pdb=" C3' ADP w 401 " pdb=" C4' ADP w 401 " ideal model delta sigma weight residual 1.524 1.301 0.223 2.00e-02 2.50e+03 1.25e+02 bond pdb=" CA7 CDL r 503 " pdb=" OA8 CDL r 503 " 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 r 503 " pdb=" OB8 CDL r 503 " ideal model delta sigma weight residual 1.334 1.452 -0.118 1.10e-02 8.26e+03 1.14e+02 bond pdb=" C4' ADP w 401 " pdb=" O4' ADP w 401 " ideal model delta sigma weight residual 1.426 1.618 -0.192 2.00e-02 2.50e+03 9.22e+01 bond pdb=" CA7 CDL V 201 " pdb=" OA8 CDL V 201 " ideal model delta sigma weight residual 1.334 1.432 -0.098 1.10e-02 8.26e+03 7.95e+01 ... (remaining 39672 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.48: 53070 3.48 - 6.95: 449 6.95 - 10.43: 74 10.43 - 13.91: 17 13.91 - 17.38: 7 Bond angle restraints: 53617 Sorted by residual: angle pdb=" C11 CDL r 503 " pdb=" CA5 CDL r 503 " pdb=" OA6 CDL r 503 " ideal model delta sigma weight residual 111.33 121.81 -10.48 1.32e+00 5.72e-01 6.28e+01 angle pdb=" C11 CDL i 401 " pdb=" CA5 CDL i 401 " pdb=" OA6 CDL i 401 " ideal model delta sigma weight residual 111.33 120.92 -9.59 1.32e+00 5.72e-01 5.26e+01 angle pdb=" C11 CDL a 201 " pdb=" CA5 CDL a 201 " pdb=" OA6 CDL a 201 " ideal model delta sigma weight residual 111.33 120.90 -9.57 1.32e+00 5.72e-01 5.24e+01 angle pdb=" C51 CDL V 201 " pdb=" CB5 CDL V 201 " pdb=" OB6 CDL V 201 " ideal model delta sigma weight residual 111.33 120.74 -9.41 1.32e+00 5.72e-01 5.07e+01 angle pdb=" C51 CDL a 201 " pdb=" CB5 CDL a 201 " pdb=" OB6 CDL a 201 " ideal model delta sigma weight residual 111.33 120.59 -9.26 1.32e+00 5.72e-01 4.90e+01 ... (remaining 53612 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.23: 22727 33.23 - 66.47: 1261 66.47 - 99.70: 91 99.70 - 132.93: 22 132.93 - 166.17: 15 Dihedral angle restraints: 24116 sinusoidal: 10490 harmonic: 13626 Sorted by residual: dihedral pdb=" CB CYS u 88 " pdb=" SG CYS u 88 " pdb=" SG CYS u 100 " pdb=" CB CYS u 100 " ideal model delta sinusoidal sigma weight residual 93.00 161.51 -68.51 1 1.00e+01 1.00e-02 6.08e+01 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 85.21 -145.21 1 2.00e+01 2.50e-03 4.37e+01 dihedral pdb=" CA ILE a 93 " pdb=" C ILE a 93 " pdb=" N GLY a 94 " pdb=" CA GLY a 94 " ideal model delta harmonic sigma weight residual -180.00 -151.57 -28.43 0 5.00e+00 4.00e-02 3.23e+01 ... (remaining 24113 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 5118 0.066 - 0.131: 662 0.131 - 0.197: 41 0.197 - 0.263: 6 0.263 - 0.328: 5 Chirality restraints: 5832 Sorted by residual: chirality pdb=" C6 PLX g 201 " pdb=" C7 PLX g 201 " pdb=" O6 PLX g 201 " pdb=" O7 PLX g 201 " both_signs ideal model delta sigma weight residual False 2.01 2.34 -0.33 2.00e-01 2.50e+01 2.69e+00 chirality pdb=" C6 PLX r 502 " pdb=" C7 PLX r 502 " pdb=" O6 PLX r 502 " pdb=" O7 PLX r 502 " both_signs ideal model delta sigma weight residual False 2.01 2.34 -0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" C6 PLX e 201 " pdb=" C7 PLX e 201 " pdb=" O6 PLX e 201 " pdb=" O7 PLX e 201 " both_signs ideal model delta sigma weight residual False 2.01 2.32 -0.31 2.00e-01 2.50e+01 2.36e+00 ... (remaining 5829 not shown) Planarity restraints: 6559 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS Q 62 " -0.070 5.00e-02 4.00e+02 1.05e-01 1.77e+01 pdb=" N PRO Q 63 " 0.182 5.00e-02 4.00e+02 pdb=" CA PRO Q 63 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO Q 63 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER o 26 " 0.049 5.00e-02 4.00e+02 7.38e-02 8.72e+00 pdb=" N PRO o 27 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO o 27 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO o 27 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY s 218 " -0.043 5.00e-02 4.00e+02 6.61e-02 6.98e+00 pdb=" N PRO s 219 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO s 219 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO s 219 " -0.037 5.00e-02 4.00e+02 ... (remaining 6556 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3372 2.74 - 3.28: 38416 3.28 - 3.82: 67599 3.82 - 4.36: 82802 4.36 - 4.90: 137842 Nonbonded interactions: 330031 Sorted by model distance: nonbonded pdb=" O THR l 13 " pdb=" OG1 THR l 16 " model vdw 2.199 3.040 nonbonded pdb=" O ALA g 58 " pdb=" O TRP w 353 " model vdw 2.210 3.040 nonbonded pdb=" OE2 GLU i 269 " pdb=" O HOH i 501 " model vdw 2.213 3.040 nonbonded pdb=" OG1 THR r 153 " pdb=" O HOH r 601 " model vdw 2.217 3.040 nonbonded pdb=" NE2 GLN r 81 " pdb=" O HOH r 602 " model vdw 2.218 3.120 ... (remaining 330026 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=0.62 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: 9.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.480 Check model and map are aligned: 0.150 Set scattering table: 0.110 Process input model: 31.270 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 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:8.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 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 : 0.007 0.223 39684 Z= 0.374 Angle : 0.857 33.805 53629 Z= 0.435 Chirality : 0.044 0.328 5832 Planarity : 0.006 0.105 6559 Dihedral : 19.438 166.168 15292 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.80 % Favored : 96.12 % Rotamer: Outliers : 1.35 % Allowed : 15.40 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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: 1.51 (0.12), residues: 4582 helix: 1.80 (0.10), residues: 2940 sheet: 1.08 (1.27), residues: 20 loop : -0.46 (0.15), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG m 173 TYR 0.030 0.002 TYR l 422 PHE 0.029 0.002 PHE i 292 TRP 0.038 0.001 TRP c 145 HIS 0.005 0.001 HIS p 26 Details of bonding type rmsd covalent geometry : bond 0.00679 (39677) covalent geometry : angle 0.84199 (53617) SS BOND : bond 0.06858 ( 6) SS BOND : angle 10.71603 ( 12) hydrogen bonds : bond 0.13306 ( 2305) hydrogen bonds : angle 5.32211 ( 6705) Misc. bond : bond 0.04948 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9164 Ramachandran restraints generated. 4582 Oldfield, 0 Emsley, 4582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9164 Ramachandran restraints generated. 4582 Oldfield, 0 Emsley, 4582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 746 residues out of total 4086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 691 time to evaluate : 1.468 Fit side-chains revert: symmetry clash REVERT: c 103 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8010 (pt0) REVERT: e 72 ASP cc_start: 0.7821 (m-30) cc_final: 0.7508 (m-30) REVERT: g 21 ARG cc_start: 0.8527 (mtm180) cc_final: 0.8298 (mtp180) REVERT: h 97 HIS cc_start: 0.6709 (OUTLIER) cc_final: 0.6317 (m-70) REVERT: l 525 MET cc_start: 0.9226 (OUTLIER) cc_final: 0.7652 (mpp) REVERT: p 54 GLU cc_start: 0.7242 (tt0) cc_final: 0.6778 (tt0) REVERT: p 127 ARG cc_start: 0.8146 (ptp90) cc_final: 0.7861 (ptt-90) REVERT: r 123 GLU cc_start: 0.8928 (OUTLIER) cc_final: 0.8587 (mp0) REVERT: w 355 LYS cc_start: 0.7910 (mttt) cc_final: 0.7585 (mttp) outliers start: 55 outliers final: 43 residues processed: 734 average time/residue: 0.8077 time to fit residues: 701.6698 Evaluate side-chains 714 residues out of total 4086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 668 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 77 SER Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 105 THR Chi-restraints excluded: chain X residue 140 CYS Chi-restraints excluded: chain Z residue 24 ILE Chi-restraints excluded: chain a residue 130 GLU Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain d residue 39 LEU Chi-restraints excluded: chain h residue 97 HIS Chi-restraints excluded: chain i residue 67 SER Chi-restraints excluded: chain i residue 257 LEU Chi-restraints excluded: chain i residue 263 LYS Chi-restraints excluded: chain j residue 57 LEU Chi-restraints excluded: chain l residue 52 LEU Chi-restraints excluded: chain l residue 59 GLN Chi-restraints excluded: chain l residue 60 GLU Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 132 VAL Chi-restraints excluded: chain l residue 293 ILE Chi-restraints excluded: chain l residue 349 SER Chi-restraints excluded: chain l residue 489 THR Chi-restraints excluded: chain l residue 500 LEU Chi-restraints excluded: chain l residue 525 MET Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 578 SER Chi-restraints excluded: chain m residue 50 SER Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain r residue 123 GLU Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 332 THR Chi-restraints excluded: chain r residue 337 VAL Chi-restraints excluded: chain s residue 17 VAL Chi-restraints excluded: chain s residue 73 ILE Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 155 LEU Chi-restraints excluded: chain u residue 62 LEU Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain u residue 106 LYS Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain w residue 67 CYS Chi-restraints excluded: chain w residue 213 GLU Chi-restraints excluded: chain w residue 241 TYR 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: 4.9990 chunk 388 optimal weight: 9.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.0870 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 7.9990 chunk 401 optimal weight: 8.9990 chunk 424 optimal weight: 6.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 124 ASN d 140 GLN g 18 ASN ** g 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 310 ASN k 91 GLN l 351 ASN m 46 ASN p 141 GLN s 171 HIS s 284 GLN u 64 ASN w 37 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.121846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.094050 restraints weight = 46361.934| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 1.31 r_work: 0.2799 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2680 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2680 r_free = 0.2680 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2680 r_free = 0.2680 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2680 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8950 moved from start: 0.0620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 39684 Z= 0.165 Angle : 0.614 9.610 53629 Z= 0.312 Chirality : 0.043 0.199 5832 Planarity : 0.005 0.080 6559 Dihedral : 17.014 166.688 6240 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.49 % Favored : 96.46 % Rotamer: Outliers : 3.22 % Allowed : 14.09 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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 (0.12), residues: 4582 helix: 2.04 (0.09), residues: 2975 sheet: 0.94 (1.25), residues: 20 loop : -0.37 (0.16), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG m 173 TYR 0.025 0.002 TYR l 422 PHE 0.030 0.002 PHE i 292 TRP 0.024 0.001 TRP l 144 HIS 0.006 0.001 HIS p 26 Details of bonding type rmsd covalent geometry : bond 0.00378 (39677) covalent geometry : angle 0.61345 (53617) SS BOND : bond 0.00820 ( 6) SS BOND : angle 1.68807 ( 12) hydrogen bonds : bond 0.06323 ( 2305) hydrogen bonds : angle 4.21002 ( 6705) Misc. bond : bond 0.00082 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9164 Ramachandran restraints generated. 4582 Oldfield, 0 Emsley, 4582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9164 Ramachandran restraints generated. 4582 Oldfield, 0 Emsley, 4582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 814 residues out of total 4086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 683 time to evaluate : 1.555 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 52 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.7799 (mmm) REVERT: S 44 GLN cc_start: 0.9089 (OUTLIER) cc_final: 0.8880 (mt0) REVERT: U 40 ASN cc_start: 0.8325 (OUTLIER) cc_final: 0.8061 (t0) REVERT: V 95 CYS cc_start: 0.7115 (t) cc_final: 0.6880 (t) REVERT: V 118 MET cc_start: 0.8698 (mtt) cc_final: 0.8401 (mtt) REVERT: c 63 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7630 (tm-30) REVERT: c 103 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8088 (pt0) REVERT: f 60 LYS cc_start: 0.8622 (ttmt) cc_final: 0.8345 (tmtp) REVERT: g 21 ARG cc_start: 0.8737 (mtm180) cc_final: 0.8356 (mtp180) REVERT: i 236 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8604 (tttm) REVERT: i 324 LYS cc_start: 0.6612 (OUTLIER) cc_final: 0.5729 (tmtm) REVERT: l 140 LEU cc_start: 0.9436 (OUTLIER) cc_final: 0.9031 (tt) REVERT: l 475 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.8046 (mtt) REVERT: l 525 MET cc_start: 0.9176 (OUTLIER) cc_final: 0.7982 (mpt) REVERT: n 58 LYS cc_start: 0.8173 (tppt) cc_final: 0.7881 (tptp) REVERT: p 48 PHE cc_start: 0.8755 (OUTLIER) cc_final: 0.8089 (t80) REVERT: p 127 ARG cc_start: 0.8275 (ptp90) cc_final: 0.7887 (ptt-90) REVERT: r 123 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8256 (mp0) REVERT: u 102 LYS cc_start: 0.8373 (ttpt) cc_final: 0.7532 (mmmt) REVERT: u 109 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7229 (tp30) REVERT: w 355 LYS cc_start: 0.7846 (mttt) cc_final: 0.7573 (mmtp) outliers start: 131 outliers final: 60 residues processed: 741 average time/residue: 0.8469 time to fit residues: 743.3461 Evaluate side-chains 738 residues out of total 4086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 666 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 44 GLN Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain U residue 40 ASN Chi-restraints excluded: chain U residue 68 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 64 ASP Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain Z residue 24 ILE Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 127 ASP Chi-restraints excluded: chain a residue 130 GLU Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain b residue 9 LYS Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain c residue 63 GLU Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 181 VAL Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain e residue 99 LEU Chi-restraints excluded: chain g residue 110 THR Chi-restraints excluded: chain h residue 97 HIS Chi-restraints excluded: chain i residue 236 LYS Chi-restraints excluded: chain i residue 237 MET Chi-restraints excluded: chain i residue 257 LEU Chi-restraints excluded: chain i residue 271 THR Chi-restraints excluded: chain i residue 278 MET Chi-restraints excluded: chain i residue 324 LYS Chi-restraints excluded: chain k residue 4 VAL Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain k residue 91 GLN Chi-restraints excluded: chain l residue 52 LEU Chi-restraints excluded: chain l residue 59 GLN Chi-restraints excluded: chain l residue 60 GLU Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 132 VAL Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 293 ILE Chi-restraints excluded: chain l residue 366 MET Chi-restraints excluded: chain l residue 475 MET Chi-restraints excluded: chain l residue 500 LEU Chi-restraints excluded: chain l residue 525 MET Chi-restraints excluded: chain m residue 5 ILE Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain o residue 88 LEU Chi-restraints excluded: chain p residue 48 PHE Chi-restraints excluded: chain p residue 151 THR Chi-restraints excluded: chain r residue 123 GLU Chi-restraints excluded: chain r residue 126 LEU Chi-restraints excluded: chain r residue 138 ASN Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 187 SER Chi-restraints excluded: chain r residue 332 THR Chi-restraints excluded: chain r residue 337 VAL Chi-restraints excluded: chain r residue 342 MET Chi-restraints excluded: chain s residue 73 ILE Chi-restraints excluded: chain s residue 91 MET Chi-restraints excluded: chain s residue 119 SER Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 155 LEU Chi-restraints excluded: chain u residue 62 LEU Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain u residue 109 GLU Chi-restraints excluded: chain v residue 14 SER Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain w residue 347 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 258 optimal weight: 6.9990 chunk 131 optimal weight: 4.9990 chunk 19 optimal weight: 20.0000 chunk 123 optimal weight: 0.7980 chunk 58 optimal weight: 0.3980 chunk 120 optimal weight: 7.9990 chunk 441 optimal weight: 6.9990 chunk 10 optimal weight: 0.3980 chunk 442 optimal weight: 3.9990 chunk 437 optimal weight: 6.9990 chunk 159 optimal weight: 8.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 18 ASN ** g 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 27 HIS k 91 GLN l 351 ASN m 46 ASN p 141 GLN r 139 GLN r 390 ASN s 287 HIS u 64 ASN w 37 GLN w 127 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.121643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.093981 restraints weight = 46103.862| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 1.29 r_work: 0.2799 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2715 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2715 r_free = 0.2715 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2715 r_free = 0.2715 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2715 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8947 moved from start: 0.0828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 39684 Z= 0.155 Angle : 0.591 9.891 53629 Z= 0.301 Chirality : 0.042 0.199 5832 Planarity : 0.005 0.072 6559 Dihedral : 15.947 167.261 6207 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.56 % Favored : 96.40 % Rotamer: Outliers : 3.62 % Allowed : 14.51 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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: 1.93 (0.12), residues: 4582 helix: 2.14 (0.09), residues: 2977 sheet: 0.47 (1.12), residues: 25 loop : -0.37 (0.16), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG m 173 TYR 0.023 0.002 TYR l 422 PHE 0.030 0.002 PHE i 292 TRP 0.024 0.001 TRP l 144 HIS 0.008 0.001 HIS r 30 Details of bonding type rmsd covalent geometry : bond 0.00357 (39677) covalent geometry : angle 0.59063 (53617) SS BOND : bond 0.00504 ( 6) SS BOND : angle 1.74708 ( 12) hydrogen bonds : bond 0.06024 ( 2305) hydrogen bonds : angle 4.08826 ( 6705) Misc. bond : bond 0.00015 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9164 Ramachandran restraints generated. 4582 Oldfield, 0 Emsley, 4582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9164 Ramachandran restraints generated. 4582 Oldfield, 0 Emsley, 4582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 837 residues out of total 4086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 690 time to evaluate : 1.612 Fit side-chains revert: symmetry clash REVERT: Q 52 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.7705 (mmm) REVERT: S 44 GLN cc_start: 0.9089 (OUTLIER) cc_final: 0.8859 (mt0) REVERT: S 66 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8119 (mp) REVERT: U 40 ASN cc_start: 0.8300 (OUTLIER) cc_final: 0.8031 (t0) REVERT: V 95 CYS cc_start: 0.7171 (t) cc_final: 0.6903 (t) REVERT: V 118 MET cc_start: 0.8727 (mtt) cc_final: 0.8476 (mtt) REVERT: Z 49 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.7368 (mm-30) REVERT: c 63 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7630 (tm-30) REVERT: c 103 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8092 (pt0) REVERT: d 134 GLN cc_start: 0.8831 (mt0) cc_final: 0.8371 (tm-30) REVERT: f 60 LYS cc_start: 0.8624 (ttmt) cc_final: 0.8419 (tmtp) REVERT: g 4 MET cc_start: 0.8910 (OUTLIER) cc_final: 0.8650 (mtt) REVERT: g 21 ARG cc_start: 0.8763 (mtm180) cc_final: 0.8474 (mtp180) REVERT: h 32 ARG cc_start: 0.8936 (ttp80) cc_final: 0.8725 (ttm170) REVERT: i 236 LYS cc_start: 0.9045 (OUTLIER) cc_final: 0.8556 (tttm) REVERT: i 324 LYS cc_start: 0.6624 (OUTLIER) cc_final: 0.5745 (tmtm) REVERT: l 60 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.7739 (mp0) REVERT: l 140 LEU cc_start: 0.9421 (OUTLIER) cc_final: 0.9012 (tt) REVERT: l 475 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.8013 (mtt) REVERT: l 500 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8658 (mp) REVERT: l 525 MET cc_start: 0.9133 (OUTLIER) cc_final: 0.7940 (mpt) REVERT: n 58 LYS cc_start: 0.8154 (tppt) cc_final: 0.7825 (mmtm) REVERT: o 5 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8561 (mtmt) REVERT: o 114 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7700 (mppt) REVERT: p 48 PHE cc_start: 0.8778 (OUTLIER) cc_final: 0.8153 (t80) REVERT: p 55 LYS cc_start: 0.7163 (OUTLIER) cc_final: 0.6572 (mtpt) REVERT: r 123 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8264 (mp0) REVERT: r 448 THR cc_start: 0.8871 (OUTLIER) cc_final: 0.8589 (m) REVERT: u 102 LYS cc_start: 0.8376 (ttpt) cc_final: 0.7580 (mmmt) REVERT: u 109 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7228 (tp30) REVERT: v 111 ARG cc_start: 0.7332 (OUTLIER) cc_final: 0.6327 (mtp180) outliers start: 147 outliers final: 64 residues processed: 763 average time/residue: 0.8575 time to fit residues: 777.9105 Evaluate side-chains 752 residues out of total 4086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 666 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 44 GLN Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain S residue 66 LEU Chi-restraints excluded: chain U residue 39 THR Chi-restraints excluded: chain U residue 40 ASN Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain V residue 4 THR Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain Z residue 24 ILE Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 127 ASP Chi-restraints excluded: chain a residue 130 GLU Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain b residue 9 LYS Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain c residue 63 GLU Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 181 VAL Chi-restraints excluded: chain d residue 39 LEU Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 99 LEU Chi-restraints excluded: chain g residue 4 MET Chi-restraints excluded: chain g residue 110 THR Chi-restraints excluded: chain h residue 74 LYS Chi-restraints excluded: chain h residue 97 HIS Chi-restraints excluded: chain i residue 146 SER Chi-restraints excluded: chain i residue 236 LYS Chi-restraints excluded: chain i residue 237 MET Chi-restraints excluded: chain i residue 257 LEU Chi-restraints excluded: chain i residue 278 MET Chi-restraints excluded: chain i residue 324 LYS Chi-restraints excluded: chain k residue 4 VAL Chi-restraints excluded: chain k residue 70 GLU Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain l residue 52 LEU Chi-restraints excluded: chain l residue 59 GLN Chi-restraints excluded: chain l residue 60 GLU Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 79 SER Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 293 ILE Chi-restraints excluded: chain l residue 405 ASN Chi-restraints excluded: chain l residue 475 MET Chi-restraints excluded: chain l residue 500 LEU Chi-restraints excluded: chain l residue 525 MET Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain o residue 5 LYS Chi-restraints excluded: chain o residue 88 LEU Chi-restraints excluded: chain o residue 114 LYS Chi-restraints excluded: chain p residue 48 PHE Chi-restraints excluded: chain p residue 55 LYS Chi-restraints excluded: chain p residue 151 THR Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 123 GLU Chi-restraints excluded: chain r residue 126 LEU Chi-restraints excluded: chain r residue 138 ASN Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 183 SER Chi-restraints excluded: chain r residue 187 SER Chi-restraints excluded: chain r residue 332 THR Chi-restraints excluded: chain r residue 337 VAL Chi-restraints excluded: chain r residue 342 MET Chi-restraints excluded: chain r residue 448 THR Chi-restraints excluded: chain s residue 73 ILE Chi-restraints excluded: chain s residue 91 MET Chi-restraints excluded: chain s residue 119 SER Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 155 LEU Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain u residue 106 LYS Chi-restraints excluded: chain u residue 109 GLU Chi-restraints excluded: chain v residue 14 SER Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain v residue 111 ARG Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain w residue 67 CYS Chi-restraints excluded: chain w residue 347 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 349 optimal weight: 6.9990 chunk 84 optimal weight: 8.9990 chunk 170 optimal weight: 0.6980 chunk 391 optimal weight: 5.9990 chunk 433 optimal weight: 0.4980 chunk 44 optimal weight: 10.0000 chunk 255 optimal weight: 5.9990 chunk 364 optimal weight: 9.9990 chunk 50 optimal weight: 7.9990 chunk 124 optimal weight: 1.9990 chunk 342 optimal weight: 0.0570 overall best weight: 1.8502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 46 GLN g 18 ASN g 63 GLN ** g 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 91 GLN l 351 ASN m 46 ASN p 62 GLN p 141 GLN s 287 HIS u 64 ASN w 37 GLN w 127 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.122172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.094522 restraints weight = 46048.522| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 1.31 r_work: 0.2813 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2705 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2705 r_free = 0.2705 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2705 r_free = 0.2705 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2705 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.0999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 39684 Z= 0.143 Angle : 0.572 10.187 53629 Z= 0.290 Chirality : 0.041 0.194 5832 Planarity : 0.005 0.067 6559 Dihedral : 14.924 169.606 6203 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.60 % Favored : 96.36 % Rotamer: Outliers : 3.96 % Allowed : 14.34 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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: 2.01 (0.12), residues: 4582 helix: 2.23 (0.09), residues: 2970 sheet: 0.30 (1.10), residues: 25 loop : -0.39 (0.16), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG m 173 TYR 0.022 0.001 TYR l 422 PHE 0.030 0.002 PHE i 292 TRP 0.026 0.001 TRP c 145 HIS 0.009 0.001 HIS p 76 Details of bonding type rmsd covalent geometry : bond 0.00324 (39677) covalent geometry : angle 0.57158 (53617) SS BOND : bond 0.00489 ( 6) SS BOND : angle 1.62139 ( 12) hydrogen bonds : bond 0.05673 ( 2305) hydrogen bonds : angle 4.00499 ( 6705) Misc. bond : bond 0.00025 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9164 Ramachandran restraints generated. 4582 Oldfield, 0 Emsley, 4582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9164 Ramachandran restraints generated. 4582 Oldfield, 0 Emsley, 4582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 850 residues out of total 4086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 689 time to evaluate : 1.681 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 52 MET cc_start: 0.8477 (OUTLIER) cc_final: 0.7713 (mmm) REVERT: S 44 GLN cc_start: 0.9067 (OUTLIER) cc_final: 0.8830 (mt0) REVERT: S 66 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8124 (mp) REVERT: U 40 ASN cc_start: 0.8293 (OUTLIER) cc_final: 0.8029 (t0) REVERT: V 95 CYS cc_start: 0.7140 (t) cc_final: 0.6879 (t) REVERT: c 63 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7640 (tm-30) REVERT: c 103 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8101 (pt0) REVERT: d 134 GLN cc_start: 0.8830 (mt0) cc_final: 0.8377 (tm-30) REVERT: e 68 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8538 (tt0) REVERT: f 63 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8267 (mtmm) REVERT: g 21 ARG cc_start: 0.8753 (mtm180) cc_final: 0.8420 (mtp180) REVERT: i 236 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8475 (tttm) REVERT: i 324 LYS cc_start: 0.6590 (OUTLIER) cc_final: 0.5733 (tmtm) REVERT: i 333 SER cc_start: 0.9320 (p) cc_final: 0.8955 (m) REVERT: l 60 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.7630 (mp0) REVERT: l 140 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.9000 (tt) REVERT: l 286 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8776 (tp) REVERT: l 383 MET cc_start: 0.9147 (OUTLIER) cc_final: 0.7620 (tpt) REVERT: l 475 MET cc_start: 0.8485 (OUTLIER) cc_final: 0.8030 (mtt) REVERT: l 541 ASN cc_start: 0.8857 (OUTLIER) cc_final: 0.8603 (t0) REVERT: n 58 LYS cc_start: 0.8139 (tppt) cc_final: 0.7780 (mtpp) REVERT: o 5 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8589 (mtmt) REVERT: o 114 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7695 (mppt) REVERT: p 48 PHE cc_start: 0.8809 (OUTLIER) cc_final: 0.8141 (t80) REVERT: p 95 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.7754 (mp0) REVERT: p 127 ARG cc_start: 0.8227 (ptp90) cc_final: 0.7879 (ptt-90) REVERT: r 103 GLN cc_start: 0.9321 (OUTLIER) cc_final: 0.8739 (tt0) REVERT: r 123 GLU cc_start: 0.8939 (OUTLIER) cc_final: 0.8253 (mp0) REVERT: r 378 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8663 (tt0) REVERT: r 448 THR cc_start: 0.8888 (OUTLIER) cc_final: 0.8633 (m) REVERT: s 26 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8175 (mptp) REVERT: u 102 LYS cc_start: 0.8349 (ttpt) cc_final: 0.7619 (mmmt) REVERT: u 106 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.8098 (tppt) REVERT: u 109 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7235 (tp30) REVERT: v 103 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7506 (tm-30) REVERT: v 106 ARG cc_start: 0.8118 (ttp-170) cc_final: 0.7411 (ttm170) REVERT: v 111 ARG cc_start: 0.7426 (OUTLIER) cc_final: 0.6213 (mtp180) REVERT: w 160 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.6025 (mp0) REVERT: w 254 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.5659 (mm-30) outliers start: 161 outliers final: 63 residues processed: 771 average time/residue: 0.8494 time to fit residues: 778.0863 Evaluate side-chains 756 residues out of total 4086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 663 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 44 GLN Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain S residue 66 LEU Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 40 ASN 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 64 ASP Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 155 TYR Chi-restraints excluded: chain Z residue 24 ILE Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 127 ASP Chi-restraints excluded: chain a residue 130 GLU Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain b residue 9 LYS Chi-restraints excluded: chain c residue 63 GLU Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 181 VAL Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain e residue 68 GLU Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 99 LEU Chi-restraints excluded: chain f residue 63 LYS Chi-restraints excluded: chain g residue 110 THR Chi-restraints excluded: chain h residue 74 LYS Chi-restraints excluded: chain h residue 77 SER Chi-restraints excluded: chain h residue 97 HIS Chi-restraints excluded: chain i residue 146 SER Chi-restraints excluded: chain i residue 236 LYS Chi-restraints excluded: chain i residue 237 MET Chi-restraints excluded: chain i residue 257 LEU Chi-restraints excluded: chain i residue 278 MET Chi-restraints excluded: chain i residue 324 LYS Chi-restraints excluded: chain k residue 4 VAL Chi-restraints excluded: chain k residue 70 GLU Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain l residue 59 GLN Chi-restraints excluded: chain l residue 60 GLU Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 79 SER Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 286 LEU Chi-restraints excluded: chain l residue 293 ILE Chi-restraints excluded: chain l residue 383 MET Chi-restraints excluded: chain l residue 405 ASN Chi-restraints excluded: chain l residue 475 MET Chi-restraints excluded: chain l residue 541 ASN Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain m residue 5 ILE Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain o residue 5 LYS Chi-restraints excluded: chain o residue 88 LEU Chi-restraints excluded: chain o residue 114 LYS Chi-restraints excluded: chain p residue 48 PHE Chi-restraints excluded: chain p residue 95 GLU Chi-restraints excluded: chain p residue 151 THR Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 103 GLN Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 123 GLU Chi-restraints excluded: chain r residue 126 LEU Chi-restraints excluded: chain r residue 138 ASN Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 183 SER Chi-restraints excluded: chain r residue 187 SER Chi-restraints excluded: chain r residue 332 THR Chi-restraints excluded: chain r residue 337 VAL Chi-restraints excluded: chain r residue 342 MET Chi-restraints excluded: chain r residue 378 GLU Chi-restraints excluded: chain r residue 448 THR Chi-restraints excluded: chain s residue 26 LYS Chi-restraints excluded: chain s residue 73 ILE Chi-restraints excluded: chain s residue 91 MET Chi-restraints excluded: chain s residue 119 SER Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 155 LEU Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain u residue 106 LYS Chi-restraints excluded: chain u residue 109 GLU Chi-restraints excluded: chain v residue 5 LEU Chi-restraints excluded: chain v residue 14 SER Chi-restraints excluded: chain v residue 103 GLU Chi-restraints excluded: chain v residue 111 ARG Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain w residue 61 THR Chi-restraints excluded: chain w residue 160 GLU Chi-restraints excluded: chain w residue 254 GLU Chi-restraints excluded: chain w residue 347 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 197 optimal weight: 4.9990 chunk 381 optimal weight: 1.9990 chunk 256 optimal weight: 2.9990 chunk 329 optimal weight: 0.9990 chunk 401 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 253 optimal weight: 6.9990 chunk 48 optimal weight: 0.7980 chunk 71 optimal weight: 7.9990 chunk 109 optimal weight: 0.9990 chunk 162 optimal weight: 5.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 46 GLN g 18 ASN ** g 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 91 GLN l 59 GLN l 351 ASN p 141 GLN u 64 ASN w 37 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.123413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.095882 restraints weight = 46088.761| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 1.29 r_work: 0.2831 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2722 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2722 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 39684 Z= 0.128 Angle : 0.552 10.247 53629 Z= 0.279 Chirality : 0.040 0.188 5832 Planarity : 0.004 0.064 6559 Dihedral : 14.273 171.406 6192 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.45 % Favored : 96.51 % Rotamer: Outliers : 3.15 % Allowed : 15.40 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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: 2.14 (0.13), residues: 4582 helix: 2.32 (0.09), residues: 2971 sheet: 0.38 (1.09), residues: 25 loop : -0.32 (0.16), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG m 173 TYR 0.022 0.001 TYR l 422 PHE 0.030 0.001 PHE i 292 TRP 0.027 0.001 TRP c 145 HIS 0.008 0.001 HIS r 30 Details of bonding type rmsd covalent geometry : bond 0.00278 (39677) covalent geometry : angle 0.55187 (53617) SS BOND : bond 0.00422 ( 6) SS BOND : angle 1.53580 ( 12) hydrogen bonds : bond 0.05288 ( 2305) hydrogen bonds : angle 3.93958 ( 6705) Misc. bond : bond 0.00023 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9164 Ramachandran restraints generated. 4582 Oldfield, 0 Emsley, 4582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9164 Ramachandran restraints generated. 4582 Oldfield, 0 Emsley, 4582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 819 residues out of total 4086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 691 time to evaluate : 1.541 Fit side-chains revert: symmetry clash REVERT: Q 52 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.7569 (mmm) REVERT: S 44 GLN cc_start: 0.9021 (OUTLIER) cc_final: 0.8785 (mt0) REVERT: S 66 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8071 (mp) REVERT: V 95 CYS cc_start: 0.7100 (t) cc_final: 0.6833 (t) REVERT: Z 49 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.7443 (mm-30) REVERT: c 63 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7634 (tm-30) REVERT: c 103 GLU cc_start: 0.8645 (mt-10) cc_final: 0.8105 (pt0) REVERT: d 134 GLN cc_start: 0.8823 (mt0) cc_final: 0.8391 (tm-30) REVERT: e 68 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8537 (tt0) REVERT: e 138 GLU cc_start: 0.8295 (tp30) cc_final: 0.8060 (mm-30) REVERT: g 21 ARG cc_start: 0.8747 (mtm180) cc_final: 0.8415 (mtp180) REVERT: g 110 THR cc_start: 0.8927 (OUTLIER) cc_final: 0.8644 (t) REVERT: i 236 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8490 (tttm) REVERT: i 324 LYS cc_start: 0.6554 (OUTLIER) cc_final: 0.5706 (tmtm) REVERT: l 60 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.7582 (mp0) REVERT: l 140 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.8943 (tt) REVERT: l 286 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8762 (tp) REVERT: l 383 MET cc_start: 0.9126 (OUTLIER) cc_final: 0.7576 (tpt) REVERT: l 475 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.8056 (mtt) REVERT: n 29 ARG cc_start: 0.8198 (mtt-85) cc_final: 0.7680 (mtp85) REVERT: n 58 LYS cc_start: 0.8119 (tppt) cc_final: 0.7780 (mtpp) REVERT: o 114 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7669 (mppt) REVERT: p 48 PHE cc_start: 0.8779 (OUTLIER) cc_final: 0.8177 (t80) REVERT: p 57 MET cc_start: 0.5505 (OUTLIER) cc_final: 0.4722 (mmp) REVERT: p 127 ARG cc_start: 0.8194 (ptp90) cc_final: 0.7919 (ptt-90) REVERT: r 103 GLN cc_start: 0.9309 (OUTLIER) cc_final: 0.8699 (tt0) REVERT: r 123 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8269 (mp0) REVERT: r 378 GLU cc_start: 0.8960 (OUTLIER) cc_final: 0.8656 (tt0) REVERT: r 448 THR cc_start: 0.8874 (OUTLIER) cc_final: 0.8621 (m) REVERT: s 26 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8188 (mptp) REVERT: s 43 TYR cc_start: 0.8649 (m-80) cc_final: 0.8194 (m-80) REVERT: u 102 LYS cc_start: 0.8304 (ttpt) cc_final: 0.7586 (mmmt) REVERT: u 106 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.8081 (tppt) REVERT: v 103 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7524 (tm-30) REVERT: v 106 ARG cc_start: 0.8107 (ttp-170) cc_final: 0.7396 (ttm170) outliers start: 128 outliers final: 56 residues processed: 751 average time/residue: 0.8516 time to fit residues: 757.8254 Evaluate side-chains 744 residues out of total 4086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 664 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 44 GLN Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain S residue 66 LEU Chi-restraints excluded: chain U residue 34 SER 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 64 ASP Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain Z residue 24 ILE Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain a residue 71 MET Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 127 ASP Chi-restraints excluded: chain a residue 130 GLU Chi-restraints excluded: chain b residue 9 LYS Chi-restraints excluded: chain c residue 63 GLU Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 181 VAL Chi-restraints excluded: chain e residue 68 GLU Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 99 LEU Chi-restraints excluded: chain g residue 110 THR Chi-restraints excluded: chain h residue 97 HIS Chi-restraints excluded: chain i residue 146 SER Chi-restraints excluded: chain i residue 236 LYS Chi-restraints excluded: chain i residue 237 MET Chi-restraints excluded: chain i residue 278 MET Chi-restraints excluded: chain i residue 324 LYS Chi-restraints excluded: chain k residue 4 VAL Chi-restraints excluded: chain k residue 21 MET Chi-restraints excluded: chain k residue 70 GLU Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain k residue 91 GLN Chi-restraints excluded: chain l residue 60 GLU Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 79 SER Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 286 LEU Chi-restraints excluded: chain l residue 293 ILE Chi-restraints excluded: chain l residue 383 MET Chi-restraints excluded: chain l residue 405 ASN Chi-restraints excluded: chain l residue 475 MET Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain o residue 114 LYS Chi-restraints excluded: chain p residue 48 PHE Chi-restraints excluded: chain p residue 57 MET Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 103 GLN Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 123 GLU Chi-restraints excluded: chain r residue 126 LEU Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 183 SER Chi-restraints excluded: chain r residue 187 SER Chi-restraints excluded: chain r residue 332 THR Chi-restraints excluded: chain r residue 342 MET Chi-restraints excluded: chain r residue 378 GLU Chi-restraints excluded: chain r residue 448 THR Chi-restraints excluded: chain s residue 26 LYS Chi-restraints excluded: chain s residue 73 ILE Chi-restraints excluded: chain s residue 91 MET Chi-restraints excluded: chain s residue 119 SER Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 155 LEU Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain u residue 106 LYS Chi-restraints excluded: chain v residue 5 LEU Chi-restraints excluded: chain v residue 14 SER Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain v residue 103 GLU Chi-restraints excluded: chain w residue 59 VAL Chi-restraints excluded: chain w residue 61 THR Chi-restraints excluded: chain w residue 219 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 297 optimal weight: 6.9990 chunk 104 optimal weight: 9.9990 chunk 266 optimal weight: 2.9990 chunk 355 optimal weight: 3.9990 chunk 185 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 178 optimal weight: 0.4980 chunk 413 optimal weight: 1.9990 chunk 199 optimal weight: 0.9980 chunk 338 optimal weight: 0.7980 chunk 29 optimal weight: 9.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 46 GLN ** S 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 18 ASN ** g 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 91 GLN l 351 ASN p 141 GLN r 139 GLN u 64 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.124641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.097271 restraints weight = 46160.888| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 1.29 r_work: 0.2851 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2738 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2738 r_free = 0.2738 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2738 r_free = 0.2738 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2738 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 39684 Z= 0.119 Angle : 0.540 10.200 53629 Z= 0.272 Chirality : 0.039 0.184 5832 Planarity : 0.004 0.063 6559 Dihedral : 13.801 173.351 6186 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.40 % Favored : 96.55 % Rotamer: Outliers : 3.42 % Allowed : 15.30 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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: 2.23 (0.13), residues: 4582 helix: 2.38 (0.09), residues: 2979 sheet: 0.40 (1.07), residues: 25 loop : -0.27 (0.16), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG m 173 TYR 0.023 0.001 TYR l 422 PHE 0.030 0.001 PHE i 292 TRP 0.028 0.001 TRP c 145 HIS 0.007 0.001 HIS r 30 Details of bonding type rmsd covalent geometry : bond 0.00254 (39677) covalent geometry : angle 0.53926 (53617) SS BOND : bond 0.00390 ( 6) SS BOND : angle 1.55376 ( 12) hydrogen bonds : bond 0.04980 ( 2305) hydrogen bonds : angle 3.88515 ( 6705) Misc. bond : bond 0.00019 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9164 Ramachandran restraints generated. 4582 Oldfield, 0 Emsley, 4582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9164 Ramachandran restraints generated. 4582 Oldfield, 0 Emsley, 4582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 830 residues out of total 4086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 691 time to evaluate : 1.707 Fit side-chains revert: symmetry clash REVERT: S 44 GLN cc_start: 0.9006 (OUTLIER) cc_final: 0.8762 (mt0) REVERT: V 95 CYS cc_start: 0.7073 (t) cc_final: 0.6824 (t) REVERT: Z 49 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.7490 (mm-30) REVERT: c 103 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8102 (pt0) REVERT: d 134 GLN cc_start: 0.8799 (mt0) cc_final: 0.8373 (tm-30) REVERT: e 68 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8538 (tt0) REVERT: e 138 GLU cc_start: 0.8283 (tp30) cc_final: 0.8055 (mm-30) REVERT: f 64 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8143 (mm-30) REVERT: g 21 ARG cc_start: 0.8733 (mtm180) cc_final: 0.8401 (mtp180) REVERT: g 110 THR cc_start: 0.8907 (OUTLIER) cc_final: 0.8624 (t) REVERT: i 236 LYS cc_start: 0.9019 (OUTLIER) cc_final: 0.8550 (tttm) REVERT: l 60 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.7565 (mp0) REVERT: l 140 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.8917 (tt) REVERT: l 541 ASN cc_start: 0.8860 (OUTLIER) cc_final: 0.8609 (t0) REVERT: n 29 ARG cc_start: 0.8170 (mtt-85) cc_final: 0.7699 (mtp85) REVERT: n 58 LYS cc_start: 0.8106 (tppt) cc_final: 0.7779 (mtpp) REVERT: o 114 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7641 (mppt) REVERT: p 43 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8692 (mp) REVERT: p 48 PHE cc_start: 0.8771 (OUTLIER) cc_final: 0.8152 (t80) REVERT: p 57 MET cc_start: 0.5391 (OUTLIER) cc_final: 0.4569 (mmp) REVERT: p 95 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.7732 (mp0) REVERT: r 103 GLN cc_start: 0.9303 (OUTLIER) cc_final: 0.8686 (tt0) REVERT: r 123 GLU cc_start: 0.8933 (OUTLIER) cc_final: 0.8290 (mp0) REVERT: r 378 GLU cc_start: 0.8963 (OUTLIER) cc_final: 0.8675 (tt0) REVERT: r 400 MET cc_start: 0.8601 (mtm) cc_final: 0.8216 (mtp) REVERT: r 448 THR cc_start: 0.8856 (OUTLIER) cc_final: 0.8629 (m) REVERT: s 26 LYS cc_start: 0.9086 (OUTLIER) cc_final: 0.8194 (mptp) REVERT: s 43 TYR cc_start: 0.8601 (m-80) cc_final: 0.8281 (m-80) REVERT: u 102 LYS cc_start: 0.8337 (ttpt) cc_final: 0.7675 (mmmt) REVERT: u 106 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.8084 (tppt) REVERT: u 109 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7230 (tp30) REVERT: w 160 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.5956 (mp0) REVERT: w 214 ILE cc_start: 0.8096 (OUTLIER) cc_final: 0.7874 (tp) outliers start: 139 outliers final: 59 residues processed: 766 average time/residue: 0.8299 time to fit residues: 755.1602 Evaluate side-chains 756 residues out of total 4086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 675 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 44 GLN Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain U residue 34 SER 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 64 ASP Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain Z residue 24 ILE Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain a residue 71 MET Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 127 ASP Chi-restraints excluded: chain a residue 130 GLU Chi-restraints excluded: chain b residue 9 LYS Chi-restraints excluded: chain c residue 113 ILE Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 181 VAL Chi-restraints excluded: chain e residue 63 ASP Chi-restraints excluded: chain e residue 68 GLU Chi-restraints excluded: chain e residue 99 LEU Chi-restraints excluded: chain g residue 110 THR Chi-restraints excluded: chain h residue 74 LYS Chi-restraints excluded: chain h residue 97 HIS Chi-restraints excluded: chain i residue 146 SER Chi-restraints excluded: chain i residue 148 SER Chi-restraints excluded: chain i residue 236 LYS Chi-restraints excluded: chain i residue 237 MET Chi-restraints excluded: chain i residue 278 MET Chi-restraints excluded: chain i residue 324 LYS Chi-restraints excluded: chain k residue 70 GLU Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain l residue 60 GLU Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 79 SER Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 293 ILE Chi-restraints excluded: chain l residue 405 ASN Chi-restraints excluded: chain l residue 541 ASN Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain o residue 114 LYS Chi-restraints excluded: chain p residue 43 LEU Chi-restraints excluded: chain p residue 48 PHE Chi-restraints excluded: chain p residue 57 MET Chi-restraints excluded: chain p residue 95 GLU Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 103 GLN Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 123 GLU Chi-restraints excluded: chain r residue 126 LEU Chi-restraints excluded: chain r residue 138 ASN Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 183 SER Chi-restraints excluded: chain r residue 187 SER Chi-restraints excluded: chain r residue 332 THR Chi-restraints excluded: chain r residue 337 VAL Chi-restraints excluded: chain r residue 342 MET Chi-restraints excluded: chain r residue 378 GLU Chi-restraints excluded: chain r residue 448 THR Chi-restraints excluded: chain s residue 26 LYS Chi-restraints excluded: chain s residue 73 ILE Chi-restraints excluded: chain s residue 91 MET Chi-restraints excluded: chain s residue 119 SER Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 155 LEU Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain u residue 106 LYS Chi-restraints excluded: chain u residue 109 GLU Chi-restraints excluded: chain v residue 5 LEU Chi-restraints excluded: chain v residue 14 SER Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain w residue 59 VAL Chi-restraints excluded: chain w residue 61 THR Chi-restraints excluded: chain w residue 160 GLU Chi-restraints excluded: chain w residue 214 ILE 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 444 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 143 optimal weight: 1.9990 chunk 367 optimal weight: 2.9990 chunk 207 optimal weight: 10.0000 chunk 114 optimal weight: 6.9990 chunk 150 optimal weight: 4.9990 chunk 425 optimal weight: 0.7980 chunk 123 optimal weight: 10.0000 chunk 113 optimal weight: 0.0870 chunk 162 optimal weight: 6.9990 overall best weight: 2.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 46 GLN g 18 ASN k 91 GLN l 351 ASN p 141 GLN r 139 GLN s 287 HIS u 64 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.121786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.094179 restraints weight = 45905.400| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 1.28 r_work: 0.2802 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2692 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2692 r_free = 0.2692 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2692 r_free = 0.2692 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2692 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8947 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 39684 Z= 0.156 Angle : 0.589 10.523 53629 Z= 0.297 Chirality : 0.042 0.197 5832 Planarity : 0.005 0.062 6559 Dihedral : 13.781 172.242 6186 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.73 % Favored : 96.22 % Rotamer: Outliers : 3.22 % Allowed : 15.69 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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 (0.12), residues: 4582 helix: 2.28 (0.09), residues: 2969 sheet: 0.49 (1.09), residues: 25 loop : -0.33 (0.16), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG m 173 TYR 0.021 0.002 TYR m 70 PHE 0.029 0.002 PHE i 292 TRP 0.032 0.001 TRP c 145 HIS 0.012 0.001 HIS p 76 Details of bonding type rmsd covalent geometry : bond 0.00362 (39677) covalent geometry : angle 0.58889 (53617) SS BOND : bond 0.00488 ( 6) SS BOND : angle 1.26646 ( 12) hydrogen bonds : bond 0.05851 ( 2305) hydrogen bonds : angle 3.98380 ( 6705) Misc. bond : bond 0.00024 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9164 Ramachandran restraints generated. 4582 Oldfield, 0 Emsley, 4582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9164 Ramachandran restraints generated. 4582 Oldfield, 0 Emsley, 4582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 825 residues out of total 4086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 694 time to evaluate : 1.737 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 44 GLN cc_start: 0.9080 (OUTLIER) cc_final: 0.8842 (mt0) REVERT: V 95 CYS cc_start: 0.7124 (t) cc_final: 0.6859 (t) REVERT: Z 49 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.7514 (mm-30) REVERT: c 103 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8111 (pt0) REVERT: d 134 GLN cc_start: 0.8824 (mt0) cc_final: 0.8385 (tm-30) REVERT: e 68 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8548 (tt0) REVERT: e 69 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8487 (mtpt) REVERT: f 64 GLU cc_start: 0.8347 (mt-10) cc_final: 0.8120 (mm-30) REVERT: g 21 ARG cc_start: 0.8751 (mtm180) cc_final: 0.8429 (mtp180) REVERT: i 236 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8497 (tttm) REVERT: l 60 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.7551 (mp0) REVERT: l 140 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.8990 (tt) REVERT: l 541 ASN cc_start: 0.8865 (OUTLIER) cc_final: 0.8609 (t0) REVERT: n 29 ARG cc_start: 0.8236 (mtt-85) cc_final: 0.7781 (mtp85) REVERT: n 58 LYS cc_start: 0.8126 (tppt) cc_final: 0.7805 (mtpp) REVERT: o 114 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7691 (mppt) REVERT: p 43 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8697 (mp) REVERT: p 48 PHE cc_start: 0.8835 (OUTLIER) cc_final: 0.8526 (m-80) REVERT: p 57 MET cc_start: 0.5523 (OUTLIER) cc_final: 0.4617 (mmp) REVERT: p 95 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.7787 (mp0) REVERT: r 103 GLN cc_start: 0.9319 (OUTLIER) cc_final: 0.8927 (tt0) REVERT: r 123 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.8290 (mp0) REVERT: r 144 ASN cc_start: 0.8879 (OUTLIER) cc_final: 0.8529 (t0) REVERT: r 378 GLU cc_start: 0.8999 (OUTLIER) cc_final: 0.8707 (tt0) REVERT: r 448 THR cc_start: 0.8933 (OUTLIER) cc_final: 0.8689 (m) REVERT: s 26 LYS cc_start: 0.9088 (OUTLIER) cc_final: 0.8207 (mptp) REVERT: s 43 TYR cc_start: 0.8605 (m-80) cc_final: 0.8338 (m-80) REVERT: u 102 LYS cc_start: 0.8419 (ttpt) cc_final: 0.7777 (mmmt) REVERT: u 106 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.8103 (tppt) REVERT: u 109 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7242 (tp30) REVERT: w 160 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.5987 (mp0) REVERT: w 214 ILE cc_start: 0.8123 (OUTLIER) cc_final: 0.7921 (tp) REVERT: w 254 GLU cc_start: 0.6717 (mm-30) cc_final: 0.6383 (mp0) outliers start: 131 outliers final: 69 residues processed: 764 average time/residue: 0.8371 time to fit residues: 762.6122 Evaluate side-chains 769 residues out of total 4086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 677 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 44 GLN Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain S residue 66 LEU Chi-restraints excluded: chain U residue 34 SER 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 64 ASP Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain Z residue 24 ILE Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain a residue 71 MET Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 130 GLU Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain b residue 9 LYS Chi-restraints excluded: chain c residue 113 ILE Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 181 VAL Chi-restraints excluded: chain e residue 68 GLU Chi-restraints excluded: chain e residue 69 LYS Chi-restraints excluded: chain e residue 99 LEU Chi-restraints excluded: chain g residue 110 THR Chi-restraints excluded: chain h residue 74 LYS Chi-restraints excluded: chain h residue 97 HIS Chi-restraints excluded: chain i residue 88 LYS Chi-restraints excluded: chain i residue 146 SER Chi-restraints excluded: chain i residue 236 LYS Chi-restraints excluded: chain i residue 237 MET Chi-restraints excluded: chain i residue 241 THR Chi-restraints excluded: chain i residue 278 MET Chi-restraints excluded: chain i residue 324 LYS Chi-restraints excluded: chain k residue 4 VAL Chi-restraints excluded: chain k residue 70 GLU Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain l residue 60 GLU Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 79 SER Chi-restraints excluded: chain l residue 132 VAL Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 293 ILE Chi-restraints excluded: chain l residue 405 ASN Chi-restraints excluded: chain l residue 541 ASN Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain m residue 5 ILE Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain n residue 15 ILE Chi-restraints excluded: chain o residue 114 LYS Chi-restraints excluded: chain p residue 43 LEU Chi-restraints excluded: chain p residue 48 PHE Chi-restraints excluded: chain p residue 57 MET Chi-restraints excluded: chain p residue 95 GLU Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 103 GLN Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 123 GLU Chi-restraints excluded: chain r residue 126 LEU Chi-restraints excluded: chain r residue 138 ASN Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 144 ASN Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 183 SER Chi-restraints excluded: chain r residue 187 SER Chi-restraints excluded: chain r residue 332 THR Chi-restraints excluded: chain r residue 337 VAL Chi-restraints excluded: chain r residue 342 MET Chi-restraints excluded: chain r residue 378 GLU Chi-restraints excluded: chain r residue 448 THR Chi-restraints excluded: chain s residue 26 LYS Chi-restraints excluded: chain s residue 73 ILE Chi-restraints excluded: chain s residue 91 MET Chi-restraints excluded: chain s residue 119 SER Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 155 LEU Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain u residue 106 LYS Chi-restraints excluded: chain u residue 109 GLU Chi-restraints excluded: chain u residue 111 VAL Chi-restraints excluded: chain v residue 5 LEU Chi-restraints excluded: chain v residue 14 SER Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain w residue 59 VAL Chi-restraints excluded: chain w residue 61 THR Chi-restraints excluded: chain w residue 67 CYS Chi-restraints excluded: chain w residue 160 GLU Chi-restraints excluded: chain w residue 184 VAL Chi-restraints excluded: chain w residue 214 ILE Chi-restraints excluded: chain w residue 219 GLN 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 157 optimal weight: 2.9990 chunk 448 optimal weight: 0.1980 chunk 130 optimal weight: 6.9990 chunk 33 optimal weight: 0.5980 chunk 384 optimal weight: 8.9990 chunk 60 optimal weight: 4.9990 chunk 322 optimal weight: 2.9990 chunk 405 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 395 optimal weight: 0.8980 chunk 342 optimal weight: 7.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 46 GLN ** S 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 18 ASN k 91 GLN l 351 ASN p 141 GLN r 139 GLN s 287 HIS u 64 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.124817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.097586 restraints weight = 45921.925| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 1.29 r_work: 0.2847 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2734 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2734 r_free = 0.2734 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2734 r_free = 0.2734 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2734 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 39684 Z= 0.121 Angle : 0.545 13.261 53629 Z= 0.274 Chirality : 0.039 0.184 5832 Planarity : 0.004 0.062 6559 Dihedral : 13.324 173.170 6186 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.43 % Favored : 96.53 % Rotamer: Outliers : 2.68 % Allowed : 16.43 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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: 2.24 (0.13), residues: 4582 helix: 2.40 (0.09), residues: 2975 sheet: 0.62 (1.08), residues: 25 loop : -0.28 (0.16), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG m 173 TYR 0.023 0.001 TYR l 422 PHE 0.030 0.001 PHE i 292 TRP 0.032 0.001 TRP c 145 HIS 0.007 0.001 HIS r 30 Details of bonding type rmsd covalent geometry : bond 0.00261 (39677) covalent geometry : angle 0.54480 (53617) SS BOND : bond 0.00395 ( 6) SS BOND : angle 1.08947 ( 12) hydrogen bonds : bond 0.05008 ( 2305) hydrogen bonds : angle 3.88247 ( 6705) Misc. bond : bond 0.00024 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9164 Ramachandran restraints generated. 4582 Oldfield, 0 Emsley, 4582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9164 Ramachandran restraints generated. 4582 Oldfield, 0 Emsley, 4582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 798 residues out of total 4086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 689 time to evaluate : 1.758 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 44 GLN cc_start: 0.8999 (OUTLIER) cc_final: 0.8740 (mt0) REVERT: V 95 CYS cc_start: 0.7065 (t) cc_final: 0.6801 (t) REVERT: Z 49 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.7557 (mm-30) REVERT: c 103 GLU cc_start: 0.8646 (mt-10) cc_final: 0.8111 (pt0) REVERT: d 134 GLN cc_start: 0.8816 (mt0) cc_final: 0.8378 (tm-30) REVERT: e 138 GLU cc_start: 0.8286 (tp30) cc_final: 0.8055 (mm-30) REVERT: f 64 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8142 (mm-30) REVERT: g 21 ARG cc_start: 0.8742 (mtm180) cc_final: 0.8415 (mtp180) REVERT: g 110 THR cc_start: 0.8895 (OUTLIER) cc_final: 0.8616 (t) REVERT: i 236 LYS cc_start: 0.9020 (OUTLIER) cc_final: 0.8560 (tttm) REVERT: i 333 SER cc_start: 0.9276 (p) cc_final: 0.8953 (m) REVERT: l 60 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.7529 (mp0) REVERT: l 140 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.8923 (tt) REVERT: l 541 ASN cc_start: 0.8859 (OUTLIER) cc_final: 0.8604 (t0) REVERT: n 29 ARG cc_start: 0.8188 (mtt-85) cc_final: 0.7750 (mtp85) REVERT: n 58 LYS cc_start: 0.8117 (tppt) cc_final: 0.7814 (mtpp) REVERT: o 114 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7651 (mppt) REVERT: p 43 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8671 (mp) REVERT: p 48 PHE cc_start: 0.8796 (OUTLIER) cc_final: 0.8230 (t80) REVERT: p 55 LYS cc_start: 0.7260 (OUTLIER) cc_final: 0.6657 (mtpt) REVERT: p 57 MET cc_start: 0.5451 (ttt) cc_final: 0.4660 (mmp) REVERT: r 103 GLN cc_start: 0.9304 (OUTLIER) cc_final: 0.8691 (tt0) REVERT: r 123 GLU cc_start: 0.8928 (OUTLIER) cc_final: 0.8336 (mp0) REVERT: r 144 ASN cc_start: 0.8808 (m110) cc_final: 0.8463 (t0) REVERT: r 378 GLU cc_start: 0.8976 (OUTLIER) cc_final: 0.8688 (tt0) REVERT: r 400 MET cc_start: 0.8582 (mtm) cc_final: 0.8220 (mtp) REVERT: r 448 THR cc_start: 0.8887 (OUTLIER) cc_final: 0.8648 (m) REVERT: s 26 LYS cc_start: 0.9087 (OUTLIER) cc_final: 0.8185 (mptp) REVERT: s 43 TYR cc_start: 0.8560 (m-80) cc_final: 0.8313 (m-80) REVERT: u 102 LYS cc_start: 0.8412 (ttpt) cc_final: 0.7773 (mmmt) REVERT: u 106 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.8103 (tppt) REVERT: u 109 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7271 (tp30) REVERT: w 160 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.5962 (mp0) REVERT: w 214 ILE cc_start: 0.8127 (OUTLIER) cc_final: 0.7797 (tp) REVERT: w 254 GLU cc_start: 0.6653 (mm-30) cc_final: 0.6325 (mp0) outliers start: 109 outliers final: 65 residues processed: 750 average time/residue: 0.8728 time to fit residues: 776.7497 Evaluate side-chains 751 residues out of total 4086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 666 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 44 GLN Chi-restraints excluded: chain S residue 66 LEU Chi-restraints excluded: chain U residue 34 SER 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 64 ASP Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain Z residue 24 ILE Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain a residue 71 MET Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 127 ASP Chi-restraints excluded: chain a residue 130 GLU Chi-restraints excluded: chain b residue 9 LYS Chi-restraints excluded: chain c residue 113 ILE Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 181 VAL Chi-restraints excluded: chain e residue 63 ASP Chi-restraints excluded: chain e residue 72 ASP Chi-restraints excluded: chain e residue 99 LEU Chi-restraints excluded: chain g residue 110 THR Chi-restraints excluded: chain h residue 74 LYS Chi-restraints excluded: chain h residue 77 SER Chi-restraints excluded: chain h residue 97 HIS Chi-restraints excluded: chain i residue 146 SER Chi-restraints excluded: chain i residue 236 LYS Chi-restraints excluded: chain i residue 237 MET Chi-restraints excluded: chain i residue 278 MET Chi-restraints excluded: chain i residue 324 LYS Chi-restraints excluded: chain j residue 105 GLU Chi-restraints excluded: chain k residue 4 VAL Chi-restraints excluded: chain k residue 70 GLU Chi-restraints excluded: chain k residue 91 GLN Chi-restraints excluded: chain l residue 60 GLU Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 79 SER Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 293 ILE Chi-restraints excluded: chain l residue 349 SER Chi-restraints excluded: chain l residue 405 ASN Chi-restraints excluded: chain l residue 541 ASN Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain m residue 5 ILE Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain o residue 114 LYS Chi-restraints excluded: chain p residue 43 LEU Chi-restraints excluded: chain p residue 48 PHE Chi-restraints excluded: chain p residue 55 LYS Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 103 GLN Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 123 GLU Chi-restraints excluded: chain r residue 126 LEU Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 183 SER Chi-restraints excluded: chain r residue 187 SER Chi-restraints excluded: chain r residue 332 THR Chi-restraints excluded: chain r residue 337 VAL Chi-restraints excluded: chain r residue 342 MET Chi-restraints excluded: chain r residue 378 GLU Chi-restraints excluded: chain r residue 448 THR Chi-restraints excluded: chain s residue 26 LYS Chi-restraints excluded: chain s residue 73 ILE Chi-restraints excluded: chain s residue 91 MET Chi-restraints excluded: chain s residue 119 SER Chi-restraints excluded: chain s residue 151 LEU Chi-restraints excluded: chain s residue 155 LEU Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain u residue 106 LYS Chi-restraints excluded: chain u residue 109 GLU Chi-restraints excluded: chain u residue 111 VAL Chi-restraints excluded: chain v residue 5 LEU Chi-restraints excluded: chain v residue 14 SER Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain w residue 59 VAL Chi-restraints excluded: chain w residue 61 THR Chi-restraints excluded: chain w residue 160 GLU Chi-restraints excluded: chain w residue 184 VAL Chi-restraints excluded: chain w residue 214 ILE Chi-restraints excluded: chain w residue 219 GLN 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 365 optimal weight: 6.9990 chunk 282 optimal weight: 2.9990 chunk 366 optimal weight: 0.9990 chunk 172 optimal weight: 0.8980 chunk 231 optimal weight: 2.9990 chunk 121 optimal weight: 8.9990 chunk 75 optimal weight: 0.8980 chunk 358 optimal weight: 1.9990 chunk 266 optimal weight: 2.9990 chunk 67 optimal weight: 0.0970 chunk 189 optimal weight: 10.0000 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 46 GLN ** S 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 18 ASN i 347 ASN k 91 GLN l 351 ASN p 141 GLN r 139 GLN s 287 HIS u 64 ASN w 37 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.125095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.097840 restraints weight = 46135.077| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 1.30 r_work: 0.2854 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2764 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2764 r_free = 0.2764 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2764 r_free = 0.2764 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2764 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 39684 Z= 0.118 Angle : 0.550 12.181 53629 Z= 0.276 Chirality : 0.039 0.185 5832 Planarity : 0.004 0.061 6559 Dihedral : 13.094 172.756 6186 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.40 % Favored : 96.55 % Rotamer: Outliers : 2.75 % Allowed : 16.63 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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: 2.28 (0.13), residues: 4582 helix: 2.43 (0.09), residues: 2975 sheet: 0.62 (1.08), residues: 25 loop : -0.26 (0.16), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG m 173 TYR 0.023 0.001 TYR l 422 PHE 0.030 0.001 PHE i 292 TRP 0.035 0.001 TRP c 145 HIS 0.007 0.001 HIS r 30 Details of bonding type rmsd covalent geometry : bond 0.00252 (39677) covalent geometry : angle 0.54961 (53617) SS BOND : bond 0.00417 ( 6) SS BOND : angle 1.53337 ( 12) hydrogen bonds : bond 0.04899 ( 2305) hydrogen bonds : angle 3.85929 ( 6705) Misc. bond : bond 0.00020 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9164 Ramachandran restraints generated. 4582 Oldfield, 0 Emsley, 4582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9164 Ramachandran restraints generated. 4582 Oldfield, 0 Emsley, 4582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 792 residues out of total 4086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 680 time to evaluate : 1.750 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 44 GLN cc_start: 0.8994 (OUTLIER) cc_final: 0.8736 (mt0) REVERT: V 95 CYS cc_start: 0.7080 (t) cc_final: 0.6815 (t) REVERT: Z 49 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.7571 (mm-30) REVERT: c 103 GLU cc_start: 0.8651 (mt-10) cc_final: 0.8123 (pt0) REVERT: d 134 GLN cc_start: 0.8820 (mt0) cc_final: 0.8378 (tm-30) REVERT: e 138 GLU cc_start: 0.8288 (tp30) cc_final: 0.8063 (mm-30) REVERT: f 64 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8132 (mm-30) REVERT: g 21 ARG cc_start: 0.8735 (mtm180) cc_final: 0.8432 (mtp180) REVERT: g 110 THR cc_start: 0.8882 (OUTLIER) cc_final: 0.8611 (t) REVERT: i 236 LYS cc_start: 0.9010 (OUTLIER) cc_final: 0.8502 (tttm) REVERT: i 333 SER cc_start: 0.9283 (p) cc_final: 0.8935 (m) REVERT: k 63 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8764 (tp) REVERT: l 60 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.7501 (mp0) REVERT: l 140 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.8902 (tt) REVERT: l 541 ASN cc_start: 0.8863 (OUTLIER) cc_final: 0.8614 (t0) REVERT: n 29 ARG cc_start: 0.8190 (mtt-85) cc_final: 0.7713 (mtp85) REVERT: n 58 LYS cc_start: 0.8099 (tppt) cc_final: 0.7810 (mtpp) REVERT: o 114 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7637 (mppt) REVERT: p 43 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8683 (mp) REVERT: p 48 PHE cc_start: 0.8798 (OUTLIER) cc_final: 0.8284 (t80) REVERT: p 55 LYS cc_start: 0.7256 (OUTLIER) cc_final: 0.6637 (mtpt) REVERT: p 57 MET cc_start: 0.5349 (ttt) cc_final: 0.4660 (mmp) REVERT: r 103 GLN cc_start: 0.9298 (OUTLIER) cc_final: 0.8722 (tt0) REVERT: r 123 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8349 (mp0) REVERT: r 144 ASN cc_start: 0.8801 (m110) cc_final: 0.8451 (t0) REVERT: r 378 GLU cc_start: 0.8961 (OUTLIER) cc_final: 0.8660 (tt0) REVERT: r 400 MET cc_start: 0.8567 (mtm) cc_final: 0.8205 (mtp) REVERT: r 448 THR cc_start: 0.8867 (OUTLIER) cc_final: 0.8643 (m) REVERT: s 26 LYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8191 (mptp) REVERT: u 102 LYS cc_start: 0.8373 (ttpt) cc_final: 0.7691 (mmmt) REVERT: u 106 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.8098 (tppt) REVERT: u 109 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7264 (tp30) REVERT: w 160 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.5914 (mp0) REVERT: w 214 ILE cc_start: 0.8075 (OUTLIER) cc_final: 0.7855 (tp) REVERT: w 254 GLU cc_start: 0.6666 (mm-30) cc_final: 0.6347 (mp0) outliers start: 112 outliers final: 60 residues processed: 743 average time/residue: 0.8597 time to fit residues: 758.2635 Evaluate side-chains 759 residues out of total 4086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 678 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 44 GLN Chi-restraints excluded: chain S residue 66 LEU Chi-restraints excluded: chain U residue 34 SER 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 64 ASP Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain Z residue 24 ILE Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain a residue 71 MET Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 127 ASP Chi-restraints excluded: chain a residue 130 GLU Chi-restraints excluded: chain b residue 9 LYS Chi-restraints excluded: chain c residue 113 ILE Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 181 VAL Chi-restraints excluded: chain e residue 63 ASP Chi-restraints excluded: chain e residue 99 LEU Chi-restraints excluded: chain g residue 110 THR Chi-restraints excluded: chain h residue 97 HIS Chi-restraints excluded: chain i residue 146 SER Chi-restraints excluded: chain i residue 236 LYS Chi-restraints excluded: chain i residue 237 MET Chi-restraints excluded: chain i residue 241 THR Chi-restraints excluded: chain i residue 278 MET Chi-restraints excluded: chain i residue 324 LYS Chi-restraints excluded: chain j residue 105 GLU Chi-restraints excluded: chain k residue 4 VAL Chi-restraints excluded: chain k residue 63 LEU Chi-restraints excluded: chain k residue 70 GLU Chi-restraints excluded: chain l residue 60 GLU Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 79 SER Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 293 ILE Chi-restraints excluded: chain l residue 349 SER Chi-restraints excluded: chain l residue 405 ASN Chi-restraints excluded: chain l residue 541 ASN Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain o residue 114 LYS Chi-restraints excluded: chain p residue 43 LEU Chi-restraints excluded: chain p residue 48 PHE Chi-restraints excluded: chain p residue 55 LYS Chi-restraints excluded: chain r residue 60 SER Chi-restraints excluded: chain r residue 103 GLN Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 123 GLU Chi-restraints excluded: chain r residue 126 LEU Chi-restraints excluded: chain r residue 138 ASN Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 183 SER Chi-restraints excluded: chain r residue 187 SER Chi-restraints excluded: chain r residue 332 THR Chi-restraints excluded: chain r residue 337 VAL Chi-restraints excluded: chain r residue 342 MET Chi-restraints excluded: chain r residue 378 GLU Chi-restraints excluded: chain r residue 448 THR Chi-restraints excluded: chain s residue 26 LYS Chi-restraints excluded: chain s residue 91 MET Chi-restraints excluded: chain s residue 119 SER Chi-restraints excluded: chain u residue 106 LYS Chi-restraints excluded: chain u residue 109 GLU Chi-restraints excluded: chain u residue 111 VAL Chi-restraints excluded: chain v residue 5 LEU Chi-restraints excluded: chain v residue 14 SER Chi-restraints excluded: chain w residue 54 THR Chi-restraints excluded: chain w residue 59 VAL Chi-restraints excluded: chain w residue 61 THR Chi-restraints excluded: chain w residue 67 CYS Chi-restraints excluded: chain w residue 160 GLU Chi-restraints excluded: chain w residue 184 VAL Chi-restraints excluded: chain w residue 214 ILE Chi-restraints excluded: chain w residue 219 GLN Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 347 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 132 optimal weight: 3.9990 chunk 372 optimal weight: 2.9990 chunk 335 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 178 optimal weight: 0.7980 chunk 313 optimal weight: 0.9980 chunk 412 optimal weight: 20.0000 chunk 46 optimal weight: 3.9990 chunk 287 optimal weight: 0.3980 chunk 411 optimal weight: 0.0770 chunk 343 optimal weight: 0.7980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 46 GLN ** S 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 18 ASN k 91 GLN l 351 ASN p 141 GLN r 139 GLN s 287 HIS w 37 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.127706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.101099 restraints weight = 46019.039| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.27 r_work: 0.2902 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2810 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2810 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 39684 Z= 0.110 Angle : 0.535 12.468 53629 Z= 0.268 Chirality : 0.039 0.177 5832 Planarity : 0.004 0.061 6559 Dihedral : 12.646 173.034 6179 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.40 % Favored : 96.55 % Rotamer: Outliers : 2.02 % Allowed : 17.34 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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: 2.37 (0.13), residues: 4582 helix: 2.49 (0.09), residues: 2982 sheet: 0.63 (1.07), residues: 25 loop : -0.22 (0.16), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG m 173 TYR 0.024 0.001 TYR l 422 PHE 0.031 0.001 PHE i 292 TRP 0.036 0.001 TRP c 145 HIS 0.006 0.001 HIS r 30 Details of bonding type rmsd covalent geometry : bond 0.00228 (39677) covalent geometry : angle 0.53384 (53617) SS BOND : bond 0.00559 ( 6) SS BOND : angle 2.08671 ( 12) hydrogen bonds : bond 0.04426 ( 2305) hydrogen bonds : angle 3.79266 ( 6705) Misc. bond : bond 0.00019 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9164 Ramachandran restraints generated. 4582 Oldfield, 0 Emsley, 4582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9164 Ramachandran restraints generated. 4582 Oldfield, 0 Emsley, 4582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 4086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 690 time to evaluate : 1.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 44 GLN cc_start: 0.8942 (OUTLIER) cc_final: 0.8688 (mt0) REVERT: W 129 THR cc_start: 0.8621 (p) cc_final: 0.8248 (t) REVERT: Z 35 LYS cc_start: 0.8616 (mmtt) cc_final: 0.8407 (mmtp) REVERT: Z 49 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.7509 (mm-30) REVERT: c 103 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8128 (pt0) REVERT: d 134 GLN cc_start: 0.8780 (mt0) cc_final: 0.8344 (tm-30) REVERT: e 138 GLU cc_start: 0.8261 (tp30) cc_final: 0.8045 (mm-30) REVERT: f 64 GLU cc_start: 0.8353 (mt-10) cc_final: 0.8127 (mm-30) REVERT: g 21 ARG cc_start: 0.8708 (mtm180) cc_final: 0.8423 (mtp180) REVERT: g 110 THR cc_start: 0.8859 (m) cc_final: 0.8586 (t) REVERT: i 236 LYS cc_start: 0.8967 (OUTLIER) cc_final: 0.8537 (tttm) REVERT: i 324 LYS cc_start: 0.6493 (OUTLIER) cc_final: 0.5787 (mmtm) REVERT: k 63 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8681 (tp) REVERT: k 91 GLN cc_start: 0.7198 (OUTLIER) cc_final: 0.6846 (pm20) REVERT: l 60 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.7498 (mp0) REVERT: l 140 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8865 (tt) REVERT: l 541 ASN cc_start: 0.8830 (OUTLIER) cc_final: 0.8570 (t0) REVERT: n 29 ARG cc_start: 0.8163 (mtt-85) cc_final: 0.7705 (mtp85) REVERT: n 58 LYS cc_start: 0.8077 (tppt) cc_final: 0.7810 (mtpp) REVERT: o 114 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7516 (mppt) REVERT: o 118 GLU cc_start: 0.7325 (mt-10) cc_final: 0.7115 (mm-30) REVERT: p 43 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8759 (mp) REVERT: p 48 PHE cc_start: 0.8758 (OUTLIER) cc_final: 0.8233 (t80) REVERT: p 55 LYS cc_start: 0.7254 (OUTLIER) cc_final: 0.6628 (mtpt) REVERT: p 57 MET cc_start: 0.5235 (ttt) cc_final: 0.4720 (mmp) REVERT: p 124 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.8148 (mt0) REVERT: r 103 GLN cc_start: 0.9270 (OUTLIER) cc_final: 0.8667 (tt0) REVERT: r 123 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.8384 (mp0) REVERT: r 138 ASN cc_start: 0.8889 (OUTLIER) cc_final: 0.8635 (m-40) REVERT: r 144 ASN cc_start: 0.8745 (m110) cc_final: 0.8396 (t0) REVERT: r 378 GLU cc_start: 0.8928 (OUTLIER) cc_final: 0.8604 (tt0) REVERT: r 400 MET cc_start: 0.8529 (mtm) cc_final: 0.8156 (mtp) REVERT: s 26 LYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8202 (mptp) REVERT: u 106 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.8105 (tppt) REVERT: u 109 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7263 (tp30) REVERT: w 214 ILE cc_start: 0.8124 (OUTLIER) cc_final: 0.7906 (tp) REVERT: w 254 GLU cc_start: 0.6600 (mm-30) cc_final: 0.6285 (mp0) outliers start: 82 outliers final: 46 residues processed: 737 average time/residue: 0.8016 time to fit residues: 702.0697 Evaluate side-chains 728 residues out of total 4086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 660 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 44 GLN Chi-restraints excluded: chain S residue 66 LEU Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain W residue 144 THR Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain Z residue 24 ILE Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 130 GLU Chi-restraints excluded: chain b residue 9 LYS Chi-restraints excluded: chain c residue 113 ILE Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 181 VAL Chi-restraints excluded: chain e residue 63 ASP Chi-restraints excluded: chain e residue 99 LEU Chi-restraints excluded: chain h residue 97 HIS Chi-restraints excluded: chain i residue 236 LYS Chi-restraints excluded: chain i residue 237 MET Chi-restraints excluded: chain i residue 241 THR Chi-restraints excluded: chain i residue 278 MET Chi-restraints excluded: chain i residue 324 LYS Chi-restraints excluded: chain j residue 105 GLU Chi-restraints excluded: chain k residue 63 LEU Chi-restraints excluded: chain k residue 70 GLU Chi-restraints excluded: chain k residue 91 GLN Chi-restraints excluded: chain l residue 60 GLU Chi-restraints excluded: chain l residue 79 SER Chi-restraints excluded: chain l residue 140 LEU Chi-restraints excluded: chain l residue 349 SER Chi-restraints excluded: chain l residue 405 ASN Chi-restraints excluded: chain l residue 481 THR Chi-restraints excluded: chain l residue 541 ASN Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain m residue 5 ILE Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain o residue 114 LYS Chi-restraints excluded: chain p residue 43 LEU Chi-restraints excluded: chain p residue 48 PHE Chi-restraints excluded: chain p residue 55 LYS Chi-restraints excluded: chain p residue 124 GLN Chi-restraints excluded: chain r residue 103 GLN Chi-restraints excluded: chain r residue 123 GLU Chi-restraints excluded: chain r residue 126 LEU Chi-restraints excluded: chain r residue 138 ASN Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 187 SER Chi-restraints excluded: chain r residue 332 THR Chi-restraints excluded: chain r residue 337 VAL Chi-restraints excluded: chain r residue 342 MET Chi-restraints excluded: chain r residue 378 GLU Chi-restraints excluded: chain s residue 26 LYS Chi-restraints excluded: chain s residue 91 MET Chi-restraints excluded: chain s residue 119 SER Chi-restraints excluded: chain u residue 88 CYS Chi-restraints excluded: chain u residue 106 LYS Chi-restraints excluded: chain u residue 109 GLU Chi-restraints excluded: chain v residue 5 LEU Chi-restraints excluded: chain v residue 14 SER Chi-restraints excluded: chain w residue 59 VAL Chi-restraints excluded: chain w residue 61 THR Chi-restraints excluded: chain w residue 184 VAL Chi-restraints excluded: chain w residue 214 ILE Chi-restraints excluded: chain w residue 219 GLN Chi-restraints excluded: chain w residue 347 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 132 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 chunk 306 optimal weight: 0.7980 chunk 328 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 368 optimal weight: 6.9990 chunk 114 optimal weight: 6.9990 chunk 451 optimal weight: 0.9980 chunk 401 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 187 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 46 GLN ** S 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 140 GLN g 18 ASN l 351 ASN p 141 GLN r 139 GLN s 287 HIS w 37 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.127576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.100898 restraints weight = 46367.109| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 1.27 r_work: 0.2900 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2784 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2784 r_free = 0.2784 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2784 r_free = 0.2784 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2784 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.186 39684 Z= 0.136 Angle : 0.644 58.971 53629 Z= 0.341 Chirality : 0.039 0.179 5832 Planarity : 0.004 0.061 6559 Dihedral : 12.626 173.045 6175 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.38 % Favored : 96.57 % Rotamer: Outliers : 1.80 % Allowed : 17.63 % Favored : 80.57 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.84 % 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: 2.37 (0.13), residues: 4582 helix: 2.49 (0.09), residues: 2981 sheet: 0.63 (1.07), residues: 25 loop : -0.22 (0.16), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG m 173 TYR 0.028 0.001 TYR m 70 PHE 0.031 0.001 PHE i 292 TRP 0.033 0.001 TRP c 145 HIS 0.006 0.001 HIS r 30 Details of bonding type rmsd covalent geometry : bond 0.00286 (39677) covalent geometry : angle 0.64065 (53617) SS BOND : bond 0.02568 ( 6) SS BOND : angle 4.32260 ( 12) hydrogen bonds : bond 0.04468 ( 2305) hydrogen bonds : angle 3.79222 ( 6705) Misc. bond : bond 0.00027 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19386.80 seconds wall clock time: 329 minutes 42.01 seconds (19782.01 seconds total)